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W Li

Publications and source records attributed to W Li.

At least 199 records · Page 11Linked to original sources
PubMed2001

Genomic imbalances in human lung adenocarcinomas and squamous cell carcinomas.

Comparative genomic hybridization analysis was performed on 67 non-small-cell lung cancers (NSCLCs), including 32 squamous cell carcinomas (SCCs) and 35 adenocarcinomas (ACs), to identify differences in the patterns of genomic imbalance between these two histologic subtypes. Among the entire tumor set, the chromosome arms most often overrepresented were 1q, 3q, 5p, and 8q, each detected in 50-55% of cases. The most frequently underrepresented arms were 9q, 3p, 8p, and 17p. The number of imbalances was similar in SCCs and ACs (median number/case: 12 and 11, respectively). Moreover, many imbalances, such as gains of 1q, 5p, and 8q, occurred at a high frequency in both histologic subgroups. Several statistically significant differences, however, were found. The most prominent difference was gain of 3q24-qter, seen in 81% of SCCs compared with 31% of ACs (P < 0.0001), with amplification at 3q25-26 being detected in eight of 32 (25%) SCCs but in only two of 35 (6%) ACs. Gain of 20p13 and loss of 4q also were seen at a significantly higher rate in SCCs than in ACs, whereas overrepresentation of 6p was more common in ACs. Gains of 7q and 8q each were associated with higher-stage tumors and either positive nodal involvement or higher tumor grade. These data suggest that genes located in several chromosomal regions, particularly 3q25-26, may be associated with phenotypic properties that differentiate lung SCCs from ACs. Furthermore, certain imbalances, prominent among them gains of 7q and 8q, may be indicative of tumor aggressiveness in NSCLCs.

Adenocarcinoma↗
PubMed2001

Marker selection by Akaike information criterion and Bayesian information criterion.

We carried out a discriminant analysis with identity by descent (IBD) at each marker as inputs, and the sib pair type (affected-affected versus affected-unaffected) as the output. Using simple logistic regression for this discriminant analysis, we illustrate the importance of comparing models with different number of parameters. Such model comparisons are best carried out using either the Akaike information criterion (AIC) or the Bayesian information criterion (BIC). When AIC (or BIC) stepwise variable selection was applied to the German Asthma data set, a group of markers were selected which provide the best fit to the data (assuming an additive effect). Interestingly, these 25-26 markers were not identical to those with the highest (in magnitude) single-locus lod scores.

Adult↗
PubMed2001

Two approaches for consolidating results from genome scans of complex traits: selection methods and scan statistics.

This work has two purposes: (i) empirically selecting levels of significance that maximize the fraction of markers close to a gene (hit rate) when performing linkage analyses of simulated data and (ii) evaluating the utility of a previously reported scan statistic on the same data. Genotype data were simulated from a trait model of seven susceptibility genes. For purpose (i), five statistics were evaluated on all marker loci in fifty replicates; two-point lod and heterogeneity lod scores maximized over dominance (mlod, mhlod), a multi-allelic TDT test, an affected sib-pair test (ASP), and a model-free test on all sib-pairs (ALL_SIBS). Within each replicate the fraction of markers (hit rate) significant at specified levels of significance and also (a) within fifty markers of, or (b) on the same chromosome as a major gene was calculated. For purpose (ii), scan statistics of length 15 were calculated for each chromosome and their empirical significance levels estimated on the basis of 500 replicates generated under no linkage. The scan statistic was applied to the mhlod scores from one replicate (Replicate 5). Empirical p-values for the scan statistic were determined by computing mhlod scores on 500 replicates of simulated null data. For purpose (i), significance levels between 0.001 and 0.01 had the greatest hit rate for all five methods and both criteria. For criterion (a) at the 0.001 level of significance, both mlod and mhlod displayed the highest hit rates, approximately 0.4 for each. For criterion (b), all methods but ALL_SIBS and ASP had hit rates ranging between 0.4 and 0.5. For purpose (ii), the scan statistic proved equally or more powerful than the single-locus statistic for two of the seven susceptibility genes while the remaining five genes were not detected.

Chromosome Mapping↗
PubMed2001

Population based linkage disequilibrium mapping of QTL: an application to simulated data in an isolated population.

