Tuan Anh Pham - Academia.edu (original) (raw)

Papers by Tuan Anh Pham

… Transactions of the …, 1997

A multiwavelength, high bandwidth (1 GHz) frequency-domain photon migration (FDPM) instrument has... more A multiwavelength, high bandwidth (1 GHz) frequency-domain photon migration (FDPM) instrument has been developed for quantitative, non-invasive measurements of tissue optical and physiological properties. The instrument produces 300 kHz to 1 GHz photon density waves (PDWs) in optically turbid media using a network analyser, an avalanche photodiode detector and four amplitude-modulated diode lasers (674 nm, 811 nm, 849 nm, and 956 nm). The frequency of PDW phase and amplitude is measured and compared to analytically derived model functions in order to calculate absorption, mu a, and reduced scattering, mu s, parameters. The wavelength-dependence of absorption is used to determine tissue haemoglobin concentration (total, oxy- and deoxy- forms), oxygen saturation and water concentration. We present preliminary results of non-invasive FDPM measurements obtained from normal and tumour-containing human breast tissue. Our data clearly demonstrate that physiological changes caused by the presence of small (about 1 cm diameter) palpable lesions can be detected using a handheld FDPM probe.

Journal of medicinal chemistry, Jan 5, 2006

Surflex-Dock employs an empirically derived scoring function to rank putative protein-ligand inte... more Surflex-Dock employs an empirically derived scoring function to rank putative protein-ligand interactions by flexible docking of small molecules to proteins of known structure. The scoring function employed by Surflex was developed purely on the basis of positive data, comprising noncovalent protein-ligand complexes with known binding affinities. Consequently, scoring function terms for improper interactions received little weight in parameter estimation, and an ad hoc scheme for avoiding protein-ligand interpenetration was adopted. We present a generalized method for incorporating synthetically generated negative training data, which allows for rigorous estimation of all scoring function parameters. Geometric docking accuracy remained excellent under the new parametrization. In addition, a test of screening utility covering a diverse set of 29 proteins and corresponding ligand sets showed improved performance. Maximal enrichment of true ligands over nonligands exceeded 20-fold in over 80% of cases, with enrichment of greater than 100-fold in over 50% of cases.

Chemical Communications, 2007

A novel negative, inorganic polymer photoresist was demonstrated to be suitable for simple and di... more A novel negative, inorganic polymer photoresist was demonstrated to be suitable for simple and direct fabrication of tribological SiCN-based ceramic microstructures via UV photolithography and subsequent pyrolysis at 800 degrees C.

Superparamagnetic iron oxide nanoparticles (SPIONs) are currently unavailable as MRI contrast age... more Superparamagnetic iron oxide nanoparticles (SPIONs) are currently unavailable as MRI contrast agents for detecting atherosclerosis in the clinical setting because of either low signal enhancement or safety concerns. Therefore, a new generation of SPIONs with increased circulation time, enhanced image contrast, and less cytotoxicity is essential. In this study, monodisperse SPIONs were synthesized and coated with polyethylene glycol (PEG) of varying molecular weights. The resulting PEGylated SPIONs were characterized, and their interactions with vascular smooth muscle cells (VSMCs) were examined. SPIONs were tested at different concentrations (100 and 500 ppm Fe) for stability, T 2 contrast, cytotoxicity, and cellular uptake to determine an optimal formulation for in vivo use. We found that at 100 ppm Fe, the PEG 2K SPIONs showed adequate stability and magnetic contrast, and exhibited the least cytotoxicity and nonspecific cellular uptake. An increase in cell viability was observed when the SPION-treated cells were washed with PBS after 1 h incubation compared to 5 and 24 h incubation without washing. Our investigation provides insight into the potential safe application of SPIONs in the clinic.

Proceedings of 2012 UKACC International Conference on Control, 2012

The emergence of RFID applications has huge influence to become pervasive in modern life. However... more The emergence of RFID applications has huge influence to become pervasive in modern life. However the vulnerability of the transmission through the air and the unique identification number of RFID tag are the drawbacks that impact the popularity of RFID technology. In this paper, a mutual authentication protocol is proposed based on the challengeresponse model. The Advanced Encryption Standard (AES) is used as a cryptographic primitive to secure the data. The experimental works are carried out to validate the protocol in term of security and privacy. The timing analysis is also presented and applied to a case study of conveyor belt system.

Mycobiology, 2011

Spores of Aspergillus sp. SU14 were treated repeatedly and sequentially with Co(60) γ-rays, ultra... more Spores of Aspergillus sp. SU14 were treated repeatedly and sequentially with Co(60) γ-rays, ultraviolet irradiation, and N-methyl-N'-nitro-N-nitrosoguanidine. One selected mutant strain, Aspergillus sp. SU14-M15, produced cellulase in a yield 2.2-fold exceeding that of the wild type. Optimal conditions for the production of cellulase by the mutant fungal strain using solid-state fermentation were examined. The medium consisted of wheat-bran supplemented with 1% (w/w) urea or NH(4)Cl, 1% (w/w) rice starch, 2.5 mM MgCl(2), and 0.05% (v/w) Tween 80. Optimal moisture content and initial pH was 50% (v/w) and 3.5, respectively, and optimal aeration area was 3/100 (inoculated wheat bran/container). The medium was inoculated with 25% 48 hr seeding culture and fermented at 35℃ for 3 days. The resulting cellulase yield was 8.5-fold more than that of the wild type strain grown on the basal wheat bran medium.

