Biomedical subjects

Hong Yu

Publications and source records attributed to Hong Yu.

162 records · Page 9Linked to original sources

PubMed2002

Automatic extraction of gene and protein synonyms from MEDLINE and journal articles.

Genes and proteins are often associated with multiple names, and more names are added as new functional or structural information is discovered. Because authors often alternate between these synonyms, information retrieval and extraction benefits from identifying these synonymous names. We have developed a method to extract automatically synonymous gene and protein names from MEDLINE and journal articles. We first identified patterns authors use to list synonymous gene and protein names. We developed SGPE (for synonym extraction of gene and protein names), a software program that recognizes the patterns and extracts from MEDLINE abstracts and full-text journal articles candidate synonymous terms. SGPE then applies a sequence of filters that automatically screen out those terms that are not gene and protein names. We evaluated our method to have an overall precision of 71% on both MEDLINE and journal articles, and 90% precision on the more suitable full-text articles alone

Electronic Data Processing↗

PubMed2002

[The application of 4-color fluorescence labeling antibodies and its significance in immunophenotyping for leukemia by flow cytometer].

To prove the significance of 4-color fluorescence labeling flow cytometric analysis for leukemia immunophenotyping, bone marrow and peripheral blood samples from 88 cases with acute leukemia were analyzed by means of flow cytometry with 4-color fluorescence labeling monoclonal antibodies (McAbs). More than 90% of cases could be classified into acute myeloid, T- or B-lymphocytic leukemia by staining with 13 different kinds of monoclonal antibodies within 4 tubes of combination of antibodies. AML-M(2) - M(7) could also be identified simultaneously. Another one tube of combination of 4 McAbs could be used for further subtyping of those who were undetermined by the above 4 tubes. Patients with AML-M(0)/M(1) which may be negative of myeloperoxidase (MPO) in cytochemistry can be identified by labeling with both membrane and cytoplasmic antibodies. In conclusion, the accuracy of leukemia immunophenotyping has been improved by 4-color flow cytometry analysis.

Adolescent↗

PubMed2002

[Detection of cytoplasmic antigens by flow cytometry and its implication for leukemia immunophenotyping].

The purpose of this study was to optimize a fixation procedure for detection of cytoplasmic antigens by flow cytometry(FCM) and to evaluate the effect of intracellular CD3, CD22, CD79a and myeloperoxidase(MPO) in lineage assignment. Four kinds of fixation procedure and three or four color direct immunofluorescence staining were used to permeate cell membrane and label cell surface and intracellular antigens by means of FCM. Results showed that percentage of cytoplasmic antigens positive cells was the highest and cell scatter and fluorescence intensity of CD45 were not changed after using of FACS permeabilization solution. MPO protein was positive in 16/18 acute myeloid leukemia(AML) patients. 4 cases of T cell-acute lymphoblastic leukemia (T-ALL) cases were positive for cytoplasmic CD3(c CD3) but surface CD3 was negative. c CD22 was only detected in 9/13 of B-ALL and cCD79a was positive in 5/5 B-ALL. 18/38 cases of acute leukemia were expressed in more than one lineage marker, 8/21 cases of acute non-lymphocytic leukemia(ANLL) were CD7 positive. 7/17 cases of acute lymphocytic leukemia (ALL) expressed CD13. After further cytoplasmic antigen detection, one was considered to be a T/myeloid biphenotypic leukemia, another one was diagnosed as biclonal or mixed leukemia. The results suggest that intracellular CD3,CD22,CD79a and MPO are lineage specific markers, they are very important for biphenotypic and biclonal/mixed acute leukemia identification

Adolescent↗

PubMed2002

[An epidemiological survey of low vision and blindness of senile persons in Beixinjing blocks, Shanghai].

OBJECTIVE: To investigate the morbidities of low vision and blindness and the leading cause of blindness in residents aged >or= 60 years in Beixinjing blocks, Shanghai. METHODS: The vision archives were first established for total old residents. The pinhole visual acuity was recorded and classified under WHO grading system. Assigned ophthalmologic doctors assured the leading blind causes of every blind person. RESULTS: The response rates in 1994, 1997 and 2000 were 83.87%, 88.32% and 91.98% respectively. The morbidities of low vision and blindness in these 3 years were 3.61% and 1.51%, 2.31% and 1.09%, 1.31% and 0.71% respectively. The leading causes of blindness were degenerative retinopathy (including age-related maculopathy), cataract, corneal diseases and retinal angiopathy (including hypertensive and diabetic retinopathy, retinal artery or venous occlusion, etc). CONCLUSIONS: The morbidities of low vision and blindness in this area decreased from 1994. The leading cause of blindness was degenerative retinopathy.

