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Expression and bioinformatic analysis of lymphoma-associated novel gene KIAA0372

BAI Xiangyang, TANG Duozhuang, ZHU Tao, SUN Lishi, YAN Lingling, LU Yunping, ZHOU Jianfeng, MA Ding

《医学前沿（英文）》 2007年 第1卷 第1期   页码 93-98 doi: 10.1007/s11684-007-0018-2

摘要： The purpose of this study was to explore the differentially expressed genes in lymph-node cells (LNC) of lymphomas and reactive lymph node hyperplasia, and to perform an initial bioinformatic analysis on a novel gene, KIAA0372, which is highly expressed in the LNC of lymphomas. mRNA extracted from LNC of lymphomas and reactive lymph node hyperplasia were respectively marked with biotin and hybridized with Gene Expression Chips, resulting in differentially expressed genes. Initial bioinformatic analysis was then performed on a novel gene named KIAA0372, whose function has not yet been explored. Its structure and genomic location, its product s physical and chemical properties, subcellular localization and functional domains, were also predicted. Further, a systematic evolution analysis was performed on similar proteins from among several species. Using Gene Expression Chips, many differentially expressed genes were uncovered. Efficient bioinformatic analysis has fundamentally determined that KIAA0372 is an extracellular protein which may be involved in TGF-β signaling. Microarray is an efficient and high throughput strategy for detection of differentially expressed genes. And KIAA0372 is thought to be a potential target for tumor research using bioinformatic analysis.

关键词： bioinformatic analysis     functional     KIAA0372     detection     Microarray    

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General expression for linear and nonlinear time series models

Ren HUANG, Feiyun XU, Ruwen CHEN

《机械工程前沿（英文）》 2009年 第4卷 第1期   页码 15-24 doi: 10.1007/s11465-009-0015-z

摘要： The typical time series models such as ARMA, AR, and MA are founded on the normality and stationarity of a system and expressed by a linear difference equation; therefore, they are strictly limited to the linear system. However, some nonlinear factors are within the practical system; thus, it is difficult to fit the model for real systems with the above models. This paper proposes a general expression for linear and nonlinear auto-regressive time series models (GNAR). With the gradient optimization method and modified AIC information criteria integrated with the prediction error, the parameter estimation and order determination are achieved. The model simulation and experiments show that the GNAR model can accurately approximate to the dynamic characteristics of the most nonlinear models applied in academics and engineering. The modeling and prediction accuracy of the GNAR model is superior to the classical time series models. The proposed GNAR model is flexible and effective.

关键词： linear and nonlinear     autoregressive model     system identification     time series analysis    

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Thermal deflection analysis of the solidified shell in continuous casting of slab

LIU Hongzhao, WANG Zhongmin

《机械工程前沿（英文）》 2007年 第2卷 第2期   页码 175-179 doi: 10.1007/s11465-007-0029-3

摘要： The thermal deformation problem in the continuous casting of a slab subjected to thermal loading because of the temperature gradient along the solidified shell thickness is investigated. On the basis of the reciprocal theorem of work or Betti-Maxwell s reciprocal theorem and the superposition principle, the deflection expressions for a rectangular plate with the two opposite edges simply supported, and the other two opposite edges clamped under the action of the uniformly distributed load and nonuniform temperature field are derived respectively. The meaning of each term in the deflection expression obtained by the reciprocal theorem of work is explained. Then the practical example is given to calculate the thermal deformation and the bulging deformation of the solidified shell under three tension speeds. This research is useful for analyzing the bulging deformation in the continuous casting of a slab under the static pressure of the molten steel and the thermal loading because of the temperature gradient along the solidified shell thickness.

关键词： s reciprocal     loading     deflection expression     reciprocal     opposite    

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Stable expression and control parameters in the numerical simulation of unsaturated flow

Zhiyuan ZHANG; Xu LI; Yongkang WU; Xiaokang LI

《结构与土木工程前沿（英文）》 2022年 第16卷 第12期   页码 1501-1514 doi: 10.1007/s11709-022-0893-2

摘要： The Richards’ equation describes the flow phenomenon in unsaturated porous media and is essential to hydrology and environmental science. This study evaluated the numerical stability of two different forms of the Richards’ equation. Sensitivity analyses were performed to investigate the control parameters of the equation. The results show that the h-form Richards’ equation has better applicability for calculating variable saturation flows than the θ-form Richards’ equation. For the h-form Richards’ equation, the hydraulic conductivity of the soil in the low-suction range and the specific moisture capacity in the high-suction range primarily influenced the solution. In addition, sensitivity analyses indicated that the saturated hydraulic conductivity, initial condition, and air-entry pressure have a higher sensitivity to the simulation results than the saturated water content, rainfall intensity, and decline rate of hydraulic conductivity. Moreover, their correctness needs to be guaranteed first in numerical simulations. The research findings can provide a helpful reference for improving the reliability of numerical simulations of unsaturated flows.

