Binh Nguyen - Academia.edu (original) (raw)

Papers by Binh Nguyen

2011 IEEE/RSJ International Conference on Intelligent Robots and Systems

To plan a robotic task involving intermittent contact, such as an assembly task, it is helpful to... more To plan a robotic task involving intermittent contact, such as an assembly task, it is helpful to be able to simulate the task accurately and efficiently. In the past ten years, the prox formulation of the equations of motion has arisen as a competitive alternative to the well-known linear and nonlinear complementarity problem (LCP and NCP) formulations. In this paper, we compare these two formulations, showing through a set-based argument that the formulations are equivalent. Second, we provide simple examples to compare the most common approaches for solving these formulations. The prox formulation is solved by fixed-point iteration while the complementarity formulation is solved by a pivoting scheme, known as Lemke's algorithm. The well-known paradox of PAINLEVÉ is used in a case where two solutions exist to illustrate that the fixed-point scheme can fail while the pivoting scheme will succeed.

Contemporary Mathematics, 2014

We consider the eigenvalue problem for the Laplace operator in a planar domain which can be decom... more We consider the eigenvalue problem for the Laplace operator in a planar domain which can be decomposed into a bounded domain of arbitrary shape and elongated "branches" of variable cross-sectional profiles. When the eigenvalue is smaller than a prescribed threshold, the corresponding eigenfunction decays exponentially along each branch. We prove this behavior for Robin boundary condition and illustrate some related results by numerically computed eigenfunctions.

Seminars in Nuclear Medicine, 2002

The goal of this article is to summarize current data on computed tomography (CT) and magnetic re... more The goal of this article is to summarize current data on computed tomography (CT) and magnetic resonance (MR) in the diagnosis of acute pulmonary embolism (PE) in relation to the radionuclide ventilation perfusion scan. It is important for the nuclear medicine, CT, and MR communities to develop a shared approach to this disorder. Triage using chest radiographs appears to be a practical method for enhancing both nuclear medicine and CT/MR performance. The realization that there is no clinically available gold standard for the diagnosis of PE suggests that the imaging community should replace impractical and

Journal of Medicinal Chemistry, 2008

A series of 75 guanidine and 2-aminoimidazoline analogue molecules were assayed in vitro against ... more A series of 75 guanidine and 2-aminoimidazoline analogue molecules were assayed in vitro against Trypanosoma brucei rhodesiense STIB900 and Plasmodium falciparum K1. The dicationic diphenyl compounds exhibited the best activities with IC 50 values against T. b. rhodesiense and P. falciparum in the nanomolar range. Five compounds (7b, 9a, 9b, 10b, and 14b) cured 100% of treated mice upon ip administration at 20mg/kg in the difficult to cure T. b. rhodesiense STIB900 mouse model. Overall, the compounds that bear the 2-aminoimidazoline cations benefit from better safety profiles than the guanidine counterparts. The observation of a correlation between DNA binding affinity at AT-sites and trypanocidal activity for three series of compounds supported the view of a mechanism of antitrypanosomal action due in part to the formation of a DNA complex. No correlation between antiplasmodial activity and in vitro inhibition of ferriprotoporphyrin IX biomineralisation was observed, suggesting that additional mechanism of action (MOA) is likely to be involved.

Journal of Biotechnology, 1993

A fed-batch method was developed which increased the density of insect cells (Spodoptera frugiper... more A fed-batch method was developed which increased the density of insect cells (Spodoptera frugiperda, Sf-9 ceils) in suspension culture and the feeding of nutrients improved the yield of a recombinant protein produced by a baculovirus expression system. Analysis of spent medium samples indicated that depletions of glucose and glutamine correlated with the retardation of cell growth. Feeding of a mixture of nutrients consisting of glucose, glutamine, yeastolate and lipids solution restored the growth rate. In fed-batch culture, cell density was increased from 3 x 10 6 cells per ml to 1.2 x 107 cells per ml and the increased cell density enhanced the yield of the desired recombinant product, in this case, human nerve growth factor (rhNGF). The optimal conditions for the production of rhNGF were also defined by selecting the appropriate viral multiplicity of infection (MOI). At a cell density of 5 × 10 6 m1-1, a MOI of 0.05 (plaque forming units per cell) gave the highest yield of rhNGF in culture fluid 3 d post-infection. The yield of rhNGF was 20 mg 1-1. The fed-batch method was scaled up to 12 1 stirred bioreactor.

