Linh Tran - Academia.edu (original) (raw)

Papers by Linh Tran

Lecture Notes in Computer Science, 2014

This paper introduces a new concept of reversible circuits based on EXOR-sum of Products-of-EXOR-... more This paper introduces a new concept of reversible circuits based on EXOR-sum of Products-of-EXOR-sums (EPOE). Two algorithms are introduced that synthesize reversible functions using these new EPOE structures. The motivation for this work is to reduce the number of multiple controlled Toffoli gates and their number of inputs. To achieve these reductions the paper generalizes from existing 2-level AND-EXOR structures (ESOP) commonly used in reversible logic to a mixture of 3level EXOR-AND-EXOR structures and ESOPs. Our approach can be applied to reversible and permutative quantum circuits to synthesize single output functions with one ancilla line per output. In addition, a variant of the algorithm with garbage lines is presented. A comparison of the ESOP minimizer EXORCISM-4 and variants of the new EPOE minimizer, called EPOEM-1s and EPOEM-1f, is presented. The results show that EPOE circuits do in fact achieve the above-stated cost reductions, in particular when expressed in terms of Maslov's quantum cost model commonly used in quantum circuit synthesis.

Journal of Automation and Control Engineering, 2015

 Abstract-A successful classification of different tumor types is essential for successful treat... more  Abstract-A successful classification of different tumor types is essential for successful treatment of cancer. However, most prior cancer classification methods are clinical-based and have inadequate diagnostic ability. Cancer classification using gene expression data is very important in cancer diagnosis and drug discovery. The introduction of DNA microarray techniques has made simultaneous monitoring of thousands of gene expression probable. With this abundance of gene expression data nowadays, the researchers have the opportunity to do cancer classification using gene expression data. In recent years, a lot of machine learning methods have been proposed to do cancer classification using gene expression data such as clustering-based methods, k-nearest neighbor method, artificial neural network method, and support vector machine method, to name a few. In this paper, we present the un-normalized graph p-Laplacian semisupervised learning methods. These methods will be applied to the patient-patient network constructed from the gene expression data to predict the tumor types of all patients in the network. These methods are based on the assumption that the labels of two adjacent patients in the network are likely to be the same. The experiments show that that the un-normalized graph p-Laplacian semi-supervised learning methods are at least as good as the current state of the art network-based method (the un-normalized graph Laplacian based semi-supervised learning method) but often lead to better classification accuracy performance measures.

Journal of Automation and Control Engineering, 2015

Most network-based protein (or gene) function prediction methods are based on the assumption that... more Most network-based protein (or gene) function prediction methods are based on the assumption that the labels of two adjacent proteins in the network are likely to be the same. However, assuming the pairwise relationship between proteins or genes is not complete. The information a group of genes that show very similar patterns of expression and tend to have similar functions (i.e. the functional modules) is missed. The natural way overcoming the information loss of the above assumption is to represent the gene expression data as the hypergraph. Thus, in this paper, the three un-normalized, random walk, and symmetric normalized hypergraph Laplacian based semisupervised learning methods applied to hypergraph constructed from the gene expression data in order to predict the functions of yeast proteins are introduced. Experiment results show that the average accuracy performance measures of these three hypergraph Laplacian based semi-supervised learning methods are the same. However, their average accuracy performance measures of these three methods are much greater than the average accuracy performance measures of un-normalized graph Laplacian based semi-supervised learning method (i.e. the baseline method of this paper) applied to gene co-expression network created from the gene expression data. 

1996 IEEE MTT-S International Microwave Symposium Digest, 1996

ABSTRACT Frequency translation circuits are key elements in communication systems. This paper prl... more ABSTRACT Frequency translation circuits are key elements in communication systems. This paper prlesents three different frequency multipliers and a frequency mixer designed using the InP HEMT technology. These successful first iteration MMICs are highlighted by a V-band ...

