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Biomedical subjects

Ming Dong

Publications and source records attributed to Ming Dong.

At least 19 recordsLinked to original sources

MWENA: a novel sample re-weighting-based algorithm for disease classification and data interpretation using extracellular vesicles omics data.

BACKGROUND AND OBJECTIVE: Extracellular vesicles (EVs), considered as a form of liquid biopsy, have gained significant attention in recent years due to their stability and the preservation of disease markers. Research studies underscore the clinical significance of molecules found in EVs, highlighting their role as communicative mediators between cells. However, analyzing this data is challenging due to noisy measurements, having far more variables than samples, and some groups (e.g., disease subtypes or experimental conditions) having much less data than others. We therefore develop an algorithm to address aforementioned challenges for the classification of imbalanced EVs omics data. METHODS AND RESULTS: We propose the EV Meta-Weight Elastic Net Algorithm (MWENA), which utilizes logistic regression with elastic net regularization for the classification and identification of EV signatures, effectively addressing the challenges posed by high-dimensional small sample sizes. To mitigate issues related to class imbalance and high noise levels, MWENA incorporates an automatic sample re-weighting function, which uses a meta-net to adaptively learn generalizable patterns directly from the data itself. We validate the MWENA algorithm on both simulated data and EVs omics data, covering six classification tasks that involve four different types of diseases (pancreatic ductal adenocarcinoma, interstitial lung diseases, colorectal cancer, and ovarian cancer) and three clinical scenarios (disease diagnosis, disease-stage screening, and disease-subtype classification). Compared to other machine learning methods, MWENA demonstrates superiority in identifying small class samples and achieves the highest scores in both sensitivity and G-means. Biological analysis is also performed to further explore the significance of selected signatures as biological markers and their roles in disease mechanisms. CONCLUSIONS: We anticipate that our proposed approach will take a modest step in harnessing EV omics data to discover biomarkers, aiding researchers in gaining a comprehensive understanding of biological processes.

Extracellular Vesicles↗

Expression of Gadd45a and p53 proteins in human pancreatic cancer: potential effects on clinical outcomes.

BACKGROUND AND OBJECTIVES: p53 gene has a dual role as a trigger of apoptosis and as an initiator of DNA repair. Gadd45a gene assumes the function to maintain the stability of genome. The present study was designed to assess the significance of Gadd45a and p53 protein expression on pancreatic cancer. METHODS: The expression of p53 and Gadd45a was immunohistochemically studied in 59 patients with pancreatic cancer. RESULTS: The positive expression rate of p53 and Gadd45a was 67.8% and 42.4%, respectively. p53 expression in the patients <65 years was significantly higher than that in the patients >or=65 years (P=0.030). Gadd 45a expression showed no correlation to the patients' age. There was no relation for p53 expression to differentiation and TNM stages. Gadd 45a expression showed significant difference in histological differentiation (P=0.007). The median survival time of p53(+) and Gadd45a(+) group was shorter than that of p53(-) and Gadd45a(-) group (P>0.05), respectively. Meanwhile, the median survival time of p53 (+)Gadd45a(+) group was also shorter than that of p53(-)Gadd45a(-) group (P>0.05). CONCLUSIONS: p53 and Gadd45a proteins are both highly expressed in pancreatic cancer. The overexpression of p53 and Gadd45a may have connection with the malignant biologic behavior of pancreatic cancer.

Adult↗

Reductive transformation of parathion and methyl parathion by Bacillus sp.

Based on the results of phenotypic features, phylogenetic similarity of 16S rRNA gene sequences and BIOLOG test, a soil bacterium was identified as Bacillus sp. DM-1. Using either growing cells or a cell-free extract, it transformed parathion and methyl parathion to amino derivatives by reducing the nitro group. Pesticide transformation by a cell-free extract was specifically inhibited by three nitroreductase inhibitors, indicating the presence of nitroreductase activity. The nitroreductase activity was NAD(P)H-dependent, O(2)-insensitive, and exhibited the substrate specificity for parathion and methyl parathion. Reductive transformation significantly decreased the toxicity of pesticides.

Bacillus↗

Assessment of water quality and identification of pollution sources of plateau lakes in Yunnan (China).