Experimental Neurology, 1990

A baculovirus expression vector, which contains the coding sequences for human prepro (0) nerve g... more A baculovirus expression vector, which contains the coding sequences for human prepro (0) nerve growth factor under control of the viral polyhedrin promoter, was constructed. Upon infection of insect cells with the recombinant virus, mature human fi nerve growth factor (rhNGF) was released into the culture fluid. The mature rhNGF was biologically active since rat pheochromocytoma (PC 12) and human neuroblastoma (SH-SYBY) cells were induced to extend neurites upon treatment with this material. This activity was abolished by treating with antiserum prepared against mature mouse @ NGF (mNGF). When compared with mNGF, rhNGF more rapidly elicited the differentiation response in both PC12 and SH-SYBY cells. In an in vivo assay of cholinergic cell survival, rhNGF was nearly as potent as mNGF in protecting choline&c neurons from degeneration following a fimbria-fornix lesion. These results show that the baculovirus expression system provides quantities of biologically potent human @ NGF suitable for a comprehensive program of research to ascertain /3 NGF's potential as a therapeutic agent for the treatment of Alzheimer's disease. o lmo Academic Press, Inc.

Bioorganic & Medicinal Chemistry, 2008

Seven N-terminus modified derivatives of a previously published minor-groove binding polyamide (f... more Seven N-terminus modified derivatives of a previously published minor-groove binding polyamide (f-ImPyIm, 1) were synthesized and the biochemical and biophysical chemistry evaluated. These compounds were synthesized with the aim of attaining a higher level of sequence selectivity over f-ImPyIm (1), a previously published strong minor-groove binder. Two compounds possessing a furan or a benzofuran moiety at the N-terminus showed a footprint of 0.5 lM at the cognate ACGCGT site (determined by DNase I footprinting); however, the specificity of these compounds was not improved. In contrast, PyImPyIm (4) produced a footprint of 0.5 lM but showed a superior specificity using the same technique. When evaluated by thermal melting experiments and circular dichroism using ACGCGT and the non-cognate AAATTT sequence, all compounds were shown to bind in the minorgroove of DNA and stabilize the cognate sequence much better than the non-cognate (except for the non-amido-compound that did not bind either sequence, as expected). PyImPyIm (4) was interesting as the DT m for this compound was only 4°C but the footprint was very selective. No binding was observed for this compound with a third DNA (non-cognate, ACCGGT). ITC studies on compound 4 showed exothermic binding with ACGCGT and no heat change was observed for titrating the compound to the other two DNA sequences. The heat capacity (DC p) of the PIPI/ACGCGT complex calculated from the hydrophobic interactions and SASA calculations was comparable to the experimental value obtained from ITC (À146 cal mol À1 K À1). SPR results provided confirmation of the sequence specificity of PyImPyIm (4), with a K eq value determined to be 7.1 • 10 6 M À1 for the cognate sequence and no observable binding to AAATTT and ACCGGT. Molecular dynamic simulations affirmed that PyImPyIm (4) binds as a dimer in an overlapped conformation, and it fits snugly in the minor-groove of the ACGCGT oligonucleotide. PyImPyIm (4) is an especially interesting molecule, because although the binding affinity is slightly reduced, the specificity with respect to f-ImPyIm (1) is significantly improved.