关键词： Richards’ equation     sensitivity analysis     unsaturated soil     hydraulic diffusivity     seepage simulation    

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SUPEROXIDE DISMUTASE FAMILY GENES IN WATERMELON AND THEIR RESPONSES TO DIFFERENT ABIOTIC STRESSES

《农业科学与工程前沿（英文）》 2021年 第8卷 第4期   页码 645-658 doi: 10.15302/J-FASE -2020350

摘要：

Superoxide dismutase (SOD) is an important enzyme in the antioxidant system of plants and plays a vital role in stress responses by maintaining the dynamic balance of reactive oxygen species (ROS) concentrations. Genome-wide analysis of the SOD gene family in various plant species has been conducted but little is known about this gene family in watermelon (Citrullus lanatus). Here, eight SOD genes were identified in the watermelon genome and are designated ClCSD1-5, ClFSD1-2 and ClMSD according to their metal cofactors. Phylogenetic analysis shows that SOD proteins from various plant species can be classified into five groups and members in the same group possess the same metal cofactor and similar subcellular localizations. Expression analysis of the ClSOD genes indicates that they had tissue-specific expression patterns with high expression in different tissues including the leaves, flowers and fruit. In addition, the expression of ClSOD genes differed appreciably under salinity, drought and abscisic acid (ABA) treatments, indicating that they may be involved in ROS scavenging under different abiotic stresses via an ABA-dependent signaling pathway. These results lay the foundation for elucidating the function of ClSOD genes in stress tolerance and fruit development in watermelon.

 

关键词： abiotic stress / expression analysis / phylogeny / SOD / superoxide dismutase / watermelon    

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Analysis of differential expression of genes induced by ethephon in elongating internodes of maize plants

Xiaoyi WEI,Weiqiang ZHANG,Qian ZHANG,Pei SUN,Zhaohu LI,Mingcai ZHANG,Jianmin LI,Liusheng DUAN

《农业科学与工程前沿（英文）》 2016年 第3卷 第3期   页码 263-282 doi: 10.15302/J-FASE-2016103

摘要： Plant growth regulators (PGRs) are commonly used in cereal cropping systems to restrict plant height and control lodging. Ethephon has been reported to shorten internodes and increase grain yield of maize. To analyze the transcriptomic profiles of maize internode elongation following ethephon treatment, differentially expressed genes were compared between the treatment and control samples of inbred line Zong 31 using the Affymetrix Maize Genome Array. According to the microarray data, 326 probe sets showed significant change in expression. Further research revealed that the most remarkable effects of ethephon on maize internodes elongation occurred during a 48 h period, when 89 differentially expressed genes were detected. There were dramatic change in transcript levels at 24 h and six Auxin transport genes and four gibberellin biosynthesis pathway genes were differentially expressed in Zong 31 in response to ethephon treatment. In summary, we showed that gaseous ethylene release is involved in internode meristem cell elongation through the regulation of plant hormone signaling in maize. This work provides a platform for studies in which candidate genes will be functionally tested for involvement in internode elongation.

关键词： maize     ethephon     internode elongation     microarray     qPCR    

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Blockage of receptor-interacting protein 2 expression by small interfering RNA in murine macrophages