Despite successes in mapping and cloning genes involved in rare Mendelian diseases, genetic dissection of quantitative traits into single Mendelian factors still remains a challenging task. As the dense map of single nucleotide polymorphism (SNP) markers becomes available in the near future, linkage disequilibrium (LD) mapping will become one of major tools for mapping and identifying quantitative trait loci (QTL). In this report, we present a population-based linkage disequilibrium mapping of QTL. This method unifies the analysis of mapping QTL in humans and in model organisms and can be used for randomly sampled individuals. The proposed method is applied to search for polymorphism sites within the candidate genes 2 and 6, which influence quantitative traits Q1 and Q2 or Q5, in a simulated data set in an isolated population.

Chromosome Mapping↗
PubMed2001

MR ventilation-perfusion imaging of human lung using oxygen-enhanced and arterial spin labeling techniques.

Magnetic resonance ventilation-perfusion (V/Q) imaging has been demonstrated using oxygen and arterial spin labeling techniques. Inhaled oxygen is used as a paramagnetic contrast agent in ventilation imaging using a multiple inversion recovery (MIR) approach. Pulmonary perfusion imaging is conducted using a flow-sensitive alternating inversion recovery with an extra radiofrequency pulse (FAIRER) technique. A half Fourier single-short turbo spin echo (HASTE) sequence is used for data acquisition in both techniques. V/Q imaging was performed in ten of the twenty volunteers, while either ventilation or perfusion was imaged in the other ten. This V/Q imaging scheme is completely noninvasive, does not involve ionized radiation, and shows promising potential for clinical use in the diagnosis of lung diseases such as pulmonary embolism.

Adult↗
PubMed2001

Long-term toxic impact of 2,3,7,8-tetrachlorodibenzo-p-dioxin on the reproduction, sexual differentiation, and development of different life stages of Gobiocypris rarus and Daphnia magna.

The sexual ratio of Gobiocypris rarus exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and 17 beta-estradiol from embryo to sexually mature revealed feminization and overdevelopment of connective tissue in male fish gonad in 2--30 pg/L TCDD concentration range. Daphnia magna was not sensitive to the high dose of TCDD (0.1--1000 ng/ml), but the reproduction of D. magna treated with TCDD decreased after the 8th day. 7-Ethoxyresorufin-O-deethylase (EROD) activities in newly fertilized eggs of G. rarus exposed to TCDD dosage groups (1000--100,000 pg/L) were significantly induced and increased with TCDD concentrations at the early life stage, while no difference was found between low TCDD dosage groups (<100 pg/L), but a good relationship between the EROD activity and the TCDD concentration was observed during a long-term developmental stage. There was a pericardial edema formed in a 2-week yolk-sac at the concentration of 1000 pg/L TCDD. But in the exposure group (2 pg/L TCDD for 120 days), the cell nuclei of hepatocytes was far from the center and packed toward the cell membrane; the cristae of most mitochondria in the cell dropped and collapsed; the rough endoplasmic reticulum broke into fragments; and numerous lipid droplets formed in the cell.

Animals↗
PubMed2001

The gene mutated in cocoa mice, carrying a defect of organelle biogenesis, is a homologue of the human Hermansky-Pudlak syndrome-3 gene.

Hermansky-Pudlak syndrome (HPS) is a group of human disorders of organelle biogenesis characterized by defective synthesis of melanosomes, lysosomes, and platelet dense granules. In the mouse, at least 15 loci are associated with mutant phenotypes similar to human HPS. We have identified the gene mutated in cocoa (coa) mice, which is associated with an HPS-like mutant phenotype and thus represents a strong candidate for human HPS. Analysis of coa-mutant mice and cultured coa-mutant mouse melanocytes indicates that the normal coa gene product is involved in early stages of melanosome biogenesis and maturation.

Alleles↗
PubMed2001

Delivery and scavenging system for small animal inhalational anesthesia.