Bioorganic & Medicinal Chemistry, 2008

Imidazole (Im) and Pyrrole (Py)-containing polyamides that can form stacked dimers can be program... more Imidazole (Im) and Pyrrole (Py)-containing polyamides that can form stacked dimers can be programmed to target specific sequences in the minor groove of DNA and control gene expression. Even though various designs of polyamides have been thoroughly investigated for DNA sequence recognition, the use of H-pin polyamides (covalently cross-linked polyamides) has not received as much attention. Therefore, experiments were designed to systematically investigate the DNA recognition properties of two symmetrical H-pin polyamides composed of PyImPyIm (5) or f-ImPyIm (3e, f = formamido) tethered with an ethylene glycol linker. These compounds were created to recognize the cognate 5-ACGCGT-3 through an overlapped and staggered binding motif, respectively. Results from DNaseI footprinting, thermal denaturation, circular dichroism, surface plasmon resonance and isothermal titration microcalorimetry studies demonstrated that both H-pin polyamides bound with higher affinity than their respective monomers. The binding affinity of formamido-containing H-pin 3e was more than a hundred times greater than that for the tetraamide H-pin 5, demonstrating the importance of having a formamido group and the staggered motif in enhancing affinity. However, compared to H-pin 3e, tetraamide H-pin 5 demonstrated superior binding preference for the cognate sequence over its non-cognates, ACCGGT and AAATTT. Data from SPR experiments yielded binding constants of 1.6 × 10 8 M −1 and 2.0 × 10 10 M −1 for PyImPyIm H-pin 5 and f-ImPyIm H-pin 3e, respectively. Both H-pins bound with significantly higher affinity (ca. 100-fold) than their corresponding unlinked PyImPyIm 4 and f-ImPyIm 2 counterparts. ITC analyses revealed modest enthalpies of reactions at 298 K (H of −3.3 and −1.0 kcal mol −1 for 5 and 3e, respectively), indicating these were entropic-driven interactions. The heat capacities (C p) were determined to be −116 and −499 cal mol −1 K −1 , respectively. These results are in general agreement with C p values determined from changes in the solvent accessible surface areas using complexes of the H-pins bound to (5-CCACGCGTGG) 2. According to the models, the H-pins fit snugly in the minor groove and the linker comfortably holds both polyamide portions in place, with the oxygen atoms pointing into

Academic Radiology, 2004

Rationale and Objectives. To compare the effectiveness of a new computational scheme for pulmonar... more Rationale and Objectives. To compare the effectiveness of a new computational scheme for pulmonary nodule detection in computed tomography images against human observers. Materials and Methods. The study involved evaluation of 81 potential nodules by four radiologists. Each radiologist separately evaluated the potential nodules and provided a confidence level for the presence of pulmonary nodules. Their performance was compared with that of the new computational scheme by mixture distribution analysis. Results. Mixture distribution analysis of the results of the four radiologists demonstrated a relative proportion agreement of 0.84. The kappa statistic was used to compare the agreement of the computational scheme with the results of the four radiologists. A kappa value of .65 (se ϭ .11) was shown to be significantly different from chance (P ϭ .99). Conclusion. The new computational scheme correlates well with the radiologists' subjective rankings of pulmonary nodules on computed tomography scans and may prove a useful tool in the evaluation of algorithms for the screening and diagnosis of lung cancer.

2011 IEEE/RSJ International Conference on Intelligent Robots and Systems

To plan a robotic task involving intermittent contact, such as an assembly task, it is helpful to... more To plan a robotic task involving intermittent contact, such as an assembly task, it is helpful to be able to simulate the task accurately and efficiently. In the past ten years, the prox formulation of the equations of motion has arisen as a competitive alternative to the well-known linear and nonlinear complementarity problem (LCP and NCP) formulations. In this paper, we compare these two formulations, showing through a set-based argument that the formulations are equivalent. Second, we provide simple examples to compare the most common approaches for solving these formulations. The prox formulation is solved by fixed-point iteration while the complementarity formulation is solved by a pivoting scheme, known as Lemke's algorithm. The well-known paradox of PAINLEVÉ is used in a case where two solutions exist to illustrate that the fixed-point scheme can fail while the pivoting scheme will succeed.

Contemporary Mathematics, 2014

We consider the eigenvalue problem for the Laplace operator in a planar domain which can be decom... more We consider the eigenvalue problem for the Laplace operator in a planar domain which can be decomposed into a bounded domain of arbitrary shape and elongated "branches" of variable cross-sectional profiles. When the eigenvalue is smaller than a prescribed threshold, the corresponding eigenfunction decays exponentially along each branch. We prove this behavior for Robin boundary condition and illustrate some related results by numerically computed eigenfunctions.

Seminars in Nuclear Medicine, 2002

The goal of this article is to summarize current data on computed tomography (CT) and magnetic re... more The goal of this article is to summarize current data on computed tomography (CT) and magnetic resonance (MR) in the diagnosis of acute pulmonary embolism (PE) in relation to the radionuclide ventilation perfusion scan. It is important for the nuclear medicine, CT, and MR communities to develop a shared approach to this disorder. Triage using chest radiographs appears to be a practical method for enhancing both nuclear medicine and CT/MR performance. The realization that there is no clinically available gold standard for the diagnosis of PE suggests that the imaging community should replace impractical and

