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Chan CY, Tang MHY, Wong KC, Chong YK, Yeung KY, Mak TWL. Acute poisoning by dexmedetomidine-containing chewing gum in a child. Pathology 2021; 54:666-667. [PMID: 34801281 DOI: 10.1016/j.pathol.2021.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/20/2021] [Indexed: 10/19/2022]
Affiliation(s)
- Candace Y Chan
- Hospital Authority Toxicology Reference Laboratory, Princess Margaret Hospital, Hong Kong; Chemical Pathology Department, Princess Margaret Hospital, Hong Kong
| | - Magdalene H Y Tang
- Hospital Authority Toxicology Reference Laboratory, Princess Margaret Hospital, Hong Kong
| | - K C Wong
- Chemical Pathology Department, Queen Mary Hospital, Hong Kong
| | - Y K Chong
- Hospital Authority Toxicology Reference Laboratory, Princess Margaret Hospital, Hong Kong; Chemical Pathology Department, Princess Margaret Hospital, Hong Kong
| | - K Y Yeung
- Pediatric and Adolescence Medicine Department, Tuen Mun Hospital, Hong Kong
| | - Tony W L Mak
- Hospital Authority Toxicology Reference Laboratory, Princess Margaret Hospital, Hong Kong; Chemical Pathology Department, Princess Margaret Hospital, Hong Kong.
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Chung PH, Wong CW, Lai CK, Siu HK, Tsang DN, Yeung KY, Ip DK, Tam PK. A prospective interventional study to examine the effect of a silver alloy and hydrogel-coated catheter on the incidence of catheter-associated urinary tract infection. Hong Kong Med J 2017; 23:239-45. [PMID: 28211358 DOI: 10.12809/hkmj164906] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
INTRODUCTION Catheter-associated urinary tract infection is a major hospital-acquired infection. This study aimed to analyse the effect of a silver alloy and hydrogel-coated catheter on the occurrence of catheter-associated urinary tract infection. METHODS This was a 1-year prospective study conducted at a single centre in Hong Kong. Adult patients with an indwelling urinary catheter for longer than 24 hours were recruited. The incidence of catheter-associated urinary tract infection in patients with a conventional latex Foley catheter without hydrogel was compared with that in patients with a silver alloy and hydrogel-coated catheter. The most recent definition of urinary tract infection was based on the latest surveillance definition of the National Healthcare Safety Network managed by Centers for Disease Control and Prevention. RESULTS A total of 306 patients were recruited with a similar ratio between males and females. The mean (standard deviation) age was 81.1 (10.5) years. The total numbers of catheter-days were 4352 and 7474 in the silver-coated and conventional groups, respectively. The incidences of catheter-associated urinary tract infection per 1000 catheter-days were 6.4 and 9.4, respectively (P=0.095). There was a 31% reduction in the incidence of catheter-associated urinary tract infection per 1000 catheter-days in the silver-coated group. Escherichia coli was the most commonly involved pathogen (36.7%) of all cases. Subgroup analysis revealed that the protective effect of silver-coated catheter was more pronounced in long-term users as well as female patients with a respective 48% (P=0.027) and 42% (P=0.108) reduction in incidence of catheter-associated urinary tract infection. The mean catheterisation time per person was the longest in patients using a silver-coated catheter (17.0 days) compared with those using a conventional (10.8 days) or both types of catheter (13.6 days) [P=0.01]. CONCLUSIONS Silver alloy and hydrogel-coated catheters appear to be effective in preventing catheter-associated urinary tract infection based on the latest surveillance definition. The effect is perhaps more prominent in long-term users and female patients.