Advances in Intelligent Systems and Computing, 2014

Phishing is a real threat on the Internet nowadays. According to a report released by an American... more Phishing is a real threat on the Internet nowadays. According to a report released by an American security firm, RSA, there have been approximately 33,000 phishing attacks globally each month in 2012, leading to a loss of $687 million. Therefore, fighting against phishing attacks is of great importance. One popular and widely-deployed solution with browsers is to integrate a blacklist sites into them. However, this solution, which is unable to detect new attacks if the database is out of date, appears to be not effective when there are a lager number of phishing attacks created very day. In this paper, we propose a solution to this problem by applying Genetic Programming to phishing detection problem. We conducted the experiments on a data set including both phishing and legitimate sites collected from the Internet. We compared the performance of Genetic Programming with a number of other machine learning techniques and the results showed that Genetic Programming produced the best solutions to phishing detection problem.

Synthetic Metals, 2010

Natural graphite powder was oxidized by Hummers' method and graphite oxide was prepared . After u... more Natural graphite powder was oxidized by Hummers' method and graphite oxide was prepared . After ultrasonication was expanded, in order to exfoliate single or/and few layered graphene oxide sheets (GO). Although, the quite low solubility of GO, which is a very important factor in organic photovoltaics, blocks the formation of stable suspensions, as well as solutions, for the exploitation of its unique mechanical properties. In this study, we report our recent results on the covalent functionalization of graphene oxide via a chemical and photochemical method; the addition of an aliphatic amine group linked with a small molecule is demonstrated to increase the dispersability of chemically and photochemically functionalized graphene oxide in organic solvents, so that to synthesize new electron acceptors, appropriate for organic photovoltaics, based on heterostructure polymer-graphene composite layers. In particular, the carboxyl groups of GO are activated using thionyl chloride (SOCl 2 ) and finally are coupled with 3,5-dinitrobenzoyl chloride (DNBC) by using 1,4-ethylenediamine as ligament. The above coupling reaction was performed by chemical, as well as by photochemical way, yielded GO-EDNB and LGO-EDNB, respectively. The photochemical method for the simultaneous functionalization of GO was held through pulsed UV laser irradiation of GO in liquid precursor media . Using this technique we have successfully synthesized GO-ethylene dinitrobenzoyl (EDNB) at room temperature in less than 2 hours, compared to 3 days required upon using a conventional chemical route . GO-EDNB and LGO-EDNB derivatives were used as the electron acceptor materials in poly-(3hexylthiophene) (P3HT) bulk heterojunction photovoltaic devices to significantly enhance the performance, yielding a power conversion efficiency improvement of two orders and one order of magnitude compared with the pristine P3HT and the P3HT-GO devices respectively.

Journal of Biotechnology, 2010

Endo ␤-1,4-mannanases (␤-mannanases, EC 3.2.1.78), belonging to CAZy GH5 and GH26 families, catal... more Endo ␤-1,4-mannanases (␤-mannanases, EC 3.2.1.78), belonging to CAZy GH5 and GH26 families, catalyze the hydrolysis of structurally different mannans. In this study, the mannanase encoding gene of Aspergillus aculeatus VN was expressed in Aspergillus niger D15#26 using pAN 52-4 vector, under the control of PgpdA promoter and TtrpC terminator. In order to improve the hydrolytic capacity of this GH5 on lignocellulosic substrate, the family 1 carbohydrate-binding module (CBM1) of Aspergillus niger cellobiohydrolase B was artificially fused at the C-terminal end of this enzyme with a natural linker. Both mannanase and mannanase-CBM genes were successfully expressed in A. niger D15#26, producing proteins with molecular masses of 54 and 79 kDa, respectively. The Michaelis-Menten constants, pH activity profiles and temperature optima of three enzymes (wild-type mannanase, recombinant mannanase and recombinant mannanase-CBM) were similar, but the fused mannanase-CBM enzyme was more thermostable. Cross-comparison of the three enzymes for softwood hydrolysis in association with Trichoderma reesei enzymatic cocktail showed that mannanase-CBM improved the glucose yield compared to wild-type and recombinant mannanases.