Brain : a journal of neurology, Jan 11, 2015

We describe a novel nephrocerebellar syndrome on the Galloway-Mowat syndrome spectrum among 30 ch... more We describe a novel nephrocerebellar syndrome on the Galloway-Mowat syndrome spectrum among 30 children (ages 1.0 to 28 years) from diverse Amish demes. Children with nephrocerebellar syndrome had progressive microcephaly, visual impairment, stagnant psychomotor development, abnormal extrapyramidal movements and nephrosis. Fourteen died between ages 2.7 and 28 years, typically from renal failure. Post-mortem studies revealed (i) micrencephaly without polymicrogyria or heterotopia; (ii) atrophic cerebellar hemispheres with stunted folia, profound granule cell depletion, Bergmann gliosis, and signs of Purkinje cell deafferentation; (iii) selective striatal cholinergic interneuron loss; and (iv) optic atrophy with delamination of the lateral geniculate nuclei. Renal tissue showed focal and segmental glomerulosclerosis and extensive effacement and microvillus transformation of podocyte foot processes. Nephrocerebellar syndrome mapped to 700 kb on chromosome 15, which contained a single ...

The Journal of Pediatrics, 2015

Objective To assess the effectiveness of supreme laryngeal mask airway (SLMA) over face mask vent... more Objective To assess the effectiveness of supreme laryngeal mask airway (SLMA) over face mask ventilation for preventing need for endotracheal intubation at birth.

1985 International Electron Devices Meeting, 1985

A lightly doped drain (LDD) structure(1) is used in our Twin-Tub IV, fourth generation Twin-Tub C... more A lightly doped drain (LDD) structure(1) is used in our Twin-Tub IV, fourth generation Twin-Tub CMOS technology to improve stability of the N-channel transistor. The LDD N-channel transistors were successfully incorporated into the technology without adding any additional photolithography steps to the conventional process. The key to the process is a differential oxidation step of BF2implanted source/drain regions, which prevents

Journal of Surgical Research, 2015

We previously identified a correlation between increased expression of the phosphoinositide 3-kin... more We previously identified a correlation between increased expression of the phosphoinositide 3-kinase (PI3K) regulatory subunit p85α and improved survival in human pancreatic ductal adenocarcinoma (PDAC). The purpose of this study was to investigate the impact of changes in p85α expression on response to chemotherapy and the regulation of p85α by microRNA-21 (miR-21). PDAC tumor cells overexpressing p85α were generated by viral transduction, and the effect of p85α overexpression on sensitivity to gemcitabine was tested by MTT assay. Primary human PDAC tumors were stained for p85α and miR-21 via immunohistochemistry and in situ hybridization, respectively. Additionally, PDAC cells were treated with miR-21 mimic, and changes in p85α and phospho-AKT were assessed by Western blot. Finally, a luciferase reporter assay system was used to test direct regulation of p85α by miR-21. Higher p85α expression resulted in increased sensitivity to gemcitabine (P < 0.01), which correlated with decreased PI3K-AKT activation. Human tumors demonstrated an inverse correlation between miR-21 and p85α expression levels (r = -0.353, P < 0.001). In vitro, overexpression of miR-21 resulted in decreased levels of p85α and increased phosphorylation of AKT. Luciferase reporter assays confirmed the direct regulation of p85α by miR-21 (P < 0.01). Our results demonstrate that p85α expression is a determinant of chemosensitivity in PDAC. Additionally, we provide novel evidence that miR-21 can influence PI3K-AKT signaling via its direct regulation of p85α. These data provide insight into potential mechanisms for the known relationship between increased p85α expression and improved survival in PDAC.

IEEE MTT-S International Microwave Symposium Digest, 2007

A new class of zero bias, room temperature ultra sensitive detectors have been introduced for det... more A new class of zero bias, room temperature ultra sensitive detectors have been introduced for detection of millimeter wave radiation. The detectors have been scaled to micron level and have shown record responsivity in three forms. A W-band waveguide detector was designed and measured to have 4500 V/W voltage responsivity. A planar antenna coupled detector was also evaluated with and measured a responsivity 16100 V-mm2IW from 75-110 GHz. Following a resonant impedance matching technique an on-wafer characterization have shown voltage responsivity to exceed 20,000 V/W. The result does not include the reflected power from the detector and have shown that these detectors could provide noise equivalent power (NEP) values in the 4xlW1'3 W/ 'IHz level.

Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering, 2015

Most network-based clustering methods are based on the assumption that the labels of two adjacent... more Most network-based clustering methods are based on the assumption that the labels of two adjacent vertices in the network are likely to be the same. However, assuming the pairwise relationship between vertices is not complete. The information a group of vertices that show very similar patterns and tend to have similar labels is missed. The natural way overcoming the information loss of the above assumption is to represent the given data as the hypergraph. Thus, in this paper, the two unnormalized and random walk hypergraph Laplacian based un-supervised learning methods are introduced. Experiment results show that the accuracy performance measures of these two hypergraph Laplacian based un-supervised learning methods are greater than the accuracy performance measure of symmetric normalized graph Laplacian based un-supervised learning method (i.e. the baseline method of this paper) applied to simple graph created from the incident matrix of hypergraph.

1999 IEEE Third Workshop on Multimedia Signal Processing (Cat. No.99TH8451), 1999

Abstract - In many multi-media applications it is desirable to sep arate the iduence of the illum... more Abstract - In many multi-media applications it is desirable to sep arate the iduence of the illumination sources and imaging equipment from the properties of the depicted scene. The ability of the human visual system to solve this task in many situations is known as color con-stancy. ...

Signal Processing, 2005

In many colour-based image retrieval systems the colour properties of an image are described by i... more In many colour-based image retrieval systems the colour properties of an image are described by its colour histogram. Histogram-based search is, however, often inefficient for large histogram sizes. Therefore we introduce several new, Karhunen-Loe`ve transform (KLT)-based methods that provide efficient representations of colour histograms and differences between two colour histograms. The methods are based on the following two observations; Ordinary KLT considers colour histograms as signals and uses the Euclidian distance for optimization; KLT with generalized colour distance measures that take into account both the statistical properties of the image database and the properties of the underlying colour space should improve the retrieval performance. Image retrieval applications compare similarities between different images. Relevant for the decision is only the local structure of the image space around the current query image since the task is to find those images in the database that are most similar to this given query image. Therefore only the local topology of the feature space is of interest and compression methods should preserve this local topology as much as possible. It is therefore more important to have a good representation of the differences between features of similar images than good representations of the features of the images themselves. The optimization should therefore be based on minimizing the approximation error in the space of local histogram differences instead of the space of colour histograms. In this paper we report the results of our experiments that are done on three image databases containing more than 130,000 images. Both objective and subjective ground truth queries are used in order to evaluate the proposed methods and to compare them with other existing methods. The results from our experiments show that compression methods based on a combination of the two observations described above provide new, powerful and efficient retrieval algorithms for colour-based image retrieval. r

Proceedings of the National Academy of Sciences, 2007

Nitric oxide (NO) is used by mammalian immune systems to counter microbial invasions and is produ... more Nitric oxide (NO) is used by mammalian immune systems to counter microbial invasions and is produced by bacteria during denitrification. As a defense, microorganisms possess a complex network to cope with NO. Here we report a combined transcriptomic, chemical, and phenotypic approach to identify direct NO targets and construct the biochemical response network. In particular, network component analysis was used to identify transcription factors that are perturbed by NO. Such information was screened with potential NO reaction mechanisms and phenotypic data from genetic knockouts to identify active chemistry and direct NO targets in Escherichia coli. This approach identified the comprehensive E. coli NO response network and evinced that NO halts bacterial growth via inhibition of the branched-chain amino acid biosynthesis enzyme dihydroxyacid dehydratase. Because mammals do not synthesize branched-chain amino acids, inhibition of dihydroxyacid dehydratase may have served to foster the role of NO in the immune arsenal.