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Affiliation(s)
- P Hy Chung
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - C Wy Wong
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - C Kc Lai
- Department of Pathology, Queen Elizabeth Hospital, Jordan, Hong Kong
| | - H K Siu
- Chief Infection Control Officer's Office, Hospital Authority, Hong Kong
| | - D Nc Tsang
- Department of Pathology, Queen Elizabeth Hospital, Jordan, Hong Kong.,Chief Infection Control Officer's Office, Hospital Authority, Hong Kong
| | - K Y Yeung
- Infection Control Team, Central Nursing Department, Kowloon Hospital, Argyle Street, Hong Kong
| | - D Km Ip
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - P Kh Tam
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
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Abstract
The mitochondrial genome has a major role to play in establishing and maintaining pluripotency. Furthermore, mitochondrial DNA (mtDNA) copy is strictly regulated during differentiation. Undifferentiated, pluripotent cells possess fewer than 300 copies of mtDNA, which establishes the mtDNA set point and promotes cell proliferation and, as a result, these cells rely on glycolysis with some support from oxidative phosphorylation (OXPHOS) for the generation of ATP. The mtDNA set point provides the starting point from which cells increase their mtDNA copy number as they differentiate into mature functional cells. Dependent on cell types, mtDNA copy number ranges from ~10 copies in sperm to several thousand in cardiomyocytes. Consequently, differentiating cell types can acquire the appropriate numbers of mtDNA copy to meet their specific requirements for ATP generated through OXPHOS. However, as reprogrammed somatic cells do not always achieve this, it is essential to analyze them for their OXPHOS potential and ability to regulate mtDNA copy number. Here, we describe how to assess mtDNA copy number in pluripotent and differentiating cells using real-time PCR protocols; assess expression of the mtDNA specific replication factors through real-time RT-PCR; identify mtDNA variants in embryonic and induced pluripotent stem cells; determine DNA methylation patterns of the mtDNA-specific replication factors; and assess mitochondrial OXPHOS capacity.
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Affiliation(s)
- William Lee
- The Mitochondrial Genetics Group, Centre for Genetic Diseases, Hudson Institute of Medical Research, Monash University, 27-31 Wright Street, Clayton, VIC, 3168, Australia
| | - Richard D W Kelly
- The Mitochondrial Genetics Group, Centre for Genetic Diseases, Hudson Institute of Medical Research, Monash University, 27-31 Wright Street, Clayton, VIC, 3168, Australia
| | - Ka Yu Yeung
- The Mitochondrial Genetics Group, Centre for Genetic Diseases, Hudson Institute of Medical Research, Monash University, 27-31 Wright Street, Clayton, VIC, 3168, Australia
- Molecular Basis of Metabolic Disease, Division of Metabolic and Vascular Health, Warwick Medical School, The University of Warwick, Clifford Bridge Road, Coventry, CV2 2DX, UK
| | - Gael Cagnone
- The Mitochondrial Genetics Group, Centre for Genetic Diseases, Hudson Institute of Medical Research, Monash University, 27-31 Wright Street, Clayton, VIC, 3168, Australia
| | - Matthew McKenzie
- The Molecular Basis of Mitochondrial Disease Group, Centre for Genetic Diseases, Hudson Institute of Medical Research, Monash University, 27-31 Wright Street, Clayton, VIC, 3168, Australia
| | - Justin C St John
- The Mitochondrial Genetics Group, Centre for Genetic Diseases, Hudson Institute of Medical Research, Monash University, 27-31 Wright Street, Clayton, VIC, 3168, Australia.
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Yeung KY, Dickinson A, Donoghue JF, Polekhina G, White SJ, Grammatopoulos DK, McKenzie M, Johns TG, John JCS. The identification of mitochondrial DNA variants in glioblastoma multiforme. Acta Neuropathol Commun 2014; 2:1. [PMID: 24383468 PMCID: PMC3912901 DOI: 10.1186/2051-5960-2-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/07/2013] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Mitochondrial DNA (mtDNA) encodes key proteins of the electron transfer chain (ETC), which produces ATP through oxidative phosphorylation (OXPHOS) and is essential for cells to perform specialised functions. Tumor-initiating cells use aerobic glycolysis, a combination of glycolysis and low levels of OXPHOS, to promote rapid cell proliferation and tumor growth. Glioblastoma multiforme (GBM) is an aggressively malignant brain tumor and mitochondria have been proposed to play a vital role in GBM tumorigenesis. RESULTS Using next generation sequencing and high resolution melt analysis, we identified a large number of mtDNA variants within coding and non-coding regions of GBM cell lines and predicted their disease-causing potential through in silico modeling. The frequency of variants was greatest in the D-loop and origin of light strand replication in non-coding regions. ND6 was the most susceptible coding gene to mutation whilst ND4 had the highest frequency of mutation. Both genes encode subunits of complex I of the ETC. These variants were not detected in unaffected brain samples and many have not been previously reported. Depletion of HSR-GBM1 cells to varying degrees of their mtDNA followed by transplantation into immunedeficient mice resulted in the repopulation of the same variants during tumorigenesis. Likewise, de novo variants identified in other GBM cell lines were also incorporated. Nevertheless, ND4 and ND6 were still the most affected genes. We confirmed the presence of these variants in high grade gliomas. CONCLUSIONS These novel variants contribute to GBM by rendering the ETC. partially dysfunctional. This restricts metabolism to anaerobic glycolysis and promotes cell proliferation.