The plateau lakes of Yunnan are important both ecologically and economically in China. Nevertheless, the human impact on water quality in these lakes has become increasingly highlighted. The water quality of 10 plateau lakes was monitored regularly over the period of 2000 through 2004 for 24 parameters. Multivariate statistical techniques, including cluster analysis (CA), factor analysis (FA), and principal component analysis (PCA), were employed to better interpret information about the water quality and its pollution sources. No obvious data reduction from CA/FA was found because three principal components (PCs) needed 14 variables to explain 85.01% of the total variance. However, three latent factors accounted for pollution mainly from the following sources: agricultural activities, residential activities and anthropogenic-toxic pollution from industrial effluents, or other special activities. Box-whiskers plots were employed to visually interpret the spatiotemporal variations of water quality variables, which were highly correlated with three PCs. Three types of water quality (i.e., low-, medium-, and high-polluted lakes) were determined through CA based on the similarity of water quality variables. Our results may provide helpful information for the authorities to effectively manage the water quality and make sound policies.

China↗

A trade-off between guerrilla and phalanx growth forms in Leymus secalinus under different nutrient supplies.

BACKGROUND AND AIMS: A phalanx growth form enables clonal plants to make better use of resource-rich patches, whereas a guerrilla growth form provides them with opportunities to escape from resource-poor sites. Leymus secalinus produces both spreading (guerrilla form) and clumping ramets (phalanx form). Here, the hypothesis that a trade-off between the two growth forms in L. secalinus exists under different resource levels is tested. METHODS: Ramets of L. secalinus were grown under three levels of nutrient supply. KEY RESULTS: With increasing nutrient supply, the proportion of clumping ramets (in total number of ramets) increased, whereas that of spreading ramets decreased. With increasing nutrient supply, the number of buds increased, whereas biomass per bud decreased. A trade-off between bud number and size further supports the above hypothesis because larger buds were more likely to develop into spreading ramets, and smaller buds into clumping ramets. Mean spacer length between spreading ramets was significantly smaller under the high than under the medium nutrient supply. CONCLUSIONS: The results suggest that a trade-off between the two growth forms in L. secalinus exists under different nutrient supplies. Such a trade-off together with plasticity in spacer morphology may enable L. secalinus to make better use of small-scale heterogeneity in resource supply.

Biomass↗

Epidermal growth factor promotes invasiveness of pancreatic cancer cells through NF-kappaB-mediated proteinase productions.

OBJECTIVES: Overexpression of epidermal growth factor (EGF) and EGF receptor has been associated with progression and invasive phenotype in pancreatic cancer. However, the underlying molecular mechanism by which EGF worked in pancreatic cancer cells has been poorly understood. In this study, we determined the effect of EGF on the invasiveness and the related regulatory mechanism in two pancreatic cancer cell lines NOR-P1 and KP4. METHODS: Invasion assay was performed to examine the invasiveness of tumor cells induced by EGF, and the expression of matrix metalloproteinase (MMP)-9, MMP-2, and plasminogen activator (uPA) was determined by reverse transcription-polymerase chain reaction and Western blot. Gelatin zymography was used to detect the activities of MMP-9 and MMP-2, and the nuclear factor-kappaB (NF-kappaB) binding activity was determined by electrophoretic mobility shift assay (EMSA). RESULTS: EGF significantly increased the invasiveness of both cell lines but did not affect cell proliferation or adhesion. Increased invasiveness was associated with the induction of MMP-9 and uPA at both mRNA and protein levels. Furthermore, EGF stimulated NF-kappaB binding activity. Moreover, pretreatment of cells with NF-kappaB inhibitors, pyrrolidine dithiocarbamate or ibuprofen, markedly attenuated EGF-induced NF-kappaB activation. Subsequently, the EGF-induced MMP-9 and uPA expression and MMP-9 activity, as well as cell invasiveness, were also inhibited by these NF-kappaB inhibitors. CONCLUSIONS: Our findings indicated that NF-kappaB-mediated MMP-9 and uPA induction was responsible for EGF-induced invasiveness in these pancreatic cancer cell lines and implicate that such anti-NF-kappaB therapy as the use of NF-kappaB inhibitors may contribute to the reduction of invasiveness of pancreatic cancer.

Cell Adhesion↗

[Adaptation strategies of seed germination and seedling growth to sand dune environment].