Journal of Medicinal Chemistry, 2008

A series of 75 guanidine and 2-aminoimidazoline analogue molecules were assayed in vitro against ... more A series of 75 guanidine and 2-aminoimidazoline analogue molecules were assayed in vitro against Trypanosoma brucei rhodesiense STIB900 and Plasmodium falciparum K1. The dicationic diphenyl compounds exhibited the best activities with IC 50 values against T. b. rhodesiense and P. falciparum in the nanomolar range. Five compounds (7b, 9a, 9b, 10b, and 14b) cured 100% of treated mice upon ip administration at 20mg/kg in the difficult to cure T. b. rhodesiense STIB900 mouse model. Overall, the compounds that bear the 2-aminoimidazoline cations benefit from better safety profiles than the guanidine counterparts. The observation of a correlation between DNA binding affinity at AT-sites and trypanocidal activity for three series of compounds supported the view of a mechanism of antitrypanosomal action due in part to the formation of a DNA complex. No correlation between antiplasmodial activity and in vitro inhibition of ferriprotoporphyrin IX biomineralisation was observed, suggesting that additional mechanism of action (MOA) is likely to be involved.

Journal of Biotechnology, 1993

A fed-batch method was developed which increased the density of insect cells (Spodoptera frugiper... more A fed-batch method was developed which increased the density of insect cells (Spodoptera frugiperda, Sf-9 ceils) in suspension culture and the feeding of nutrients improved the yield of a recombinant protein produced by a baculovirus expression system. Analysis of spent medium samples indicated that depletions of glucose and glutamine correlated with the retardation of cell growth. Feeding of a mixture of nutrients consisting of glucose, glutamine, yeastolate and lipids solution restored the growth rate. In fed-batch culture, cell density was increased from 3 x 10 6 cells per ml to 1.2 x 107 cells per ml and the increased cell density enhanced the yield of the desired recombinant product, in this case, human nerve growth factor (rhNGF). The optimal conditions for the production of rhNGF were also defined by selecting the appropriate viral multiplicity of infection (MOI). At a cell density of 5 × 10 6 m1-1, a MOI of 0.05 (plaque forming units per cell) gave the highest yield of rhNGF in culture fluid 3 d post-infection. The yield of rhNGF was 20 mg 1-1. The fed-batch method was scaled up to 12 1 stirred bioreactor.

Experimental Neurology, 1990

A baculovirus expression vector, which contains the coding sequences for human prepro (0) nerve g... more A baculovirus expression vector, which contains the coding sequences for human prepro (0) nerve growth factor under control of the viral polyhedrin promoter, was constructed. Upon infection of insect cells with the recombinant virus, mature human fi nerve growth factor (rhNGF) was released into the culture fluid. The mature rhNGF was biologically active since rat pheochromocytoma (PC 12) and human neuroblastoma (SH-SYBY) cells were induced to extend neurites upon treatment with this material. This activity was abolished by treating with antiserum prepared against mature mouse @ NGF (mNGF). When compared with mNGF, rhNGF more rapidly elicited the differentiation response in both PC12 and SH-SYBY cells. In an in vivo assay of cholinergic cell survival, rhNGF was nearly as potent as mNGF in protecting choline&c neurons from degeneration following a fimbria-fornix lesion. These results show that the baculovirus expression system provides quantities of biologically potent human @ NGF suitable for a comprehensive program of research to ascertain /3 NGF's potential as a therapeutic agent for the treatment of Alzheimer's disease. o lmo Academic Press, Inc.