Aged↗

PubMed2002

[A monitoring study of electromyography median frequency on fatigue of erector spinalis in drivers working at high altitude].

OBJECTIVE: To evaluate the role of muscle fatigue in the pathogenesis of high prevalence of low back pain(LBP) in drivers who work at high altitude, in order to seek the effective measures for prevention and treatment of LBP. METHOD: The spectral electromyographic(EMG) changes during isometric contraction of erector spinalis to fatigue in 26 drivers in the field were consecutively recorded after daily driving for 5 days. The relationship between the decline of median frequency and the development of the back extensor fatigue were analyzed. RESULTS: The decline rates of EMG median frequency of the erector spinalis on 1-5 working day [(-0.258 +/- 0.087), (-0.248 +/- 0.070), (-0.256 +/- 0.097), (-0.267 +/- 0.093), (-0.274 +/- 0.081)%/s respectively] were significantly different from that of baseline measured before work [(-0.175 +/- 0.114)%/s, P < 0.05 or P < 0.01]. A positive correlation was also found between the decline rate and the working time(r = -0.809, P < 0.05). CONCLUSION: The high prevalence of LBP in the drivers working at high altitude is due to acumulative fatigue of back extensor resulting from long-distance driving, lack of proper rest, decrease of muscle endurance and increase of liability to fatigue, consequently leading to the muscle dysfunction and finally LBP.

Altitude↗

PubMed2002

[Lower back pain in truck drivers working in plateau areas and its prevention].

OBJECTIVE: To investigate the epidemiological characteristics of lower back pain of truck drivers in plateau areas with an analysis of the causes and evaluated the effects of the protective measures. METHODS: The self-reported lower back symptom was investigated by questionnaire in 1,132 male drivers in plateau areas. Vibration of the driver lumbar back was measured real time with or without wearing corset. Study the effect of the special corset for drivers and the massage on back by self-control design of big sample intervention experiments. RESULTS: The prevalence of lower back pain of drivers in plateau areas was 86.1%. High level of its prevalence is due to many factors. Special corset for drivers and massage on back by themselves can reduce the degree of the pain. CONCLUSION: Driving in plateau areas is a special occupational work with high level of prevalence of lower back pain which can be prevented.

Automobile Driving↗

PubMed2002

[Determination of amino acids and glucose in amino acid injection by anion exchange chromatography with integrated pulsed amperometric detection].

A direct, sensitive, simple and practical method for the determination of amino acids and glucose in amino acid injection by anion exchange chromatography with integrated pulsed amperometric detection was developed. There is no need for sample pretreatment. The retention behavior of amino acids and glucose on the anion exchange column was investigated using sodium hydroxide and sodium acetate as eluent. When the concentration of sodium hydroxide was changed, the change in the retention times was generally greater for amino acids than for glucose. The difference can be used to improve the separation between amino acids and glucose. When the concentration of sodium acetate was changed, the change in the retention times was generally greater for amino acids containing two carboxyl groups than for amino acids containing only one carboxyl group. The difference can be used to improve the separation between di-carboxylic amino acids and mono-carboxylic amino acids. In order to separate amino acids and glucose, a ternary gradient elution method with water, sodium hydroxide and sodium acetate as mobile phases was employed. The optimized gradient elution condition for the analysis of 17 amino acids and glucose in amino acid injection was obtained. The time of the gradient elution program was 74 min. Under the optimized conditions and the column temperature of 30 degrees C, the detection limits for 17 amino acids and glucose were 0.3 pmol- 10.3 pmol. The calibration graphs of peak area for all the analytes were linear in the ranges about two orders of magnitude. The relative standard deviations (RSDs) (n = 5) were 0.7% - 3.8%. The recoveries of added standard were 88.3% - 104.6%.