LIU Hongchun, CAO Zhongwei, JIN Jianjun, WANG Jiyao

《医学前沿（英文）》 2008年 第2卷 第2期   页码 166-170 doi: 10.1007/s11684-008-0030-1

摘要： This study aims to demonstrate that blocking the receptor-interacting protein2 (Rip2) expression can decrease inflammatory cytokine production by macrophage and protect mice from endotoxin lethality. Murine Rip2 small interfering RNA (siRNA) plasmids were constructed and transfected into macrophage and Rip2 expression was detected with reverse transcription-polymerase chain reaction (RT-PCR) and western blot. Cell proliferation was assayed with MTT. TNF-? concentration was assayed with ELISA and high-mobility group box 1 protein (HMGB1) level with semi-quantitative western blot after lipopolysaccharide (LPS) stimulation. LPS challenge was given after the plasmids were injected into mice and the survival rate was calculated. Rip2 siRNA plasmid could block the mRNA and protein expression of Rip2 and promote cell proliferation. Blocking Rip2 could attenuate LPS-induced TNF-? and HMGB1 production. The HMGB1 expression in the liver decreased to (40.21 ± 11.03) pg/g, and serum TNF-? level decreased to (300.43 ± 59.26) ng/L ( < 0.05). The survival rate of mice from endotoxemia was also improved ( < 0.05). The results demonstrate that Rip2 siRNA plasmid can block the expression of Rip2, decrease the production of TNF-? and HMGB1 and protect mice from fatal endotoxemia.
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MSI/LOH and extron expression of the FHIT gene in gastric carcinoma

XIAO Yuping, MAO Lili, HAN Chengbo, LI Jinyi, XU Lei, XIN Yan

《医学前沿（英文）》 2007年 第1卷 第1期   页码 99-103 doi: 10.1007/s11684-007-0019-1

摘要： We detected loss of heterozygosity (LOH) and microsatellite instabilities (MSI), as well as extron expression of the fragile histidine triad (FHIT) gene in gastric carcinoma (GC), in order to evaluate their association with clinicopathological processes in gastric carcinogenesis. LOH and MSI of the FHIT were detected by using PCR at 4 microsatellite loci: D3S 1300, D3S 4103, D3S 1481, D3S 1234 in cancer tissues from 50 patients with primary GC, with normal mucosa acting as matched controls. FHIT transcripts were detected by nested RT-PCR in 30 cases of GC and their products were sequenced. Results show that the average frequencies of LOH and MSI of the FHIT gene in GC were 32.4% and 26.4%, respectively. There was no correlation between LOH and MSI of the FHIT gene in GC and the histological characteristics of gastric carcinoma (Bormann s or Lauren s classification). LOH of the FHIT gene in GC was related to depth invasiveness, and its frequency in GC where serosa was penetrated was significantly higher than that in GC without serosa penetration (73.5% 37.5%, <0.05). The frequency of MSI in GC without lymph node metastasis was significantly higher than that in GC with lymph node metastasis (66.7% 34.3%, <0.05). Aberrant transcripts were found in 11/30 GC tissues. Sequencing analysis of the aberrant fragments found a RT-PCR product missing exons 5 7 in one case of GC, and another product missing exons 4 7. Four of 10 (40.0%) cases of primary GC showed absent or decreased expression of the FHIT protein as compared to their matched normal tissues. The findings in this study suggest that LOH and MSI of FHIT gene may induce aberrant extron expression, which might play a role in gastric carcinogenesis.
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Gene expression disparity in giant cell tumor of bone

Xiaohua PAN, Shuhua YANG, Deming XIAO, Yong DAI, Lili REN

《医学前沿（英文）》 2009年 第3卷 第1期   页码 49-56 doi: 10.1007/s11684-009-0012-y

摘要： The aim of this paper was to study the differential gene expression of giant cell tumor of bone (GCTB) by gene chip technology. Total RNA of 8 fresh GCTB specimens (Jaffe I∶6 cases, II∶1 case, III∶1 case; Campanacci I∶6 cases, II∶1 case, III∶1 case; Enneking Staging G T M : 5 cases, G T M : 2 cases, G T M : 1 case) and 4 normal bony callus specimens (the control group) were extracted and purified to get mRNA and then reverse transcribed to complementary DNA, respectively. Microarray screening with a set of 8064 human cDNA genes was conducted to analyze the difference among the samples and the control. The hybridization signals were scanned. The gene expression disparity between the GCTB samples and normal bony callus was significantly different ( <0.01), and the disparity of over 5-fold was found in 47 genes in the GCTB specimens, with 25 genes up-regulated and 22 down-regulated including the extracellular matrix and transforming-related genes, oncogene and its homolog genes, cytokine and its receptor genes. Specific gene spectrum associated with GCTB can be identified by cDNA microarray, which will be the foundation of progressive etiology elucidation, diagnosis and treatment of GCTB.