PLoS ONE, 2012

PTEN-controlled PI3K-AKT-mTOR pathway represents one of the most deregulated signaling pathways i... more PTEN-controlled PI3K-AKT-mTOR pathway represents one of the most deregulated signaling pathways in human cancers. With many small molecule inhibitors that target PI3K-AKT-mTOR pathway being exploited clinically, sensitive and reliable ways of stratifying patients according to their PTEN functional status and determining treatment outcomes are urgently needed. Heterogeneous loss of PTEN is commonly associated with human cancers and yet PTEN can also be regulated on epigenetic, transcriptional or post-translational levels, which makes the use of simple protein or gene expression-based analyses in determining PTEN status less accurate. In this study, we used network component analysis to identify 20 transcription factors (TFs) whose activities deduced from their target gene expressions were immediately altered upon the re-expression of PTEN in a PTEN-inducible system. Interestingly, PTEN controls the activities (TFA) rather than the expression levels of majority of these TFs and these PTEN-controlled TFAs are substantially altered in prostate cancer mouse models. Importantly, the activities of these TFs can be used to predict PTEN status in human prostate, breast and brain tumor samples with enhanced reliability when compared to straightforward IHC-based or expression-based analysis. Furthermore, our analysis indicates that unique sets of PTEN-controlled TFAs significantly contribute to specific tumor types. Together, our findings reveal that TFAs may be used as ''signatures'' for predicting PTEN functional status and elucidate the transcriptional architectures underlying human cancers caused by PTEN loss.

PLoS ONE, 2012

New therapies for late stage and castration resistant prostate cancer (CRPC) depend on defining u... more New therapies for late stage and castration resistant prostate cancer (CRPC) depend on defining unique properties and pathways of cell sub-populations capable of sustaining the net growth of the cancer. One of the best enrichment schemes for isolating the putative stem/progenitor cell from the murine prostate gland is Lin -;Sca1 + ;CD49f hi (LSC hi ), which results in a more than 10-fold enrichment for in vitro sphere-forming activity. We have shown previously that the LSC hi subpopulation is both necessary and sufficient for cancer initiation in the Pten-null prostate cancer model. To further improve this enrichment scheme, we searched for cell surface molecules upregulated upon castration of murine prostate and identified CD166 as a candidate gene. CD166 encodes a cell surface molecule that can further enrich sphere-forming activity of WT LSC hi and Pten null LSC hi . Importantly, CD166 could enrich sphere-forming ability of benign primary human prostate cells in vitro and induce the formation of tubule-like structures in vivo. CD166 expression is upregulated in human prostate cancers, especially CRPC samples. Although genetic deletion of murine CD166 in the Pten null prostate cancer model does not interfere with sphere formation or block prostate cancer progression and CRPC development, the presence of CD166 on prostate stem/progenitors and castration resistant sub-populations suggest that it is a cell surface molecule with the potential for targeted delivery of human prostate cancer therapeutics.

Plasmid, 2005

A series of plasmid-based expression vectors have been constructed allowing stable intracellular ... more A series of plasmid-based expression vectors have been constructed allowing stable intracellular expression of recombinant proteins in Bacillus subtilis strains. These expression vectors are based on the recently described Escherichia coli-B. subtilis shuttle vector pMTLBS72 which replicates as theta circles. Besides the weak constitutive promoter P lepA , we inserted three diVerent controllable promoters: P gsiB which can be induced by heat and acid shock, and by ethanol, P xylA and P spac which respond to the addition of xylose and IPTG, respectively. The versatility of these expression vectors was demonstrated by fusing their promoters to a reporter gene and by overexpression of the HtpG protein with three of them. All recombinant vectors exhibited full structural stability. 

Phytochemistry, 2006

Cytotoxic Phenylpropanoids and an Additional Thapsigargin Analogue Isolated from Thapsia garganic... more Cytotoxic Phenylpropanoids and an Additional Thapsigargin Analogue Isolated from Thapsia garganica. -Four new phenylpropanoids (I) and a new thapsigargin analogue (II) are isolated from the fruits of the title plant. The former are found to be potent cytotoxins. -(LIU, H.; JENSEN, K. G.; TRAN, L. M.; CHEN, M.; ZHAI, L.; OLSEN, C. E.; SOEHOEL, H.; DENMEADE, S. R.; ISAACS, J. T.; CHRISTENSEN*, S. B.; Phytochemistry 67 (2006) 24, 2651-2658; Dep. Med. Chem., Dan. Univ. Pharm. Sci., DK-2100 Copenhagen, Den.; Eng.) -H. Haber 15-207