Bioorganic & Medicinal Chemistry, 2008

Seven N-terminus modified derivatives of a previously published minor-groove binding polyamide (f... more Seven N-terminus modified derivatives of a previously published minor-groove binding polyamide (f-ImPyIm, 1) were synthesized and the biochemical and biophysical chemistry evaluated. These compounds were synthesized with the aim of attaining a higher level of sequence selectivity over f-ImPyIm (1), a previously published strong minor-groove binder. Two compounds possessing a furan or a benzofuran moiety at the N-terminus showed a footprint of 0.5 lM at the cognate ACGCGT site (determined by DNase I footprinting); however, the specificity of these compounds was not improved. In contrast, PyImPyIm (4) produced a footprint of 0.5 lM but showed a superior specificity using the same technique. When evaluated by thermal melting experiments and circular dichroism using ACGCGT and the non-cognate AAATTT sequence, all compounds were shown to bind in the minorgroove of DNA and stabilize the cognate sequence much better than the non-cognate (except for the non-amido-compound that did not bind either sequence, as expected). PyImPyIm (4) was interesting as the DT m for this compound was only 4°C but the footprint was very selective. No binding was observed for this compound with a third DNA (non-cognate, ACCGGT). ITC studies on compound 4 showed exothermic binding with ACGCGT and no heat change was observed for titrating the compound to the other two DNA sequences. The heat capacity (DC p) of the PIPI/ACGCGT complex calculated from the hydrophobic interactions and SASA calculations was comparable to the experimental value obtained from ITC (À146 cal mol À1 K À1). SPR results provided confirmation of the sequence specificity of PyImPyIm (4), with a K eq value determined to be 7.1 • 10 6 M À1 for the cognate sequence and no observable binding to AAATTT and ACCGGT. Molecular dynamic simulations affirmed that PyImPyIm (4) binds as a dimer in an overlapped conformation, and it fits snugly in the minor-groove of the ACGCGT oligonucleotide. PyImPyIm (4) is an especially interesting molecule, because although the binding affinity is slightly reduced, the specificity with respect to f-ImPyIm (1) is significantly improved.

Bioorganic & Medicinal Chemistry, 2008

Imidazole (Im) and Pyrrole (Py)-containing polyamides that can form stacked dimers can be program... more Imidazole (Im) and Pyrrole (Py)-containing polyamides that can form stacked dimers can be programmed to target specific sequences in the minor groove of DNA and control gene expression. Even though various designs of polyamides have been thoroughly investigated for DNA sequence recognition, the use of H-pin polyamides (covalently cross-linked polyamides) has not received as much attention. Therefore, experiments were designed to systematically investigate the DNA recognition properties of two symmetrical H-pin polyamides composed of PyImPyIm (5) or f-ImPyIm (3e, f = formamido) tethered with an ethylene glycol linker. These compounds were created to recognize the cognate 5-ACGCGT-3 through an overlapped and staggered binding motif, respectively. Results from DNaseI footprinting, thermal denaturation, circular dichroism, surface plasmon resonance and isothermal titration microcalorimetry studies demonstrated that both H-pin polyamides bound with higher affinity than their respective monomers. The binding affinity of formamido-containing H-pin 3e was more than a hundred times greater than that for the tetraamide H-pin 5, demonstrating the importance of having a formamido group and the staggered motif in enhancing affinity. However, compared to H-pin 3e, tetraamide H-pin 5 demonstrated superior binding preference for the cognate sequence over its non-cognates, ACCGGT and AAATTT. Data from SPR experiments yielded binding constants of 1.6 × 10 8 M −1 and 2.0 × 10 10 M −1 for PyImPyIm H-pin 5 and f-ImPyIm H-pin 3e, respectively. Both H-pins bound with significantly higher affinity (ca. 100-fold) than their corresponding unlinked PyImPyIm 4 and f-ImPyIm 2 counterparts. ITC analyses revealed modest enthalpies of reactions at 298 K (H of −3.3 and −1.0 kcal mol −1 for 5 and 3e, respectively), indicating these were entropic-driven interactions. The heat capacities (C p) were determined to be −116 and −499 cal mol −1 K −1 , respectively. These results are in general agreement with C p values determined from changes in the solvent accessible surface areas using complexes of the H-pins bound to (5-CCACGCGTGG) 2. According to the models, the H-pins fit snugly in the minor groove and the linker comfortably holds both polyamide portions in place, with the oxygen atoms pointing into

Academic Radiology, 2004

Rationale and Objectives. To compare the effectiveness of a new computational scheme for pulmonar... more Rationale and Objectives. To compare the effectiveness of a new computational scheme for pulmonary nodule detection in computed tomography images against human observers. Materials and Methods. The study involved evaluation of 81 potential nodules by four radiologists. Each radiologist separately evaluated the potential nodules and provided a confidence level for the presence of pulmonary nodules. Their performance was compared with that of the new computational scheme by mixture distribution analysis. Results. Mixture distribution analysis of the results of the four radiologists demonstrated a relative proportion agreement of 0.84. The kappa statistic was used to compare the agreement of the computational scheme with the results of the four radiologists. A kappa value of .65 (se ϭ .11) was shown to be significantly different from chance (P ϭ .99). Conclusion. The new computational scheme correlates well with the radiologists' subjective rankings of pulmonary nodules on computed tomography scans and may prove a useful tool in the evaluation of algorithms for the screening and diagnosis of lung cancer.