关键词： giant cell tumor of bone     gene     microarray     cDNA    

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Distinct gene expression pattern of mutations coordinated by target repression and promoter hypermethylation

《医学前沿（英文）》 2022年 第16卷 第4期   页码 627-636 doi: 10.1007/s11684-020-0815-4

摘要： Runt-related transcription factor 1 (RUNX1) is an essential regulator of normal hematopoiesis. Its dysfunction, caused by either fusions or mutations, is frequently reported in acute myeloid leukemia (AML). However, RUNX1 mutations have been largely under-explored compared with RUNX1 fusions mainly due to their elusive genetic characteristics. Here, based on 1741 patients with AML, we report a unique expression pattern associated with RUNX1 mutations in AML. This expression pattern was coordinated by target repression and promoter hypermethylation. We first reanalyzed a joint AML cohort that consisted of three public cohorts and found that RUNX1 mutations were mainly distributed in the Runt domain and almost mutually exclusive with NPM1 mutations. Then, based on RNA-seq data from The Cancer Genome Atlas AML cohort, we developed a 300-gene signature that significantly distinguished the patients with RUNX1 mutations from those with other AML subtypes. Furthermore, we explored the mechanisms underlying this signature from the transcriptional and epigenetic levels. Using chromatin immunoprecipitation sequencing data, we found that RUNX1 target genes tended to be repressed in patients with RUNX1 mutations. Through the integration of DNA methylation array data, we illustrated that hypermethylation on the promoter regions of RUNX1-regulated genes also contributed to dysregulation in RUNX1-mutated AML. This study revealed the distinct gene expression pattern of RUNX1 mutations and the underlying mechanisms in AML development.

关键词： RUNX1     gene mutation     acute myeloid leukemia     transcriptional repression     DNA methylation    

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Immunohistochemical measurement and expression of Mcl-1 in infertile testes

null

《医学前沿（英文）》 2015年 第9卷 第3期   页码 361-367 doi: 10.1007/s11684-015-0395-x

摘要：

The diagnosis of azoospermia represents a major challenge to andrologists as this condition may occur despite normal spermatogenesis and genital tracts. Myeloid cell leukemia-1 (Mcl-1) is a member of the Bcl-2 family of proteins involved in regulation of apoptosis in various cell types. This study aimed to investigate the immunohistochemical expression of Mcl-1 in testicular biopsies of subjects with azoospermia. Eighty-six cases with azoospermia were obtained from 509 infertile patients admitted to the Andrology Unit of the Zagazig University Hospitals from January 2010 to December 2011. Biopsies were diagnosed and classified using H&E-stained slide sections. The specimens were subjected to immunohistochemical staining for Mcl-1 and examined through light microscopy. Forty-five cases of maturation arrest (25 at spermatids and 20 at the spermatocytes), 31 cases of hypospermatogenesis (20 moderate and 11 severe), 5 cases of Sertoli?cell-only syndrome, 2 cases of basement membrane hyalinization, and 1 case of tubular and peritubular sclerosis were observed. Normal spermatogenesis was detected in 2 cases. A strong positive immunoreaction in Leydig cells was observed among all investigated specimens. A moderate reaction was detected in spermatocytes and spermatozoa in cases of normal spermatogenesis and hypospermatogenesis, but a negative reaction was detected in cases of maturation arrest and germ cell aplasia. Apoptosis was found to be associated with decreased rate of spermatogenesis. High apoptosis rates may result in azoospermia, which can occur despite normal spermatogenesis and absence of duct obstruction.

关键词： spermatogenesis     testis     Mcl-1 expression     immunohistochemical study     infertility    

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Single-cell RNA-seq data analysis on the receptor ACE2 expression reveals the potential risk of different