Lecture Notes in Computer Science, 2014

This paper introduces a new concept of reversible circuits based on EXOR-sum of Products-of-EXOR-... more This paper introduces a new concept of reversible circuits based on EXOR-sum of Products-of-EXOR-sums (EPOE). Two algorithms are introduced that synthesize reversible functions using these new EPOE structures. The motivation for this work is to reduce the number of multiple controlled Toffoli gates and their number of inputs. To achieve these reductions the paper generalizes from existing 2-level AND-EXOR structures (ESOP) commonly used in reversible logic to a mixture of 3level EXOR-AND-EXOR structures and ESOPs. Our approach can be applied to reversible and permutative quantum circuits to synthesize single output functions with one ancilla line per output. In addition, a variant of the algorithm with garbage lines is presented. A comparison of the ESOP minimizer EXORCISM-4 and variants of the new EPOE minimizer, called EPOEM-1s and EPOEM-1f, is presented. The results show that EPOE circuits do in fact achieve the above-stated cost reductions, in particular when expressed in terms of Maslov's quantum cost model commonly used in quantum circuit synthesis.

Journal of Automation and Control Engineering, 2015

 Abstract-A successful classification of different tumor types is essential for successful treat... more  Abstract-A successful classification of different tumor types is essential for successful treatment of cancer. However, most prior cancer classification methods are clinical-based and have inadequate diagnostic ability. Cancer classification using gene expression data is very important in cancer diagnosis and drug discovery. The introduction of DNA microarray techniques has made simultaneous monitoring of thousands of gene expression probable. With this abundance of gene expression data nowadays, the researchers have the opportunity to do cancer classification using gene expression data. In recent years, a lot of machine learning methods have been proposed to do cancer classification using gene expression data such as clustering-based methods, k-nearest neighbor method, artificial neural network method, and support vector machine method, to name a few. In this paper, we present the un-normalized graph p-Laplacian semisupervised learning methods. These methods will be applied to the patient-patient network constructed from the gene expression data to predict the tumor types of all patients in the network. These methods are based on the assumption that the labels of two adjacent patients in the network are likely to be the same. The experiments show that that the un-normalized graph p-Laplacian semi-supervised learning methods are at least as good as the current state of the art network-based method (the un-normalized graph Laplacian based semi-supervised learning method) but often lead to better classification accuracy performance measures.

Journal of Automation and Control Engineering, 2015

Most network-based protein (or gene) function prediction methods are based on the assumption that... more Most network-based protein (or gene) function prediction methods are based on the assumption that the labels of two adjacent proteins in the network are likely to be the same. However, assuming the pairwise relationship between proteins or genes is not complete. The information a group of genes that show very similar patterns of expression and tend to have similar functions (i.e. the functional modules) is missed. The natural way overcoming the information loss of the above assumption is to represent the gene expression data as the hypergraph. Thus, in this paper, the three un-normalized, random walk, and symmetric normalized hypergraph Laplacian based semisupervised learning methods applied to hypergraph constructed from the gene expression data in order to predict the functions of yeast proteins are introduced. Experiment results show that the average accuracy performance measures of these three hypergraph Laplacian based semi-supervised learning methods are the same. However, their average accuracy performance measures of these three methods are much greater than the average accuracy performance measures of un-normalized graph Laplacian based semi-supervised learning method (i.e. the baseline method of this paper) applied to gene co-expression network created from the gene expression data. 

1996 IEEE MTT-S International Microwave Symposium Digest, 1996

ABSTRACT Frequency translation circuits are key elements in communication systems. This paper prl... more ABSTRACT Frequency translation circuits are key elements in communication systems. This paper prlesents three different frequency multipliers and a frequency mixer designed using the InP HEMT technology. These successful first iteration MMICs are highlighted by a V-band ...