Sand dune plants possess many adaptation strategies to withstand sand environment, e. g., some desert plant seeds are dormant when matured, which helps them to escape from unfeasible environment conditions and be preserved as seed bank. The seed germination and seedling establishment of psammophytes need moderate sand burial, while excessive burial will inhibit seed germination and seedling emergence. Seeds without germination in deeper sand are in enforced dormancy, and form soil seed bank. Sand dune plant seedlings could tolerant finite sand burial by increasing the number of nodes per culm and elongating internodes. When the seedlings are partially buried, they could survive through the maintenance of photosynthesis organism. Once sand burial exceed the threshold of the plant, seedlings growth will be restrained and the growth ability even permanently lost. Other factors such as salt spray, insect herbivory, and lack of soil nutrients also affect seed germination and seedling establishment. The precipitation in desert and sand land is unpredictable and irregular. Sand erosion leads roots be exposed to the air and dehydrated to die. However, seedlings of some desert plant have the ability to tolerate desiccation for a period of time after germination. Once there is rain, the seedlings will rivive.

Adaptation, Physiological↗

Clinicopathological significance of Bcl-2 and Bax protein expression in human pancreatic cancer.

AIM: To assess the clinicopathological significance of the expression of the apoptosis-inhibitory Bcl-2 protein (pBcl-2) and the apoptosis-promoting Bax protein (pBax) in human invasive ductal carcinomas (IDCs) of the pancreas. METHODS: Fifty-nine surgical specimens of IDCs of the pancreas were stained immunohistochemically to detect pBcl-2 and pBax expressions whose correlation to tumor classification, staging, and prognosis was analyzed by univariate and multivariate analyses. RESULTS: The expression of pBcl-2 and pBax was detected in 21 of 59 (35.6%) and in 29 of 59 (49.2%) patients with IDCs of the pancreas, respectively. Neither pBcl-2 nor pBax alone was correlated to TNM staging and differentiation degree of IDCs of the pancreas according to univariate analysis. By Mantel-Cox test, the median survival time after surgery for pBcl-2(+) and pBcl-2(-) groups were 14.3 and 7.3 mo, respectively (chi(2) = 9.357, P = 0.002) and that for pBax(+) and pBax(-) groups were 12.9 and 10.2 mo, respectively (chi(2) = 0.285, P>0.05). Contingency coefficient between pBcl-2 and pBax expression was 0.298, indicating that there was correlation between them (chi(2) = 5.74, P<0.05). The median survival time after surgery for pBcl-2(+)pBax(+) and pBcl-2(+)pBax(-) groups were 14.3 and 14.1 mo, respectively, and that for pBcl-2(-)pBax(+) and pBcl-2(-)pBax(-) groups were 5.9 and 9.9 mo, respectively. There was a significant difference between pBcl-2(+)pBax(+) and pBcl-2(-)pBax(+) (chi(2) = 5.06, P<0.05), such was the case for pBcl-2(+)pBax(+) and pBcl-2(-)pBax(-) (chi(2) = 7.18, P<0.01). Cox proportional hazards model for multivariate analysis was applied, indicating that pBcl-2, TNM staging, age and pBax were high risk factors of post-surgical survival time. CONCLUSION: Both pBcl-2 and pBax have high expression in IDCs of the pancreas, indicating that co-expression of pBcl-2 and pBax is a good indicator of favorable prognosis in IDCs of the pancreas.

Aged↗

Clinicopathological significance of p53 and mdm2 protein expression in human pancreatic cancer.

AIM: To study the clinicopathological significance of p53 and mdm2 protein expression in human pancreatic cancer. METHODS: To investigate the expression of p53 and mdm2 in pancreatic cancer by immunohistochemistry, and the relationships between the p53 and mdm2 protein expression and clinicopathological parameters in pancreatic cancer. RESULTS: The positive expression of p53 protein was found in 40 of 59 patients (67.8%) and that of mdm2 protein in 17 of 59 patients (28.8%). No obvious relationships were found between p53 as well as mdm2 expression and sex, tumor site, TNM staging and histological differentiation. p53 expression was increased in patients younger than 65 years old, while mdm2 had no relationship with age. The survival time of the patients with the positive expression of p53 and mdm2 proteins was obviously shorter than the other groups. CONCLUSION: Both p53 and mdm2 presented relatively high expression in human pancreatic cancer. The overexpression of p53 and mdm2 might reflect the malignant proliferation of pancreatic cancer and their co-expression might be helpful to evaluate the prognosis of the patients with pancreatic cancer.