Xin Zou, Ke Chen, Jiawei Zou, Peiyi Han, Jie Hao, Zeguang Han

《医学前沿（英文）》   页码 185-192 doi: 10.1007/s11684-020-0754-0

摘要：

It has been known that, the novel coronavirus, 2019-nCoV, which is considered similar to SARS-CoV and originated from Wuhan (China), invades human cells via the receptor angiotensin converting enzyme II (ACE2). Moreover, lung cells that have ACE2 expression may be the main target cells during 2019-nCoV infection. However, some patients also exhibit non-respiratory symptoms, such as kidney failure, implying that 2019-nCoV could also invade other organs. To construct a risk map of different human organs, we analyzed the single-cell RNA sequencing (scRNA-seq) datasets derived from major human physiological systems, including the respiratory, cardiovascular, digestive, and urinary systems. Through scRNA-seq data analyses, we identified the organs at risk, such as lung, heart, esophagus, kidney, bladder, and ileum, and located specific cell types (i.e., type II alveolar cells (AT2), myocardial cells, proximal tubule cells of the kidney, ileum and esophagus epithelial cells, and bladder urothelial cells), which are vulnerable to 2019-nCoV infection. Based on the findings, we constructed a risk map indicating the vulnerability of different organs to 2019-nCoV infection. This study may provide potential clues for further investigation of the pathogenesis and route of 2019-nCoV infection.

关键词： 2019-nCoV     ACE2     single-cell RNA-seq    

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Construction of a universal recombinant expression vector that regulates the expression of human lysozyme

Shen LIU, Shengzhe SHANG, Xuezhen YANG, Huihua ZHANG, Dan LU, Ning LI

《农业科学与工程前沿（英文）》 2018年 第5卷 第3期   页码 382-389 doi: 10.15302/J-FASE-2018211

摘要：

The mammary gland provides a novel method for producing recombinant proteins in milk of transgenic animals. A key component in the technology is the construction of an efficient milk expression vector. Here, we established a simple method to construct a milk expression vector, by a combination of homologous recombination and digestion-ligation. Our methodology is expected to have the advantages of both plasmid and bacterial artificial chromosome (BAC) vectors. The BAC of mouse whey acidic protein gene (mWAP) was modified twice by homologous recombination to produce a universal expression vector, and the human lysozyme gene (hLZ) was then inserted into the vector by a digestion-ligation method. The final vector containing the 8.5 kb mWAP 5′ promoter, 4.8 kb hLZ genomic DNA, and 8.0 kb mWAP 3′ genomic DNA was microinjected into pronuclei of fertilized mouse embryos, to successfully generate two transgenic mouse lines that expressed recombinant human lysozyme (rhLZ) in milk. The highest expression level of rhLZ was 0.45 g·L−1, and rhLZ exhibited the same antibacterial activity as native hLZ. Our results have provided a simple approach to construct a universal milk expression vector, and demonstrated that the resulting vector regulates the expression of hLZ in milk.

关键词： BAC recombinant methods     gene expression     human lysozyme     transgenic mice     milk expression vector    

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Genome-wide identification and expression analysis of the β-amylase genes strongly associated with fruit

Hongxia MIAO,Peiguang SUN,Yulu MIAO,Juhua LIU,Jianbin ZHANG,Caihong JIA,Jingyi WANG,Zhuo WANG,Zhiqiang JIN,Biyu XU

《农业科学与工程前沿（英文）》 2016年 第3卷 第4期   页码 346-356 doi: 10.15302/J-FASE-2016127

摘要： β-amylase (BAM) is an important enzyme involved in conversion of starch to maltose in multiple biological processes in plants. However, there is currently insufficient information on the BAM gene family in the important fruit crop banana. This study identified 16 genes in the banana genome. Phylogenetic analysis showed that MaBAMs were classified into four subfamilies. Most in each subfamily shared similar gene structures. Conserved motif analysis showed that all identified MaBAM proteins had the typical glyco hydro 14 domains. Comprehensive transcriptomic analysis of two banana genotypes revealed the expression patterns of in different tissues, at various stages of fruit development and ripening, and in responses to abiotic stresses. Most s showed strong transcript accumulation changes during fruit development and late-stage ripening. Some showed significant changes under cold, salt, and osmotic stresses. This finding indicated that might be involved in regulating fruit development, ripening, and responses to abiotic stress. Analysis of five hormone-related and seven stress-relevant elements in the promoters of further revealed that BAMs participated in various biological processes. This systemic analysis provides new insights into the transcriptional characteristics of the genes in banana and may serve as a basis for further functional studies of such genes.