Brain : a journal of neurology, Jan 11, 2015

We describe a novel nephrocerebellar syndrome on the Galloway-Mowat syndrome spectrum among 30 ch... more We describe a novel nephrocerebellar syndrome on the Galloway-Mowat syndrome spectrum among 30 children (ages 1.0 to 28 years) from diverse Amish demes. Children with nephrocerebellar syndrome had progressive microcephaly, visual impairment, stagnant psychomotor development, abnormal extrapyramidal movements and nephrosis. Fourteen died between ages 2.7 and 28 years, typically from renal failure. Post-mortem studies revealed (i) micrencephaly without polymicrogyria or heterotopia; (ii) atrophic cerebellar hemispheres with stunted folia, profound granule cell depletion, Bergmann gliosis, and signs of Purkinje cell deafferentation; (iii) selective striatal cholinergic interneuron loss; and (iv) optic atrophy with delamination of the lateral geniculate nuclei. Renal tissue showed focal and segmental glomerulosclerosis and extensive effacement and microvillus transformation of podocyte foot processes. Nephrocerebellar syndrome mapped to 700 kb on chromosome 15, which contained a single ...

The Journal of Pediatrics, 2015

Objective To assess the effectiveness of supreme laryngeal mask airway (SLMA) over face mask vent... more Objective To assess the effectiveness of supreme laryngeal mask airway (SLMA) over face mask ventilation for preventing need for endotracheal intubation at birth.

1985 International Electron Devices Meeting, 1985

A lightly doped drain (LDD) structure(1) is used in our Twin-Tub IV, fourth generation Twin-Tub C... more A lightly doped drain (LDD) structure(1) is used in our Twin-Tub IV, fourth generation Twin-Tub CMOS technology to improve stability of the N-channel transistor. The LDD N-channel transistors were successfully incorporated into the technology without adding any additional photolithography steps to the conventional process. The key to the process is a differential oxidation step of BF2implanted source/drain regions, which prevents

Journal of Surgical Research, 2015

We previously identified a correlation between increased expression of the phosphoinositide 3-kin... more We previously identified a correlation between increased expression of the phosphoinositide 3-kinase (PI3K) regulatory subunit p85α and improved survival in human pancreatic ductal adenocarcinoma (PDAC). The purpose of this study was to investigate the impact of changes in p85α expression on response to chemotherapy and the regulation of p85α by microRNA-21 (miR-21). PDAC tumor cells overexpressing p85α were generated by viral transduction, and the effect of p85α overexpression on sensitivity to gemcitabine was tested by MTT assay. Primary human PDAC tumors were stained for p85α and miR-21 via immunohistochemistry and in situ hybridization, respectively. Additionally, PDAC cells were treated with miR-21 mimic, and changes in p85α and phospho-AKT were assessed by Western blot. Finally, a luciferase reporter assay system was used to test direct regulation of p85α by miR-21. Higher p85α expression resulted in increased sensitivity to gemcitabine (P < 0.01), which correlated with decreased PI3K-AKT activation. Human tumors demonstrated an inverse correlation between miR-21 and p85α expression levels (r = -0.353, P < 0.001). In vitro, overexpression of miR-21 resulted in decreased levels of p85α and increased phosphorylation of AKT. Luciferase reporter assays confirmed the direct regulation of p85α by miR-21 (P < 0.01). Our results demonstrate that p85α expression is a determinant of chemosensitivity in PDAC. Additionally, we provide novel evidence that miR-21 can influence PI3K-AKT signaling via its direct regulation of p85α. These data provide insight into potential mechanisms for the known relationship between increased p85α expression and improved survival in PDAC.

IEEE MTT-S International Microwave Symposium Digest, 2007

A new class of zero bias, room temperature ultra sensitive detectors have been introduced for det... more A new class of zero bias, room temperature ultra sensitive detectors have been introduced for detection of millimeter wave radiation. The detectors have been scaled to micron level and have shown record responsivity in three forms. A W-band waveguide detector was designed and measured to have 4500 V/W voltage responsivity. A planar antenna coupled detector was also evaluated with and measured a responsivity 16100 V-mm2IW from 75-110 GHz. Following a resonant impedance matching technique an on-wafer characterization have shown voltage responsivity to exceed 20,000 V/W. The result does not include the reflected power from the detector and have shown that these detectors could provide noise equivalent power (NEP) values in the 4xlW1'3 W/ 'IHz level.

Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering, 2015

Most network-based clustering methods are based on the assumption that the labels of two adjacent... more Most network-based clustering methods are based on the assumption that the labels of two adjacent vertices in the network are likely to be the same. However, assuming the pairwise relationship between vertices is not complete. The information a group of vertices that show very similar patterns and tend to have similar labels is missed. The natural way overcoming the information loss of the above assumption is to represent the given data as the hypergraph. Thus, in this paper, the two unnormalized and random walk hypergraph Laplacian based un-supervised learning methods are introduced. Experiment results show that the accuracy performance measures of these two hypergraph Laplacian based un-supervised learning methods are greater than the accuracy performance measure of symmetric normalized graph Laplacian based un-supervised learning method (i.e. the baseline method of this paper) applied to simple graph created from the incident matrix of hypergraph.

1999 IEEE Third Workshop on Multimedia Signal Processing (Cat. No.99TH8451), 1999

Abstract - In many multi-media applications it is desirable to sep arate the iduence of the illum... more Abstract - In many multi-media applications it is desirable to sep arate the iduence of the illumination sources and imaging equipment from the properties of the depicted scene. The ability of the human visual system to solve this task in many situations is known as color con-stancy. ...

Signal Processing, 2005

In many colour-based image retrieval systems the colour properties of an image are described by i... more In many colour-based image retrieval systems the colour properties of an image are described by its colour histogram. Histogram-based search is, however, often inefficient for large histogram sizes. Therefore we introduce several new, Karhunen-Loe`ve transform (KLT)-based methods that provide efficient representations of colour histograms and differences between two colour histograms. The methods are based on the following two observations; Ordinary KLT considers colour histograms as signals and uses the Euclidian distance for optimization; KLT with generalized colour distance measures that take into account both the statistical properties of the image database and the properties of the underlying colour space should improve the retrieval performance. Image retrieval applications compare similarities between different images. Relevant for the decision is only the local structure of the image space around the current query image since the task is to find those images in the database that are most similar to this given query image. Therefore only the local topology of the feature space is of interest and compression methods should preserve this local topology as much as possible. It is therefore more important to have a good representation of the differences between features of similar images than good representations of the features of the images themselves. The optimization should therefore be based on minimizing the approximation error in the space of local histogram differences instead of the space of colour histograms. In this paper we report the results of our experiments that are done on three image databases containing more than 130,000 images. Both objective and subjective ground truth queries are used in order to evaluate the proposed methods and to compare them with other existing methods. The results from our experiments show that compression methods based on a combination of the two observations described above provide new, powerful and efficient retrieval algorithms for colour-based image retrieval. r

Proceedings of the National Academy of Sciences, 2007

Nitric oxide (NO) is used by mammalian immune systems to counter microbial invasions and is produ... more Nitric oxide (NO) is used by mammalian immune systems to counter microbial invasions and is produced by bacteria during denitrification. As a defense, microorganisms possess a complex network to cope with NO. Here we report a combined transcriptomic, chemical, and phenotypic approach to identify direct NO targets and construct the biochemical response network. In particular, network component analysis was used to identify transcription factors that are perturbed by NO. Such information was screened with potential NO reaction mechanisms and phenotypic data from genetic knockouts to identify active chemistry and direct NO targets in Escherichia coli. This approach identified the comprehensive E. coli NO response network and evinced that NO halts bacterial growth via inhibition of the branched-chain amino acid biosynthesis enzyme dihydroxyacid dehydratase. Because mammals do not synthesize branched-chain amino acids, inhibition of dihydroxyacid dehydratase may have served to foster the role of NO in the immune arsenal.