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Dickinson A, Yeung KY, Donoghue J, Baker MJ, Kelly RD, McKenzie M, Johns TG, St John JC. The regulation of mitochondrial DNA copy number in glioblastoma cells. Cell Death Differ 2013; 20:1644-53. [PMID: 23995230 PMCID: PMC3824586 DOI: 10.1038/cdd.2013.115] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 07/10/2013] [Accepted: 07/22/2013] [Indexed: 01/07/2023] Open
Abstract
As stem cells undergo differentiation, mitochondrial DNA (mtDNA) copy number is strictly regulated in order that specialized cells can generate appropriate levels of adenosine triphosphate (ATP) through oxidative phosphorylation (OXPHOS) to undertake their specific functions. It is not understood whether tumor-initiating cells regulate their mtDNA in a similar manner or whether mtDNA is essential for tumorigenesis. We show that human neural stem cells (hNSCs) increased their mtDNA content during differentiation in a process that was mediated by a synergistic relationship between the nuclear and mitochondrial genomes and results in increased respiratory capacity. Differentiating multipotent glioblastoma cells failed to match the expansion in mtDNA copy number, patterns of gene expression and increased respiratory capacity observed in hNSCs. Partial depletion of glioblastoma cell mtDNA rescued mtDNA replication events and enhanced cell differentiation. However, prolonged depletion resulted in impaired mtDNA replication, reduced proliferation and induced the expression of early developmental and pro-survival markers including POU class 5 homeobox 1 (OCT4) and sonic hedgehog (SHH). The transfer of glioblastoma cells depleted to varying degrees of their mtDNA content into immunocompromised mice resulted in tumors requiring significantly longer to form compared with non-depleted cells. The number of tumors formed and the time to tumor formation was relative to the degree of mtDNA depletion. The tumors derived from mtDNA depleted glioblastoma cells recovered their mtDNA copy number as part of the tumor formation process. These outcomes demonstrate the importance of mtDNA to the initiation and maintenance of tumorigenesis in glioblastoma multiforme.
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Affiliation(s)
- A Dickinson
- 1] The Mitochondrial Genetics Group, Centre for Genetic Diseases, Monash Institute of Medical Research, Monash University, 27-31 Wright Street, Clayton, Victoria 3168, Australia [2] Molecular Basis of Metabolic Disease, Division of Metabolic and Vascular Health, Warwick Medical School, The University of Warwick, Clifford Bridge Road, Coventry, CV2 2DX, UK
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6
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Yeung KY, Dickinson A, John JS. Identification of Mitochondrial DNA Variants in Cancer Stem Cells Using Next Generation Sequencing. Biol Reprod 2012. [DOI: 10.1093/biolreprod/87.s1.591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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7
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Yeung KY, Gooley TA, Zhang A, Raftery AE, Radich JP, Oehler VG. Predicting relapse prior to transplantation in chronic myeloid leukemia by integrating expert knowledge and expression data. ACTA ACUST UNITED AC 2012; 28:823-30. [PMID: 22296787 DOI: 10.1093/bioinformatics/bts059] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
MOTIVATION Selecting a small number of signature genes for accurate classification of samples is essential for the development of diagnostic tests. However, many genes are highly correlated in gene expression data, and hence, many possible sets of genes are potential classifiers. Because treatment outcomes are poor in advanced chronic myeloid leukemia (CML), we hypothesized that expression of classifiers of advanced phase CML when detected in early CML [chronic phase (CP) CML], correlates with subsequent poorer therapeutic outcome. RESULTS We developed a method that integrates gene expression data with expert knowledge and predicted functional relationships using iterative Bayesian model averaging. Applying our integrated method to CML, we identified small sets of signature genes that are highly predictive of disease phases and that are more robust and stable than using expression data alone. The accuracy of our algorithm was evaluated using cross-validation on the gene expression data. We then tested the hypothesis that gene sets associated with advanced phase CML would predict relapse after allogeneic transplantation in 176 independent CP CML cases. Our gene signatures of advanced phase CML are predictive of relapse even after adjustment for known risk factors associated with transplant outcomes.
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Affiliation(s)
- K Y Yeung
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA.