BACKGROUND: Inhalational agents have been widely used for anesthesia in laboratory animals. However, the safe use of inhalational agents in small laboratory animals has been limited by the lack of a suitable and effective scavenging system for the removal of waste anesthetic gases. The aim of the present study is to develop an anesthetic system that can be manufactured using common household and laboratory items. MATERIALS AND METHODS: An anesthetic system was designed for rats weighing from 300 to 350 g. A face mask for the rat was made by cutting off the distal part of a 50-ml centrifuge tube. A scavenging hood was made from a transparent plastic food storage box. Exhaust of anesthetic gases from the scavenger hood was facilitated by fitting an outlet connected to a pump. Four experienced researchers or technicians tested the scavenger hood. RESULTS: In 79.2% of the trials the participants could smell halothane when the pump from the scavenger system was not operational. However, when the pump was switched on, halothane was detected only 16.7% of the time (P < 0.001). CONCLUSION: We have developed a simple and effective method of delivering inhalational anesthesia to small laboratory animals and of removing waste anesthetic gases.

Anesthesia, Inhalation↗
PubMed2001

An improved rat model of obstructive jaundice and its reversal by internal and external drainage.

BACKGROUND: A simple and reproducible rat model that allows studies of the reversal of obstructive jaundice (OJ) by internal (ID) and external (ED) drainage is not available at present. METHODS: OJ was induced in rats by double ligation and division of the common bile duct. To minimize tissue handling and dissection the duodenum was extracted with a ophthalmic muscle hook and the common bile duct isolated using very fine forceps. One week after bile duct ligation, ID was accomplished by implanting a length of infant feeding tube between the dilated bile duct and the duodenum. ED was achieved by placing a PVC tube into the dilated bile duct and exteriorizing the other end at the nape of the neck. RESULTS: Minimal adhesions were found around the dilated common bile duct, which made relaparotomy for drainage easy. Alanine transaminase, total bilirubin, alkaline phosphatase, and gamma-glutamyltransferase were significantly raised after bile duct ligation. All parameters returned to control levels after ID for 7 days. In the ED group plasma albumin was significantly decreased and alkaline phosphatase remained marginally elevated. CONCLUSIONS: We have developed a simple and reproducible rat model that allows for the study of reversal of OJ by ID or ED. We also demonstrated that ID is superior to ED in reversing impaired liver function in OJ.

Animals↗
PubMed2001

Congenital lactic acidosis: evaluation of the properties of the a199t natural variant of human pyruvate dehydrogenase e1alpha by in vitro mutation.

One cause of congenital lactic acidosis is a mutation in the E1 alpha-subunit of the pyruvate dehydrogenase multienzyme complex. Little is known about the consequences of these mutations at the enzymatic level. Here we study the A199T mutation by expressing the protein in Escherichia coli. The specific activity is 25% of normal and the K(m) for pyruvate is elevated by 10-fold. Inhibitors of lactate dehydrogenase might be a useful therapy for patients with such mutations.

Acidosis, Lactic↗
PubMed2001

Feature (gene) selection in gene expression-based tumor classification.

There is increasing interest in changing the emphasis of tumor classification from morphologic to molecular. Gene expression profiles may offer more information than morphology and provide an alternative to morphology-based tumor classification systems. Gene selection involves a search for gene subsets that are able to discriminate tumor tissue from normal tissue, and may have either clear biological interpretation or some implication in the molecular mechanism of the tumorigenesis. Gene selection is a fundamental issue in gene expression-based tumor classification. In the formation of a discriminant rule, the number of genes is large relative to the number of tissue samples. Too many genes can harm the performance of the tumor classification system and increase the cost as well. In this report, we discuss criteria and illustrate techniques for reducing the number of genes and selecting an optimal (or near optimal) subset of genes from an initial set of genes for tumor classification. The practical advantages of gene selection over other methods of reducing the dimensionality (e.g., principal components), include its simplicity, future cost savings, and higher likelihood of being adopted in a clinical setting. We analyze the expression profiles of 2000 genes in 22 normal and 40 colon tumor tissues, 5776 sequences in 14 human mammary epithelial cells and 13 breast tumors, and 6817 genes in 47 acute lymphoblastic leukemia and 25 acute myeloid leukemia samples. Through these three examples, we show that using 2 or 3 genes can achieve more than 90% accuracy of classification. This result implies that after initial investigation of tumor classification using microarrays, a small number of selected genes may be used as biomarkers for tumor classification, or may have some relevance in tumor development and serve as a potential drug target. In this report we also show that stepwise Fisher's linear discriminant function is a practicable method for gene expression-based tumor classification.

Humans↗
PubMed2001

The clinical relevance of molecular staging for melanoma.