Amino Acids↗

PubMed2001

[Effect of Autocrine VEGF on Chronic Myeloid Leukemia Cell Line K562]

Vascular endothelial growth factor (VEGF) is a specific mitogen for vascular endothelial cells. It has been associated with angiogenesis, growth, metastasis and poor prognosis in solid tumors. Lately, it has been known that VEGF expression is higher in bone marrow from chronic myeloid leukemia (CML) patients than that in normal subjects. However, it is not clarified that the effect of VEGF on the abnormal proliferation of CML cells. In order to explore the effect of autocrine VEGF on CML cells, K562 cells were transfected with the VEGF(121) cDNA sense vector (K562/S) or with the VEGF(121) cDNA antisense vector (K562/As). K562 cells were transfected with the pcDNA(3) vector (K562/V) as the control. Cell proliferation was determined by MTT and colony forming assay in vitro. Flow cytometric Annexin-V-FITC/PI dual labeling technique was performed to observe the effect of VEGF(121) cDNA transfection on apoptosis of K562 cells. Results indicated that K562/S transfectants exhibited a 3-fold increase in VEGF secretion, and K562/As transfectants exhibited a 49% reduction in VEGF secretion. K562/As showed a reduced growth rate and colony forming efficiency as compared to K562/V. K562/S showed an increasing growth rate and colony forming efficiency as compared to K562/V. K562/As had more apoptotic cells than K562/V and K562/S in the same culture condition. These data suggest that VEGF plays an important role in the abnormal proliferation and apoptosis in CML cells through an autocrine mechanism.

Journal Article↗

PubMed2001

[Expression of AC133 Antigen on Acute Leukemia Cells]

To investigate the expression of AC133 antigen on acute leukemia cells and its clinical significance, samples of 29 patients with acute lymphocytic leukemia (ALL) and 32 patients with acute myelocytic leukemia (AML) were analyzed by flow cytometric three-color direct immunofluorescence methods. It was found that 13 of 29 ALL, 6 of 8 AML-M(0)/M(1), 4 of 16 AML-M(2) and 4 of 8 AML-M(4)/M(5) expressed AC133. The mean fluoresence intensity of AC133 in each subtype of AML-M(0)/M(1), AML-M(2) and AML-M(4)/M(5) was 227.1, 143.1 and 142.5, respectively. Among 27 AC133(+) cases (44.3%), 25 cases coexpressed CD34 (92.6%) and 13 cases coex- pressed CD117 (48.1%). In contrast to other reports, our data do not support the findings that AML-M(4)/M(5) expressed very high levels of AC133. In conclusion, AC133 antigen, coexpressed with CD34 and CD117, appears more frequently and more intensely in AML-M(0)/M(1).

Journal Article↗

PubMed2000

Effect of hepatocyte apoptosis induced by TNF-alpha on acute severe hepatitis in mouse models.

AIM:To study the effect of hepatocyte apoptosis and necrosis induced by TNF-alpha on the pathogenesis of acute severe hepatitis (ASH).METHODS:The model of ASH was prepared in D-galactosamine (GalN) sensitized BALB/c mice by injection of either endotoxin (ET) or tumor necrosis factor-alpha(TNF-alpha. Morphological changes of apoptotic hepatocytes were studied by both light and electron microscope and in site end labeling method (ISEL). Molecular biological changes of DNA ladder were observed by electrophoresis of extract from liver tissues. Biochemical changes were measured by alanine aminotransferase (ALT), aspartic aminotransferase (AST) and TNF-alpha. The relation between apoptosis and necrosis was evaluated simultaneously.RESULTS:The sequence of hepatocyte apoptosis, necrosis, and final death from ASH was observed both in GalN/ET and GalN/TNF-alpha group. Apoptosis was prominent at 3.5h and 6h after injection of inducer, while necrosis became dominant at 9h after challenge. The appearance of apoptosis was earlier in GalN/TNF-alpha group than that in GalN/ET group. Pretreatment of mice with antiTNF IgG1 may completely prevent the liver injury induced by GalN/ET.CONCLUSION:TNF-alpha can cause liver amage by inducing hepatic apoptosis and necrosis in mice with endotoxemia.