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Liu X, Sivaganesan S, Yeung KY, Guo J, Bumgarner RE, Medvedovic M. Context-specific infinite mixtures for clustering gene expression profiles across diverse microarray dataset. Bioinformatics 2006; 22:1737-44. [PMID: 16709591 PMCID: PMC1617036 DOI: 10.1093/bioinformatics/btl184] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Identifying groups of co-regulated genes by monitoring their expression over various experimental conditions is complicated by the fact that such co-regulation is condition-specific. Ignoring the context-specific nature of co-regulation significantly reduces the ability of clustering procedures to detect co-expressed genes due to additional 'noise' introduced by non-informative measurements. RESULTS We have developed a novel Bayesian hierarchical model and corresponding computational algorithms for clustering gene expression profiles across diverse experimental conditions and studies that accounts for context-specificity of gene expression patterns. The model is based on the Bayesian infinite mixtures framework and does not require a priori specification of the number of clusters. We demonstrate that explicit modeling of context-specificity results in increased accuracy of the cluster analysis by examining the specificity and sensitivity of clusters in microarray data. We also demonstrate that probabilities of co-expression derived from the posterior distribution of clusterings are valid estimates of statistical significance of created clusters. AVAILABILITY The open-source package gimm is available at http://eh3.uc.edu/gimm.
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Affiliation(s)
- X Liu
- Department of Environmental Health, University of Cincinnati, 3223 Eden Avenue ML 56, Cincinnati, OH 45267, USA
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9
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Abstract
MOTIVATION Identifying patterns of co-expression in microarray data by cluster analysis has been a productive approach to uncovering molecular mechanisms underlying biological processes under investigation. Using experimental replicates can generally improve the precision of the cluster analysis by reducing the experimental variability of measurements. In such situations, Bayesian mixtures allow for an efficient use of information by precisely modeling between-replicates variability. RESULTS We developed different variants of Bayesian mixture based clustering procedures for clustering gene expression data with experimental replicates. In this approach, the statistical distribution of microarray data is described by a Bayesian mixture model. Clusters of co-expressed genes are created from the posterior distribution of clusterings, which is estimated by a Gibbs sampler. We define infinite and finite Bayesian mixture models with different between-replicates variance structures and investigate their utility by analyzing synthetic and the real-world datasets. Results of our analyses demonstrate that (1) improvements in precision achieved by performing only two experimental replicates can be dramatic when the between-replicates variability is high, (2) precise modeling of intra-gene variability is important for accurate identification of co-expressed genes and (3) the infinite mixture model with the 'elliptical' between-replicates variance structure performed overall better than any other method tested. We also introduce a heuristic modification to the Gibbs sampler based on the 'reverse annealing' principle. This modification effectively overcomes the tendency of the Gibbs sampler to converge to different modes of the posterior distribution when started from different initial positions. Finally, we demonstrate that the Bayesian infinite mixture model with 'elliptical' variance structure is capable of identifying the underlying structure of the data without knowing the 'correct' number of clusters. AVAILABILITY The MS Windows based program named Gaussian Infinite Mixture Modeling (GIMM) implementing the Gibbs sampler and corresponding C++ code are available at http://homepages.uc.edu/~medvedm/GIMM.htm SUPPLEMENTAL INFORMATION: http://expression.microslu.washington.edu/expression/kayee/medvedovic2003/medvedovic_bioinf2003.html
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Affiliation(s)
- M Medvedovic
- Department of Environmental Health, Center for Genome Information, University of Cincinnati Medical Center, 3223 Eden Avenue ML 56, Cincinnati, OH 45267-0056, USA.
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Abstract
BACKGROUND At least 1 million people worldwide have retinitis pigmentosa (RP), making it relatively common among the inherited forms of blindness. Mutations in many genes may cause RP. The most common known mutation, Pro347Leu in rhodopsin, is found in no more than about 1% of unrelated patients, implying the impracticality of a diagnostic test which would screen only for a few, common mutation sites. CONCLUSIONS Ongoing discovery and study of RP genes makes it feasible to consider a molecular diagnostic test which would screen coding regions of all known RP genes by a mutation detection method such as conformation-sensitive gel electrophoresis followed by sequencing. The parallel development of RP genetic knowledge and treatments such as gene therapy will make such tests both possible and necessary.