Adult↗

Classifiability-based omnivariate decision trees.

Top-down induction of decision trees is a simple and powerful method of pattern classification. In a decision tree, each node partitions the available patterns into two or more sets. New nodes are created to handle each of the resulting partitions and the process continues. A node is considered terminal if it satisfies some stopping criteria (for example, purity, i.e., all patterns at the node are from a single class). Decision trees may be univariate, linear multivariate, or nonlinear multivariate depending on whether a single attribute, a linear function of all the attributes, or a nonlinear function of all the attributes is used for the partitioning at each node of the decision tree. Though nonlinear multivariate decision trees are the most powerful, they are more susceptible to the risks of overfitting. In this paper, we propose to perform model selection at each decision node to build omnivariate decision trees. The model selection is done using a novel classifiability measure that captures the possible sources of misclassification with relative ease and is able to accurately reflect the complexity of the subproblem at each node. The proposed approach is fast and does not suffer from as high a computational burden as that incurred by typical model selection algorithms. Empirical results over 26 data sets indicate that our approach is faster and achieves better classification accuracy compared to statistical model select algorithms.

Algorithms↗

Protection of rhesus monkeys against infection with minimally pathogenic simian-human immunodeficiency virus: correlations with neutralizing antibodies and cytotoxic T cells.

We studied the capacity of active immunization of rhesus monkeys with HIV-1 envelope protein (Env) to induce primary virus cross-reactive neutralizing antibodies to prevent infection following intravenous challenge with simian-human immunodeficiency virus (SHIV). Monkeys were immunized with the human immunodeficiency type 1 (HIV-1) strain R2 Env. Initially, the Env was expressed in vivo by an alphavirus replicon particle system, and then it was administered as soluble oligomeric gp140. Concurrently, groups of monkeys received expression vectors that encoded either simian immunodeficiency virus (SIV) gag/pol genes or no SIV genes in vivo to test the additional protective benefit of concurrent induction of virus-specific cell-mediated immune (CMI) responses. Groups of control monkeys received either the gag/pol regimen or sham immunizations. The antibodies induced by the Env immunization regimen neutralized diverse primary HIV-1 strains. Similarly, potent CMI responses were induced by the gag/pol regimen, as measured by gamma interferon enzyme-linked immunospot assays. Differences in the responses among groups of monkeys strongly suggested that there was interference between the Env and gag/pol immunization regimens. Complete protection of some of the monkeys against infection after intravenous challenge with the partially pathogenic SHIV(DH12R (Clone 7)) was associated independently with both neutralizing antibody and CMI responses. Protection was associated with SHIV(DH12 (Clone 7)) serum neutralizing antibody titers of > or =1:80 or with cellular immune responses corresponding to >2,000 spot forming cells per 10(6) peripheral blood mononuclear cells. Immunization was also associated with a reduction in the magnitude and duration of virus load. Induction of cross-reactive, primary HIV-1-neutralizing antibodies is feasible and, when potent, may result in complete protection against infection with a heterologous challenge virus strain.

AIDS Vaccines↗

[Expression of programmed cell death 4 and its clinicopathological significance in human pancreatic cancer].

OBJECTIVE: To investigate the expression of programmed cell death 4 (PDCD4) protein and its clinicopathological significance in human pancreatic cancer. METHODS: Immunohistochemistry was used to examine the expression of PDCD4 protein in 69 specimens of pancreatic cancer and Western blot in 8 fresh specimens. RESULTS: The expression of PDCD4 protein was significantly lower in all 8 fresh pancreatic cancer tissues than that in non-cancerous tissues detected by Western blot. Compared with non-cancerous pancreatic tissue (> 80% of positive cells), low PDCD4 expression was shown in 69 pancreatic cancer tissues (< 30% of positive cells in 36 cases and 30%-80% of positive expression cells in 33 cases). In the 33 cases with 30% and 80% of positive expression cells, the expression rates of PDCD4 protein were 57.6%, 24.2%, and 18.2% in well, moderately, and poorly differentiated cancers, respectively. In the 36 cases less than 30% of positive expression cells, however, the expression rate of PDCD4 protein in well, moderately, and poorly differentiated cases were 19.4%, 41.7%, and 38.9%, respectively. 67.4% (15/23) of the moderately differentiated cases and 70% (14/20) of the poorly differentiated cases showed < 30% of positive expression cells. Only 26.9% (7/26) of the well differentiated cases, however, showed < 30% of positive expression cells, indicating that low PDCD4 expression was associated with histological grade (P < 0.01). There was no relationship between PDCD4 expression and other clinicopathological parameters including patients' sex, age, and TNM stage. CONCLUSIONS: Expression of PDCD4 protein is low in human pancreatic cancer and is correlated with the differentiation levels of human pancreatic cancer. PDCD4 may play an important role in the occurrence and development of pancreatic carcinomas.