Journal Article↗

PubMed2000

[Standardization and Quality Control in Flow Cytometric Enumeration of CD34(+) cells]

The enumeration of CD34(+) cells by flow cytometry is commonly employed to assess hematopoietic stem/progenitor cells in cord blood, peripheral blood and apheresis products. Interlaboratory variation of CD34(+) cells enumeration is exceedingly large. Factors contributing to those variation, currently established flow cytometry protocols and comparison between these protocols were reviewed. CD34(+) cells in 45 cord blood samples, 12 normal bone marrows and 4 apheresis products were also enumerated in our laboratory by using ProCUNT kit, and results showed that the ProCUNT is highly standardizaed and could assist in reducing interlaboratory variation of CD34(+) cells.

Journal Article↗

PubMed2000

[The Function of Dendritic Cells Derived from Chronic Myeloid Leukemia]

The purpose of this study was to investigate the function of dendritic cells derived from chronic myeloid leukemia (CML-DC). Mononuclear cells were prepared from bone marrow and peripheral blood of 24 patients with CML, and the DCs were obtained by incubation of MNCs with media containing GM-CSF, IL-4 and TNF-alpha. The phenotype of CML-DCs was identified by flow cytometry. FITC-dextran uptake, (3)H-TdR incorporation or MTT assay and lactate dehydrogenase release assay were used to detect uptake of exogenous antigen in immature DCs, the antigen presenting ability in mature DCs and specific cytotoxicity of CTL to leukemic cells, respectively. The DCs with high expression of CD1a, CD86, CD80, HLA-DR, CD54 and CD4 were obtained from marrow and blood of patients with CML. The uptake of FITC-DX was observed in early DCs. There was a potent stimulation to allo-MLR in DCs cultured for 7 - 10 days, and a lightly lower stimulation to auto-MLR. CML-DCs can induce the generation of specific cytotoxic T cells. These results suggest that CML-DCs are functional DCs with the ability to induce anti-leukemia effect.

Journal Article↗

PubMed2000

[beta1 Integrin Dysfunction in Adult Chronic Myeloid Leukemia Bone Marrow Cells]

According to our previous experiments, Ph(+) chronic myeloid leukemia (CML) cell line K562 cells have defects in beta 1 integrin activation. In order to search the same regularity in Ph(+) CML bone marrow cells, bone marrow mononuclear cells (BMMNC) from 12 cases of Ph(+) CML and 10 cases of normal individuals were studied. Their expression rate of 9EG7 epitope on beta1 integrin post treatment by 8A2 or GM- or G-CSF and cell adhesion ability with soluble fibronectin (FN) were evaluated by flow cytometry; in addition, the effects of CGP57148B, a highly specific ABL tyrosine kinase inhibitor, were observed. Our results showed that 9EG7 expression rate and FN binding rate were very low in all the inactivated cells. The parameter increased markedly post 8A2 activation in both NBMMNCs and CMLBMMNCs, but the degree of increase in CMLBMMNCs was significantly lower than that in NBMMNCs; GM-CSF or G-CSF could significantly increase the parameters in NBMMNCs while had no effects on that in CMLBMMNCs. CGP57148B could increase the beta1 integrin activation potential of CMLBMMNCs but had no effects on that of NBMMNCs. The results indicate that decreased activation potential of beta1 integrin in CMLBMMNCs is the major cause of adhesion defects of Ph(+) CML cells; beta1 integrin functional insufficiency in CMLBMMNCs could not be directly reversed by ABL tyrosine kinase inhibitor CGP57148B.

Journal Article↗

PubMed1998

High Expression of a cDNA Coding for Human Lymphotoxin alpha Derivative in E. coli and Purification of Its Protein Product.

Using PCR, a cDNA coding for human lymphotoxin alpha derivative (hLTalphaDa) lacking 27 amino acids at N-terminal of natural hLT was constructed. The expression construct was expressed in E. coli BL21 (DE3). The product of expression was in the form of inclusion bodies, and accounted for 60%-80% of total bacterial proteins. The product protein was purified to over 95% by treatments of inclusion bodies. The specific activity of hLTalphaDa was above 2x10(8) IU(per mg protein). Its cytotoxic activity can be neutralized by monoclone antibody against hLT. The anti-tumor effects of hLTalphaDa were also tested in vitro and in vivo.

Journal Article↗

PubMedDate not supplied

Idiopathic postoperative ascites after laparoscopic salpingectomy for ectopic pregnancy.

Postoperative ascites is a rare and serious complication of laparoscopic procedures. Urinary tract injury, bowel injury, and lymph duct injury are the common causes; however, in some patients no definitive cause can be identified after an extensive diagnostic work-up. We present a case of postoperative ascites of unknown origin. The patient recovered with general treatments. We presume that diffuse peritoneal injury may have been caused by unidentified substances in our patient.