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Affiliation(s)
- K Y Yeung
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
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11
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Abstract
MOTIVATION Clustering is a useful exploratory technique for the analysis of gene expression data. Many different heuristic clustering algorithms have been proposed in this context. Clustering algorithms based on probability models offer a principled alternative to heuristic algorithms. In particular, model-based clustering assumes that the data is generated by a finite mixture of underlying probability distributions such as multivariate normal distributions. The issues of selecting a 'good' clustering method and determining the 'correct' number of clusters are reduced to model selection problems in the probability framework. Gaussian mixture models have been shown to be a powerful tool for clustering in many applications. RESULTS We benchmarked the performance of model-based clustering on several synthetic and real gene expression data sets for which external evaluation criteria were available. The model-based approach has superior performance on our synthetic data sets, consistently selecting the correct model and the number of clusters. On real expression data, the model-based approach produced clusters of quality comparable to a leading heuristic clustering algorithm, but with the key advantage of suggesting the number of clusters and an appropriate model. We also explored the validity of the Gaussian mixture assumption on different transformations of real data. We also assessed the degree to which these real gene expression data sets fit multivariate Gaussian distributions both before and after subjecting them to commonly used data transformations. Suitably chosen transformations seem to result in reasonable fits. AVAILABILITY MCLUST is available at http://www.stat.washington.edu/fraley/mclust. The software for the diagonal model is under development. CONTACT kayee@cs.washington.edu. SUPPLEMENTARY INFORMATION http://www.cs.washington.edu/homes/kayee/model.
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Affiliation(s)
- K Y Yeung
- Computer Science and Engineering, Box 352350, University of Washington, Seattle, WA 98195, USA.
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12
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Abstract
AIM To determine the pattern of rhodopsin mutations in Chinese retinitis pigmentosa (RP) patients. METHODS The rhodopsin gene was examined in 101 RP patients and 190 controls from Hong Kong. RESULTS Three coding changes were identified: Pro347Leu, Ala299Ser, and 5211delC. Each protein sequence alteration was found in one patient. Ala299Ser also existed in two controls. CONCLUSION The C-terminal nonsense mutation may cause mis-sorting of rhodopsin protein. The finding of controls with Ala299Ser suggests this is only the third missense alteration reported that does not cause RP. The expected frequency of rhodopsin mutations in RP is <7% (2/101=2.0%, 95% confidence interval: 0.2%-7.0%).
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Affiliation(s)
- W M Chan
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
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13
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Abstract
MOTIVATION There is a great need to develop analytical methodology to analyze and to exploit the information contained in gene expression data. Because of the large number of genes and the complexity of biological networks, clustering is a useful exploratory technique for analysis of gene expression data. Other classical techniques, such as principal component analysis (PCA), have also been applied to analyze gene expression data. Using different data analysis techniques and different clustering algorithms to analyze the same data set can lead to very different conclusions. Our goal is to study the effectiveness of principal components (PCs) in capturing cluster structure. Specifically, using both real and synthetic gene expression data sets, we compared the quality of clusters obtained from the original data to the quality of clusters obtained after projecting onto subsets of the principal component axes. RESULTS Our empirical study showed that clustering with the PCs instead of the original variables does not necessarily improve, and often degrades, cluster quality. In particular, the first few PCs (which contain most of the variation in the data) do not necessarily capture most of the cluster structure. We also showed that clustering with PCs has different impact on different algorithms and different similarity metrics. Overall, we would not recommend PCA before clustering except in special circumstances.
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Affiliation(s)
- K Y Yeung
- Computer Science and Engineering, Box 352350, University of Washington, Seattle, WA 98195, USA.
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Baum L, Chan WM, Yeung KY, Lam DS, Kwok AK, Pang CP. RP1 in Chinese: Eight novel variants and evidence that truncation of the extreme C-terminal does not cause retinitis pigmentosa. Hum Mutat 2001; 17:436. [PMID: 11317367 DOI: 10.1002/humu.1127] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Heterozygous truncating mutations in the RP1 gene cause approximately 7% of autosomal dominant retinitis pigmentosa (RP) cases. To examine the role of RP1 mutations in RP, we screened 101 unrelated Chinese RP patients (unselected for mode of inheritance) and 190 elderly normal control subjects for sequence changes in the coding exons for the 2156 amino acid RP1 protein. One patient had a mutation, thus RP1 mutations cause about 0.0% to 5.4% (95% confidence interval) of all RP among Chinese. The mutation was R677X, the most common found in Americans. Five other known sequence changes were found. In addition, nine novel sequence alterations were identified: 746G>A (R249H), 1437G>T (M479I), 2116G>C (G706R), 3024G>A (Q1008Q), 3188G>A (Q1063R), 5797C>T (R1933X), 6423A>G (I2141M), and the variants 6542C>T and 6676T>A, both in the 3' untranslated region. One control subject and three members of a non-RP family were heterozygous for R1933X, which is therefore likely to be a non-disease-causing variant. The most C-terminal truncation previously reported was due to Tyr1053 (1-bp del) and occurred in RP patients. Thus the presence of a normal level of at least part of RP1 between amino acids 1052 and 1933 appears necessary to prevent RP. Hum Mutat 17:436, 2001.