Adult↗

[Comparison of pBcl-2 and pBax expression in primary invasive ductal pancreatic cancer between Chinese and Japanese patients].

OBJECTIVE: To clarify the clinicopathologic significance of the expression of the Bcl-2 protein (pBcl-2) and the Bax protein (pBax), and their clinical implications in Chinese and Japanese patients with human invasive ductal carcinomas (IDCs) of the pancreas. METHODS: The study included 59 Chinese and 65 Japanese patients with IDCs of the pancreas. pBcl-2 and pBax expression were immuno-stained with streptavidin-biotin (SAB) method. RESULTS: pBcl-2 (+) was seen in 35.6% of Chinese and in 23.1% of Japanese patients. pBax (+) was seen in 49.2% of Chinese and 64.7% of Japanese patients. A comparison between them showed that there were significant differences in the male patients, in the patients with the moderately differentiated cancer, and in the elderly patients (chi squared = 4.447, P = 0.035; chi squared = 4.114, P = 0.043; chi squared = 6.657, P = 0.010 respective). In both Chinese and Japanese patients, those with pBcl-2 positive expression had a significantly higher survival rate than those with negative one (chi squared = 9.99, P = 0.0016; chi squared = 7.63, P = 0.0058). The group with pBax positive expression had a significantly higher survival rate in Japanese patients (chi squared = 9.37, P = 0.0022). Japanese patients whose tumors exhibited pBcl-2 and pBax positive immunostaining survived significantly longer than Chinese patients did (chi squared = 4.48, P = 0.0342; chi squared = 5.23, P = 0.023). CONCLUSIONS: The expressions of both pBcl-2 and pBax are high found in Chinese and Japanese patients. The pBcl-2 positive expression implies a better prognosis in both Chinese and Japanese patients with IDCs of the pancreas. The effect of pBax expression on prognosis is different between Chinese and Japanese patients.

Adult↗

[Expressions of p53 and Gadd45a proteins in human pancreatic cancer and their clinicopathological significance].

OBJECTIVE: To study the expressions of p53 and Gadd45a proteins and their clinicopathological significance in human pancreatic cancer. METHODS: The expression of p53 and Gadd45a proteins was detected with immunohistochemistry in a series of 59 pancreatic cancers. Their relationships with the clinicopathological parameters including gender, tumor site, TNM stage, histological differentiation, and the prognosis of pancreatic cancer patients were analyzed. RESULTS: The positive expression rate of p53 protein was 67.8% (40/59) and that of Gadd45a protein was 42.4% (25/59). The positive expression rate of p53 protein is significantly higher in patients < 65 years than in patients > or = 65 years (chi squared = 4.711, P = 0.030). Gadd45a expression was not correlated to the age of the patients. No significant difference was found between the expression of p53 proteins and histological differentiation and TNM stage of the tumors. Gadd45a expression was correlated with histological differentiation of pancreatic cancer (chi squared = 10.052, P = 0.007), but not with TNM stage of the tumors. No significant differences in the prognosis were found between the groups with and without p53 expression (chi squared = 0.09, P = 0.764) and the groups with and without Gadd45a expression (chi squared = 0.14, P = 0.704). CONCLUSIONS: Both p53 and Gadd45a are highly expressed in human pancreatic cancer and may be associated with biological features of pancreatic cancer. Their expression alone or co-expression may be not helpful to evaluate the prognosis of patients with pancreatic cancer.

Adult↗

Effects of Antiadhesion preparation on free fibrinogen and fibrin degrading products in abdominal exudates of rabbits postoperatively.