The presence of metastatic disease in the regional nodal basin is the most important prognostic indicator for patients with malignant melanoma. The metastatic status of the sentinel lymph node (SLN), defined as the first node in the basin to drain a primary tumor, has been shown to represent that of the entire basin. Since routine histologic examination of lymph nodes often underestimates the presence of micrometastatic disease, a more sensitive assay for detecting tumor cells is needed. We have previously shown that a molecular assay based on the reverse transcriptase polymerase chain reaction (RT-PCR) was able to define a population of patients at higher risk for both recurrence and death, compared with routine H&E histology. Recently, we have compared "molecular staging" of patients by RT-PCR with conventional S-100 immunohistochemistry (IHC) staining of the SLNs. In these studies, SLN specimens were bivaled, and half of each specimen was examined by routine histology, including both H&E and S-100 IHC. The other half of each specimen was analyzed by a nested RT-PCR assay. H&E histology alone detected metastatic disease in 36 of 233 (16%) patients tested. Serial sectioning and IHC detected micrometastatic disease in another 16 patients, thus increasing the proportion of patients with nodal disease to 22%. RT-PCR detected micrometastatic disease in 114 of 181 patients who were negative by conventional methods, further increasing the proportion of patients with evidence of nodal disease to 70% overall. The clinical significance of these findings is still uncertain. The value of additional therapy (including elective lymph node dissection and interferon therapy) for patients who are positive only by the molecular method is currently being investigated by the national multi-center Sunbelt Melanoma Trial.

Biomarkers, Tumor↗
PubMed2001

Anti-idiotypic antibody (ab2) vaccines: coupling of Ab2 BR3E4 to KLH increases humoral and/or cellular immune responses in animals and colorectal cancer patients.

The colorectal carcinoma (CRC)-associated CO17-1A/GA733 antigen (Ag) has been the target of a phase II/III randomized trial of passive immunotherapy with monoclonal antibody CO17-1A (Ab1), and phase I active immunotherapy trials with polyclonal anti-idiotypic antibodies (Ab2) mimicking the CO17-1A or GA733 epitope of the Ag. However, monoclonal rat Ab2 BR3E4 directed against Ab1 CO17-1A was superior to polyclonal Ab2 in inducing antigen-specific humoral and cellular immune responses in mice and rabbits. Various forms of Ab2 BR3E4, i.e., BR3E4-F(ab')2 precipitated with aluminum-hydroxide (alum), BR3E4-F(ab')2 coupled to KLH and precipitated or non-precipitated with alum, and BR3E4-IgG in alum or incomplete Freund's adjuvant were compared for their capacity to induce in rabbits anti-anti-idiotypic antibodies (Ab3) that specifically bind to the CO17-1A Ag. BR3E4-F(ab')2 coupled to KLH and precipitated with alum was shown to induce the highest Ab3 titers, followed by Ab2 BR3E4-IgG in alum. Therefore Ab2 BR3E4 as intact IgG (IgG group) or as F(ab')2 coupled to KLH (KLH group), was administered in a phase I trial to 45 patients with CRC, stage Dukes'D (UICC stage IV), with the goal to modulate patients' immune responses to their tumors. Fifteen of 23 patients in the IgG group developed Ab3 binding specifically to Ab2, and in four of these patients the Ab3 also specifically bound to Ag-positive CRC cells. Lymphoproliferative responses to Ab2 and/or GA733-2E Ag stimulation were observed in three of these patients. Eighteen of the 22 KLH group patients tested developed Ab3 and the Ab3 bound specifically to CRC cells in eight patients. Five of the 15 KLH group patients tested developed lymphoproliferative responses to Ab2 and/or GA733-2E Ag. Thus, there was a trend for the KLH group demonstrating higher immune response rates than the IgG group. Clinical responses were rare in these patients with liver metastases.

Animals↗
PubMed2001

Application of CD45/SSC gating multiparameter flow cytometry in the classification of acute leukemia--an analysis of 139 cases.

In order to study the significance of flow cytometry immunophenotyping in the diagnosis of acute leukemia, CD45/SSC gating multiparameter flow cytometry (FCM) was utilized to analyze the immunophenotypes of 139 cases of acute leukemia. 139 cases of acute leukemia were enrolled in our hospital from April 1998 to April 2000. Morphological analysis and FCM immunophenotypic tests were conducted on all cases. Our results showed that CD45/SSC gating multiparameter flow cytometry immunophenotyping could reflect the origin of leukemic cells specifically. It is one of the important methods for the diagnosis of ALL, AML, and HAL. CD45/SSC gating multiparameter FCM analysis is a good technique for immunophenotyping. FCM immunophenotypic analysis can help improve the diagnosis and classification of acute leukemia, and extend the use of FCM in clinical practice.