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Affiliation(s)
- L Baum
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong
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15
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Abstract
MOTIVATION Many clustering algorithms have been proposed for the analysis of gene expression data, but little guidance is available to help choose among them. We provide a systematic framework for assessing the results of clustering algorithms. Clustering algorithms attempt to partition the genes into groups exhibiting similar patterns of variation in expression level. Our methodology is to apply a clustering algorithm to the data from all but one experimental condition. The remaining condition is used to assess the predictive power of the resulting clusters-meaningful clusters should exhibit less variation in the remaining condition than clusters formed by chance. RESULTS We successfully applied our methodology to compare six clustering algorithms on four gene expression data sets. We found our quantitative measures of cluster quality to be positively correlated with external standards of cluster quality.
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Affiliation(s)
- K Y Yeung
- Computer Science and Engineering, Box 352350, University of Washington, Seattle, WA 98195, USA
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Ahlgren JD, Ellison NM, Gottlieb RJ, Laluna F, Lokich JJ, Sinclair PR, Ueno W, Wampler GL, Yeung KY, Alt D. Hormonal palliation of chemoresistant ovarian cancer: three consecutive phase II trials of the Mid-Atlantic Oncology Program. J Clin Oncol 1993; 11:1957-68. [PMID: 7691999 DOI: 10.1200/jco.1993.11.10.1957] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
PURPOSE To evaluate the efficacy of three hormonal manipulations in the palliation of chemoresistant ovarian cancer, and to analyze the results in the light of other clinical trials. PATIENTS AND METHODS Three sequential phase II trials were performed in patients with refractory epithelial ovarian carcinoma, using high-dose megestrol acetate (800 mg/d for 30 days, then 400 mg/d), high-dose tamoxifen (80 mg/d for 30 days, then 40 mg/d), and aminoglutethimide (1 g/d plus tapering doses of hydrocortisone). Results were compared with those described in the world literature from trials of the same or similar agents. RESULTS No responses were seen among 30 assessable patients treated with megestrol acetate, and most (but not all) similar trials have reported low response rates. Five responses (17%) were seen among 29 patients treated with tamoxifen. Two responses exceeded 5 years in duration. No responses were seen among 15 patients treated with aminoglutethimide. CONCLUSION Antiestrogen therapy may offer the possibility of useful and, occasionally, long-term palliation of refractory epithelial ovarian carcinoma, with little toxicity. There may be a trend toward a dose-response effect, which represents a suitable topic for a future prospective trial.
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Affiliation(s)
- J D Ahlgren
- Division of Hematology/Oncology, George Washington University Medical Center, Washington, DC 20037
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17
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Abstract
The standard membrane filtration method of the UK has been modified in order to improve its specificity for enumerating Escherichia coli in the subtropical waters of Hong Kong. This involves incorporating into the membrane lauryl sulphate (mLS) method either an in situ urease test (the mLS-UA method), or an in situ beta-glucuronidase test (the mLS-GUD method). The false-positive errors of the mLS-UA and mLS-GUD methods are low, ranging from 3-5%. A comparison between the membrane filtration (mLS-UA) method and the multiple tube technique in testing E. coli in subtropical beach-waters has demonstrated that the former can give much more precise counts, and is the method of choice for such a purpose. The mLS-GUD method, for which automated counting of E. coli colonies is possible, is a good alternative to mLS-UA in routine enumeration of this bacterial indicator in environmental waters.