PLoS ONE, 2012

PTEN-controlled PI3K-AKT-mTOR pathway represents one of the most deregulated signaling pathways i... more PTEN-controlled PI3K-AKT-mTOR pathway represents one of the most deregulated signaling pathways in human cancers. With many small molecule inhibitors that target PI3K-AKT-mTOR pathway being exploited clinically, sensitive and reliable ways of stratifying patients according to their PTEN functional status and determining treatment outcomes are urgently needed. Heterogeneous loss of PTEN is commonly associated with human cancers and yet PTEN can also be regulated on epigenetic, transcriptional or post-translational levels, which makes the use of simple protein or gene expression-based analyses in determining PTEN status less accurate. In this study, we used network component analysis to identify 20 transcription factors (TFs) whose activities deduced from their target gene expressions were immediately altered upon the re-expression of PTEN in a PTEN-inducible system. Interestingly, PTEN controls the activities (TFA) rather than the expression levels of majority of these TFs and these PTEN-controlled TFAs are substantially altered in prostate cancer mouse models. Importantly, the activities of these TFs can be used to predict PTEN status in human prostate, breast and brain tumor samples with enhanced reliability when compared to straightforward IHC-based or expression-based analysis. Furthermore, our analysis indicates that unique sets of PTEN-controlled TFAs significantly contribute to specific tumor types. Together, our findings reveal that TFAs may be used as ''signatures'' for predicting PTEN functional status and elucidate the transcriptional architectures underlying human cancers caused by PTEN loss.

PLoS ONE, 2012

New therapies for late stage and castration resistant prostate cancer (CRPC) depend on defining u... more New therapies for late stage and castration resistant prostate cancer (CRPC) depend on defining unique properties and pathways of cell sub-populations capable of sustaining the net growth of the cancer. One of the best enrichment schemes for isolating the putative stem/progenitor cell from the murine prostate gland is Lin -;Sca1 + ;CD49f hi (LSC hi ), which results in a more than 10-fold enrichment for in vitro sphere-forming activity. We have shown previously that the LSC hi subpopulation is both necessary and sufficient for cancer initiation in the Pten-null prostate cancer model. To further improve this enrichment scheme, we searched for cell surface molecules upregulated upon castration of murine prostate and identified CD166 as a candidate gene. CD166 encodes a cell surface molecule that can further enrich sphere-forming activity of WT LSC hi and Pten null LSC hi . Importantly, CD166 could enrich sphere-forming ability of benign primary human prostate cells in vitro and induce the formation of tubule-like structures in vivo. CD166 expression is upregulated in human prostate cancers, especially CRPC samples. Although genetic deletion of murine CD166 in the Pten null prostate cancer model does not interfere with sphere formation or block prostate cancer progression and CRPC development, the presence of CD166 on prostate stem/progenitors and castration resistant sub-populations suggest that it is a cell surface molecule with the potential for targeted delivery of human prostate cancer therapeutics.

Plasmid, 2005

A series of plasmid-based expression vectors have been constructed allowing stable intracellular ... more A series of plasmid-based expression vectors have been constructed allowing stable intracellular expression of recombinant proteins in Bacillus subtilis strains. These expression vectors are based on the recently described Escherichia coli-B. subtilis shuttle vector pMTLBS72 which replicates as theta circles. Besides the weak constitutive promoter P lepA , we inserted three diVerent controllable promoters: P gsiB which can be induced by heat and acid shock, and by ethanol, P xylA and P spac which respond to the addition of xylose and IPTG, respectively. The versatility of these expression vectors was demonstrated by fusing their promoters to a reporter gene and by overexpression of the HtpG protein with three of them. All recombinant vectors exhibited full structural stability. 

Phytochemistry, 2006

Cytotoxic Phenylpropanoids and an Additional Thapsigargin Analogue Isolated from Thapsia garganic... more Cytotoxic Phenylpropanoids and an Additional Thapsigargin Analogue Isolated from Thapsia garganica. -Four new phenylpropanoids (I) and a new thapsigargin analogue (II) are isolated from the fruits of the title plant. The former are found to be potent cytotoxins. -(LIU, H.; JENSEN, K. G.; TRAN, L. M.; CHEN, M.; ZHAI, L.; OLSEN, C. E.; SOEHOEL, H.; DENMEADE, S. R.; ISAACS, J. T.; CHRISTENSEN*, S. B.; Phytochemistry 67 (2006) 24, 2651-2658; Dep. Med. Chem., Dan. Univ. Pharm. Sci., DK-2100 Copenhagen, Den.; Eng.) -H. Haber 15-207