Adolescent↗
PubMed2001

Neuronal responses from beyond the classic receptive field in V1 of alert monkeys.

Responses of primary visual cortex (V1) neurons to stimuli inside the classic receptive field (CRF) can be modulated by stimuli outside the CRF. We recently reported that responses of most V1 neurons to a line in the CRF center are inhibited by large surround-stimuli and that this modulation is stimulus selective. Here we report that a significant proportion of V1 neurons in alert monkeys respond directly to stimuli outside the CRF with very long latency and much reduced selectivity. When surround stimuli are presented alone, three response patterns can be distinguished in 153 single- or multiunits tested: (1) 31.4% have no significant response; (2) 50.3% show excitatory responses that are significantly higher than spontaneous activity. The average latency of these responses is about 145 ms, 2-3 times longer than center responses; (3) 18.3% show suppressed spontaneous activity after stimulus onset. The direct surround responses are found to be only weakly selective for the orientation of contextual lines, and not selective for other contextual patterns tested. While the outburst of responses to stimuli within the CRF is not affected by reducing stimulus duration from 500 ms to 50 ms, late excitatory surround responses are virtually eliminated. We propose that the late excitatory surround responses to extra-CRF stimulation alone are the reflection of feedback from higher cortical areas and may contribute to reduced contextual inhibition of cells in V1. This could play a role in figure-ground segregation.

Animals↗
PubMed2001

Highly efficient expression of rabbit neutrophil peptide-1 gene in Chlorella ellipsoidea cells.

A highly efficient system was developed for the expression of foreign genes in Chlorella ellipsoidea cells. The effect of five promoters on the expression efficiency of beta-glucuronidase (GUS) gene was evaluated by transient expression of the UidA gene. Among these promoters, Ubiquitin-omega was found to be the most efficient and was selected to drive the expression of foreign genes in Chlorella cells. A gene encoding the mature rabbit neutrophil peptide-1 (NP-1) was introduced into the cells. Integration of the gene for NP-1 into the Chlorella genome was confirmed by PCR and Southern blot analysis. In, vitro anti-microbial testes demonstrated the expression of biologically active NP-1 by the transgenic Chlorella cells.

Animals↗
PubMed2001

Isolation and characterization of a novel cDNA, UBAP1, derived from the tumor suppressor locus in human chromosome 9p21-22.

PURPOSE: To clone the putative tumor suppressor gene(s) in a refined region at 9p21-22 undergoing loss of heterozygosity in nasopharyngeal carcinoma (NPC). METHODS: We systematically screened the expression patterns of 25 novel ESTs (expressed sequence tags) in a minimal common deleted region of 9p21-22 in NPC. One of these ESTs was found down-regulated in NPC. Subsequently, the corresponding gene sequence of this EST was established by cDNA cloning and RACE (rapid amplification of cDNA end) procedures. Furthermore, a mouse homologue of this gene was identified. The expression of this gene was examined using Northern blot or reverse transcription-polymerase chain reaction (RT-PCR) in various human and mouse tissues. A limited screen for mutation of coding sequence of this novel human gene was undertaken using RT-PCR and direct sequencing analysis. RESULTS: A novel gene was cloned. This gene is a new member of the UBA domain family, so we named it UBAPI for ubiquitin-associated protein 1 (HUGO Gene Nomenclature Committee-approved symbol). Northern blot and RT-PCR analysis demonstrate a ubiquitous pattern of gene expression in human and mouse tissues. The direct sequencing analysis of the coding region of hUBAP1 following RT-PCR failed to reveal any mutations in a preliminary screen of NPC cell line HNE1 and primary nasopharyngeal carcinoma samples. CONCLUSIONS: We cloned a novel gene UBAPI, which is highly conserved between human and mouse. Clearly, as a novel member of UBA domain protein family and taking its map location into account, a more extensive analysis is essential to establish whether subtle mutations are present in nasopharyngeal carcinomas.

Amino Acid Sequence↗