关键词： β-amylase     banana     genome-wide identification     fruit development     abiotic stress    

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Relationship of adrenomedullin expression and microvessel density and prognosis in smooth muscle tumor

JIANG Yuan, TIAN Xuehong, YUAN Jie, JIN Yuemei, TAN Yusong

《医学前沿（英文）》 2007年 第1卷 第4期   页码 398-400 doi: 10.1007/s11684-007-0077-4

摘要： The aim of this paper was to investigate the relationship between the expression of adrenomedullin (ADM) and microvessel density (MVD) and prognosis in smooth muscle tumor of uterus. The expression of ADM was detected using immunohistochemical staining in specimens from 15 normal controls, 28 cases of uterine leiomyoma (LE) and 19 cases of uterine leiomyosarcoma (LES). The MVD was assayed by immunostainting with CD. There was a positive correlation between the ADM expression and MVD in LE and LES respectively ( = 0.823, <0.01; = 0.793, <0.01). The expression of ADM in LE was statistically lower than that in LES (<0.05). There was a positive correlation between the ADM expression and mitotic figures in LES (<0.05): the more mitotic figures, the higher levels of the ADM expression and poor prognosis. The ADM is an important angiogenic factor in smooth muscle tumor of uterus. The ADM can be used as an accessory marker in estimating the malignant potency of LE and judging the pro gnosis of LES, and as a novel molecular target of anti-angiogenic and anticarcinogenic strategies.

关键词： anticarcinogenic     microvessel density     malignant potency     muscle     uterine leiomyosarcoma    

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标题 作者 时间 类型 操作

Expression and bioinformatic analysis of lymphoma-associated novel gene KIAA0372

BAI Xiangyang, TANG Duozhuang, ZHU Tao, SUN Lishi, YAN Lingling, LU Yunping, ZHOU Jianfeng, MA Ding

期刊论文

General expression for linear and nonlinear time series models

Ren HUANG, Feiyun XU, Ruwen CHEN

期刊论文

Thermal deflection analysis of the solidified shell in continuous casting of slab

LIU Hongzhao, WANG Zhongmin

期刊论文

Stable expression and control parameters in the numerical simulation of unsaturated flow

Zhiyuan ZHANG; Xu LI; Yongkang WU; Xiaokang LI

期刊论文

SUPEROXIDE DISMUTASE FAMILY GENES IN WATERMELON AND THEIR RESPONSES TO DIFFERENT ABIOTIC STRESSES

期刊论文

Analysis of differential expression of genes induced by ethephon in elongating internodes of maize plants

Xiaoyi WEI,Weiqiang ZHANG,Qian ZHANG,Pei SUN,Zhaohu LI,Mingcai ZHANG,Jianmin LI,Liusheng DUAN

期刊论文

Blockage of receptor-interacting protein 2 expression by small interfering RNA in murine macrophages

LIU Hongchun, CAO Zhongwei, JIN Jianjun, WANG Jiyao

期刊论文

MSI/LOH and extron expression of the FHIT gene in gastric carcinoma

XIAO Yuping, MAO Lili, HAN Chengbo, LI Jinyi, XU Lei, XIN Yan

期刊论文

Gene expression disparity in giant cell tumor of bone

Xiaohua PAN, Shuhua YANG, Deming XIAO, Yong DAI, Lili REN

期刊论文

Distinct gene expression pattern of mutations coordinated by target repression and promoter hypermethylation

期刊论文

Immunohistochemical measurement and expression of Mcl-1 in infertile testes

null

期刊论文

Single-cell RNA-seq data analysis on the receptor ACE2 expression reveals the potential risk of different

Xin Zou, Ke Chen, Jiawei Zou, Peiyi Han, Jie Hao, Zeguang Han

期刊论文

Construction of a universal recombinant expression vector that regulates the expression of human lysozyme

Shen LIU, Shengzhe SHANG, Xuezhen YANG, Huihua ZHANG, Dan LU, Ning LI

期刊论文

Genome-wide identification and expression analysis of the β-amylase genes strongly associated with fruit

Hongxia MIAO,Peiguang SUN,Yulu MIAO,Juhua LIU,Jianbin ZHANG,Caihong JIA,Jingyi WANG,Zhuo WANG,Zhiqiang JIN,Biyu XU

期刊论文

Relationship of adrenomedullin expression and microvessel density and prognosis in smooth muscle tumor

JIANG Yuan, TIAN Xuehong, YUAN Jie, JIN Yuemei, TAN Yusong

期刊论文