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Affiliation(s)
- W H Cheung
- Environmental Protection Department, Southorn Centre, Wanchai, Hong Kong
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Kavanagh JJ, Yeung KY, Savaraj N, Krakoff IH. Phase I clinical evaluation of oral and intravenous 4-demethoxydaunorubicin. Eur J Cancer Clin Oncol 1985; 21:1187-9. [PMID: 3865774 DOI: 10.1016/0277-5379(85)90013-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Thirteen patients were treated with both the oral and intravenous preparations of 4-demethoxydaunorubicin (DMDR). The drug was well tolerated in both forms. Neutropenia was the dose-limiting side-effect. Approximately 30% of the compound was absorbed when given orally. The maximum tolerated dose was 12.5 mg/m2 intravenously or 50 mg/m2 (10 mg/m2 q d X 5) orally, given every 21-28 days.
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Posada JG, Marantz AB, Yeung KY, Smith FP, Delgado G, Edwards BK, Schein PS. The cyclophosphamide, hexamethylmelamine, 5 fluorouracil (CHF) regimen in the treatment of advanced and recurrent ovarian cancer. Gynecol Oncol 1985; 20:23-31. [PMID: 3917421 DOI: 10.1016/0090-8258(85)90121-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Fifty-one patients with advanced ovarian carcinoma were treated with a combination of cyclophosphamide, hexamethylmelamine, and 5-fluorouracil, CHF. Compared to the hexamethylmelamine, cyclophosphamide, methotrexate, and 5-fluorouracil (Hexa-CAF) regimen, the omission of methotrexate in CHF did not detract from its antitumor activity and it was well tolerated with only mild to moderate toxicity. The CHF combination was as effective as Hexa-CAF and was particularly active in patients who had nonmeasurable/residual disease, classified as less than 2 cm in its greatest diameter at the initiation of chemotherapy. In future studies, CHF should be prospectively compared to other combination using Adriamycin and cis-platinum that with extended use can cause renal and cardiac damage in long-term survivors.
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Abstract
Three different neoplasms of B cell lineage, chronic lymphocytic leukemia, immunoglobulin A (IgA) myeloma and immunoglobulin G (IgG) myeloma were detected in three patients who had heavy occupational exposure to asbestos dust. Two of the patients had coexistent pulmonary asbestosis, whereas the third patient had a pleural mesothelioma subsequent to his initial presentation with myeloma. Defective cell-mediated immunity and hyperactivity of B cell function have previously been noted in patients with asbestosis. We suggest the possibility that these asbestos-related immunologic derangements may predispose to the development of immunoproliferative and lymphoproliferative neoplasms, since such tumors have been observed in a variety of other settings, characterized by protracted hyperactivity of the immune system.
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Yeung KY, Haidak DJ, Brown JA, Anderson D. Metastasis-induced acute pancreatitis in small cell bronchogenic carcinoma. Arch Intern Med 1979; 139:552-4. [PMID: 220925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Despite frequent metastatic involvement of the pancreas at postmortem examination in patients with small cell lung cancer, clinically observed pancreatitis due to metastatic pancreatic tumor rarely has been reported. This communication describes three cases of clinical acute pancreatitis occurring in a consecutive series of 40 patients with oat cell lung cancer. This complication may appear either as the initial manifestation of the neoplasm or during a recrudescent phase of the malignant growth. The diagnosis should be suspected in the presence of the clinical, laboratory, and radiologic features of acute pancreatitis in patients with known small cell carcinoma of the lung, especially if there is evidence of progression of the neoplastic disease elsewhere and no response to conservative medical management. Aggressive treatment with polychemotherapy can produce rapid clinical improvement and useful prolongation of survival.
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Kline RL, Yeung KY, Calaresu FR. Role of somatic nerves in the cardiovascular responses to stimulation of an acupuncture point in anesthetized rabbits. Exp Neurol 1978; 61:561-70. [PMID: 710567 DOI: 10.1016/0014-4886(78)90023-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Poleksic S, Yeung KY. Rapid development of keratoacanthoma and accelerated transformation into squamous cell carcinoma of the skin: a mutagenic effect of polychemotherapy in a patient with Hodgkin's disease? Cancer 1978; 41:12-6. [PMID: 626922 DOI: 10.1002/1097-0142(197801)41:1<12::aid-cncr2820410104>3.0.co;2-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A 59-year-old white man developed keratoacanthoma of the nose immediately following one course of MOPP polychemotherapy for clinical state IV B mixed cellularity Hodgkin's disease. Despite the dramatic response of Hodgkin's disease to intensive chemotherapy, the skin lesion was rapidly transformed into squamous cell carcinoma in 10 weeks. The immunosuppressive effect of intensive polychemotherapy may play a significant role in accelerating the malignant transformation. We report here our results concerning this complication which may occur in any patient with Hodgkin's disease undergoing intensive therapy.