Abdominal Pain↗

PubMedDate not supplied

Automatically identifying gene/protein terms in MEDLINE abstracts.

MOTIVATION: Natural language processing (NLP) techniques are used to extract information automatically from computer-readable literature. In biology, the identification of terms corresponding to biological substances (e.g., genes and proteins) is a necessary step that precedes the application of other NLP systems that extract biological information (e.g., protein-protein interactions, gene regulation events, and biochemical pathways). We have developed GPmarkup (for "gene/protein-full name mark up"), a software system that automatically identifies gene/protein terms (i.e., symbols or full names) in MEDLINE abstracts. As a part of marking up process, we also generated automatically a knowledge source of paired gene/protein symbols and full names (e.g., LARD for lymphocyte associated receptor of death) from MEDLINE. We found that many of the pairs in our knowledge source do not appear in the current GenBank database. Therefore our methods may also be used for automatic lexicon generation. RESULTS: GPmarkup has 73% recall and 93% precision in identifying and marking up gene/protein terms in MEDLINE abstracts. AVAILABILITY: A random sample of gene/protein symbols and full names and a sample set of marked up abstracts can be viewed at http://www.cpmc.columbia.edu/homepages/yuh9001/GPmarkup/. Contact. hy52@columbia.edu. Voice: 212-939-7028; fax: 212-666-0140.

Abstracting and Indexing↗

PubMedDate not supplied

Parallel synthesis of diarylureas and their evaluation as inhibitors of insulin-like growth factor receptor.

Diarylurea (DAU) compounds, particularly species composed of a heteroaryl ring system conjugated through a urea linkage to a substituted arene, were previously identified by the screening of a diverse chemical library to be active against the insulin growth factor receptor (IGF-1R). DAU compounds 4{a,b} were synthesized in parallel by the coupling of aryl amines 2{a} with aryl isocyanates 3{b}. Preparative RP-HPLC purification was found necessary to remove an impurity 5{b}, the symmetric urea resulting from the hydrolytic degradation of aryl isocyanates. Two libraries of DAU compounds were prepared to perform preliminary optimization of the two-ring systems for inhibitory activity against IGF-1R. In the first library, we explored a series of heteroaryl ring systems and found the 4-aminoquinaldine ring system to be optimal among those evaluated. The second library fixed the 4-aminoquinaldine ring system and we evaluated a series of substituted arenes conjugated to it. Overall, eight compounds based on the 4-aminoquinaldine heteroaryl system were found to have moderate activity against IGF-1R with IC(50) values better than 40 microM.

Animals↗

PubMedDate not supplied

Mapping abbreviations to full forms in biomedical articles.

OBJECTIVE: To develop methods that automatically map abbreviations to their full forms in biomedical articles. METHODS: The authors developed two methods of mapping defined and undefined abbreviations (defined abbreviations are paired with their full forms in the articles, whereas undefined ones are not). For defined abbreviations, they developed a set of pattern-matching rules to map an abbreviation to its full form and implemented the rules into a software program, AbbRE (for "abbreviation recognition and extraction"). Using the opinions of domain experts as a reference standard, they evaluated the recall and precision of AbbRE for defined abbreviations in ten biomedical articles randomly selected from the ten most frequently cited medical and biological journals. They also measured the percentage of undefined abbreviations in the same set of articles, and they investigated whether they could map undefined abbreviations to any of four public abbreviation databases (GenBank LocusLink, SWISSPROT, LRABR of the UMLS Specialist Lexicon, and BioABACUS). RESULTS: AbbRE had an average 0.70 recall and 0.95 precision for the defined abbreviations. The authors found that an average of 25 percent of abbreviations were defined in biomedical articles and that of a randomly selected subset of undefined abbreviations, 68 percent could be mapped to any of four abbreviation databases. They also found that many abbreviations are ambiguous (i.e., they map to more than one full form in abbreviation databases). CONCLUSION: AbbRE is efficient for mapping defined abbreviations. To couple AbbRE with abbreviation databases for the mapping of undefined abbreviations, not only exhaustive abbreviation databases but also a method to resolve the ambiguity of abbreviations in the databases are needed.

Abbreviations as Topic↗