AIM: To observe effects of ACOL on fibrinogen (FIB), fibrin degrading products (FDP) and changes of FIB and FDP concentration in rabbits with intro-abdominal exudates during 7 d after major abdominal surgery. METHODS: Sixty New Zealand rabbits were randomly divided into 4 groups: ACOL group, the control group, DCT group and the normal group. After being modeled, except the normal group, the other 3 groups were treated with different ways for a week; the intro-abdominal exudates of rabbits in the 4 groups were drawn for FIB and FDP measurement once daily during 7 d after major abdominal surgery. RESULTS: FIB and FDP in the intro-abdominal exudates altered in a regular way and ACOL could change the concentration of FIB and FDP in the intra-abdominal exudates after major abdominal surgery. CONCLUSION: ACOL can prevent intestinal adhesion by reducing the concentration of FIB and raising that of FDP in the intro-abdominal exudates after major abdominal surgery.

Abdomen↗

Theoretical modeling study of the necrotic field during high-intensity focused ultrasound surgery.

BACKGROUND: High-intensity focused ultrasound (HIFU) is a type of micro-invasive treatment of tumor. It is important to create a guideline for the volume and position of the necrotic field by means of a theoretical model, this being one of the key problems in the clinic application of HIFU. MATERIAL/METHODS: Based on cellular thermo-necrotic theory, a computational model of temperature distribution and, therefore, the necrotic field was developed. A multi-transducer system with non-interferential and self-focused property was devised to provide experimental verification of the theoretical model. RESULTS: The necrotic field resulting from the modeling simulation did not show any evident difference from that of the experiment. The necrotic field of the same heating duration (4 seconds) was found with both modeling and experiment to be spheroid, with its center at the system's geometric focus and a volume of 1x1x2 cm3. CONCLUSIONS: The model of this study may predict the practical volume of the necrotic field as well as the time needed for it to form.

Computer Simulation↗

[Clonal architecture and ramet population characteristics of Lysimachia congestiflora growing under different light conditions].

The response of clonal architecture and ramet population characteristics to resource heterogeneity is of great ecological significance. This paper studied the variations of clonal architecture and ramet population characteristics of stoloniferous herb Lysimachia congestiflora growing at the open land of forest edge, forest edge, and forest understory of evergreen broad-leaved forest in Mt. Lingyan of Dujiangyan, Sichuan Province, and compared the stolon internode length, frequency distribution of stolon internode length, braching intensity, branching angle, frequency distribution of branching angle, ramet population density, ramet population height, ramet population biomass, and root/shoot of ramet population among the three habitats. The results showed that the stolon internode length, branching intensity, ramet population density and ramet population biomass were different among three habitats. Kruskal Wallis test indicated that the distributions of stolon internode length and branching angle were significantly different among three habitats. The skewness in distribution of stolon internode length was in the order of open land of forest edge>forest edge>forest understory; and the branching angle, ramet population height, and root/shoot of ramet population were significant greater in open land of forest edge than in forest edge and forest understory. The skewness in distribution of branching angle in open land of forest edge was smaller than that in forest edge and forest understory. The branching angle, ramet population height, and root/shoot of ramet population were not significantly different between forest edge and forest understory. These results were discussed in the context of resource acquisition strategy by clonal plants.

Analysis of Variance↗

[Novel mutation of fibrillin 1 gene cause ectopia lentis in a Chinese family].

OBJECTIVE: To identify the mutation gene of a Chinese family with ectopia lentis. METHODS: Clinical observation and pedigree analysis were undertaken in a family with ectopia lentis. Venous blood was drawn from 7 affected and 3 unaffected subjects. Genomic DNA was extracted. Linkage to the fibrillin 1 (FBN1) locus was not excluded. Mutation of this gene was screened by PCR of FBN1 exons and direct sequencing. PCR and restrictive endonuclease digestion were applied for population study. RESULTS: A missense mutation G640A in exon six of FBN1 gene was identified in affected patients of this Chinese family. The correspond amino acid change was Gly214Ser. Restrictive endonuclease site Eag I was eliminated. This mutation was not found in unaffected family members of this family nor it was found among 50 unrelated normal controls. CONCLUSIONS: A novel mutation of FBN1 gene with Glycine to Serine change is responsible for the ectopia lentis patients in a Chinese family.

Asian People↗