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Abstract
An unusual case of mucinous adenocarcinoma of the sweat glands originating from the right axilla is described. Despite complete control of the primary tumor after local excision, diffuse metastatic lesions continued to appear in the scalp, face, upper and lower extremities, sacral and pelvic bones, and left posterior iliac bone marrow space. The tumors were radioresistant. Multiple trials of various chemotherapeutic regimens, including alkylating agents, antifolates, antipyrimidines, vinca alkaloids, and antineoplastic antibiotics, were ineffective. The cutaneous neoplasms were grossly round, smooth, red, glistening, and cystic and were filled with a gelatinous mucinous material. Microscopic and ultrastructural findings are described.
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Abstract
Six months after right-sided spontaneous pneumothorax developed in a 56-year-old man, squamous cell carcinoma was discovered in the ipsilateral lung. Fifteen cases of bronchogenic carcinoma presenting as spontaneous pneumothorax have been reported in the English language literature. Possible pathogenetic mechanisms include: direct tumor invasion of pleura; rupture of a subpleural bleb (in an area of obstructive emphysema) or an emphysematous bulla (in an overexpanded portion of the lung associated with lobar or segmental collapse); or unknown. Patients with spontaneous pneumothorax who fail to achieve complete expansion after three weeks of therapy or who have persistent roentgenographic pulmonary infiltration should undergo further investigation for bronchogenic carcinoma.
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Abstract
The following is an example of a typical case of Hodgkin's disease, which illustrates the use of clinical and pathologic staging procedures. A 40-year-old man had fever and swelling of the left side of the neck for two weeks. Physical examination showed enlargement of the left supraclavicular and left axillary lymph nodes but no hepatosplenomegaly. Biopsy of the affected lymph nodes showed Hodgkin's disease, mixed cellularity type. A chest roentgenogram, lymphangiogram. 67Ga scan, and results of bone marrow biopsy of the right iliac crest were normal. The clinical stage was classified as IIB2. (Subscript 2 indicates the number of regions of lymph node involvement. The patient subsequently underwent laparotomy. The spleen weighed 150 gm and contained microfoci of Hodgkin disease. Biopsy of an upper para-aortic lymph node at the L-1 showed involvement by Hodgkin disease, but specimens from either lobe of the liver, lower para-aortic and iliac lymph nodes, and left iliac crest did not. The pathologic stage was therefore classified as IIIN+H-S+M- Polychemotherapy was prescribed.
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Abstract
Non-Hodgkin lymphoma is a heterogenous group of lymphoreticular malignancies that can be classified into six major cell types. In comparison with Hodgkin disease, non-Hodgkin lymphoma is more common and tends to occur in older persons. The investigative procedures for clinical and pathologic staging are similar to those used in Hodgkin disease, except that staging laparotomy is performed less frequently. Results of biopsy reflect a high incidence of bone marrow, liver, and splenic hilar and mesenteric lymph node involvement in Non-Hodgkin lymphoma than in Hodgkin disease.
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Yeung KY, Trowbridge AA. Chronic granulocytic leukemia: hypokalemia in acute blastic crisis. Ann Intern Med 1976; 85:533-4. [PMID: 1067780 DOI: 10.7326/0003-4819-85-4-533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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Abstract
Described here is a case of multiple myeloma in a patient with sickle cell anemia. Viscometric studies were made by comparing the patient's whole blood, plasma and washed red blood cells with those of a normal control subject and a patient with sickle cell anemia. Results showed that the increased viscosity of the patient's whole blood as compared with that of the control patient with sickle cell anemia was mainly due to erythrocytic interaction with the circulating abnormal immunoglobulin. It is postulated that the increased frequency of vaso-occlusive crisis that occurred in our patient in the months before the diagnosis and treatment of multiple myeloma, was due to this cell-protein interaction with the resulting enhancement of whole blood viscosity and the sickling phenomena.
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Yeung KY, Corn M. Letter: Fatal aplastic anemia with piperacetazine therapy. Ann Intern Med 1974; 81:411. [PMID: 4152939 DOI: 10.7326/0003-4819-81-3-411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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33
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Yeung KY, Shann MK. The clinical observation and hemodynamic study on the surgically proved pure patent ductus arteriosus. Taiwan Yi Xue Hui Za Zhi 1968; 67:375-85. [PMID: 5259190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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