Current Microbiology, 2011

Transformation is an indispensable method for the manipulation of Saccharomyces cerevisiae cell. ... more Transformation is an indispensable method for the manipulation of Saccharomyces cerevisiae cell. The spf1 cell, in which the gene encoding an endoplasmic reticulum-located P-type ATPase is deleted, has been known to show the high-transformation phenotype. In this study, fluorescent microscopic observation of transformation process of S. cerevisiae using plasmid DNA labelled with fluorescent DNA probe, YOYO-1, suggested that the spf1 cell absorbed more plasmid DNA on cellular surface than did the wild-type cell and the unwashed cell did more plasmid DNA than the washed cell. The amounts of the absorbed DNA correlated with the transformation efficiency (number of transformants per μg plasmid DNA) and frequency (transformation efficiency per viable cell number). The high-transformation phenotype of spf1 cell and the effect of heat shock, which effectively induces the transformation of intact cell, disappeared upon cell wall digestion. Electron microscopic observation of the transformation process using negatively charged Nanogold as a mimic of plasmid DNA supported the result obtained using YOYO-1 and implied that plasmid DNA enters into cell together with membrane structure. These data strongly suggest that during the transformation of intact cell, plasmid DNA is initially absorbed on the cell wall, passes through the cell wall with the aid of heat shock, reaches to the membrane, and enters into the cell together with the membrane structure and that the capacity of the cell wall to absorb DNA is at least one of the determinants of transformation efficiency and frequency.

Current Genetics, 2011

Transformation is an indispensable method for the genetic manipulation of cells. Saccharomyces ce... more Transformation is an indispensable method for the genetic manipulation of cells. Saccharomyces cerevisiae can be transformed by incubating intact cells and plasmid DNA in the presence of polyethylene glycol alone. Lithium acetate (LiAc) and single-stranded carrier DNA (ssDNA) enhance the transformation efficiency, but the mechanism underlying this enhancement has remained elusive. In this study, we first confirmed that LiAc and ssDNA synergistically improve the transformation efficiency of S. cerevisiae intact cells. We then used transmission electron microscopy to observe the cell walls of yeast incubated with both LiAc and ssDNA in the presence of negatively charged Nanogold (in this context, a mimic of DNA). Under these conditions, the cell walls exhibited protruded, loose, and porous structures. The Nanogold was observed within the cell wall, rather than on the surface. We also made observations using YOYO-1, a fluorescent DNA probe. Based on the transmission electron microscopy and fluorescence data, we speculated that ssDNA covers the whole cell and enters, at least partially, into the cell wall structure, causing the cell wall to become protruded, loose, and porous; meanwhile, LiAc produces effect on the cell wall. Together, the two compounds synergistically enhance the transformation efficiency and frequency.

Journal of computer-aided molecular design, 2008

Empirical scoring functions used in proteinligand docking calculations are typically trained on a... more Empirical scoring functions used in proteinligand docking calculations are typically trained on a dataset of complexes with known affinities with the aim of generalizing across different docking applications. We report a novel method of scoring-function optimization that supports the use of additional information to constrain scoring function parameters, which can be used to focus a scoring function's training towards a particular application, such as screening enrichment. The approach combines multiple instance learning, positive data in the form of ligands of protein binding sites of known and unknown affinity and binding geometry, and negative (decoy) data of ligands thought not to bind particular protein binding sites or known not to bind in particular geometries. Performance of the method for the Surflex-Dock scoring function is shown in cross-validation studies and in eight blind test cases. Tuned functions optimized with a sufficient amount of data exhibited either improved or undiminished screening performance relative to the original function across all eight complexes. Analysis of the changes to the scoring function suggest that modifications can be learned that are related to protein-specific features such as active-site mobility.

Biochemical and Biophysical Research Communications, 2004

Understanding of the molecular system for DNA delivery into eucaryotic cells, a key to human DNA ... more Understanding of the molecular system for DNA delivery into eucaryotic cells, a key to human DNA therapy, remains obscure. To understand this system, we undertook a study using the Saccharomyces cerevisiae model into which DNA delivery is easily assessed through competence (transformability) and for which all nonessential gene mutants (about 5000 strains) are available. We analyzed the competence of each of these mutants and identified three low-competence mutants, i.e., sin3D, she4D, and arc18D, and three high-competence mutants, i.e., pde2D, spf1D, and pmr1D. Through further studies using the six mutants, we concluded that the Arp2/3 activation machinery involving the Myo3/5p, Vrp1p, Las17p, Pan1p, and Arp2/3 complex is crucial to delivery (competence), and that high cAMP enhances competence via protein kinase A installing Tpk3p. We also propose that DNA is taken up via an endocytosis-like event, being at least partially different from well-known endocytosis.

Annals of Emergency Medicine, 2010

The study included prospective, simulated patient scenarios with an eye-tracking device that show... more The study included prospective, simulated patient scenarios with an eye-tracking device that showed where the health care workers looked. Simulations involved nurses administering an intravenous medication, technicians labeling a blood specimen, and clerks applying an identity band. Participants were asked to perform their assigned task on 3 simulated patients, and the third patient had a different date of birth and medical record number than the identity information on the artifact label specific to the health care workers' task. Health care workers were unaware that the focus of the study was patient identity.

Nanotechnology, 2010

A facile approach for the preparation of a novel hybrid material containing graphene and an inorg... more A facile approach for the preparation of a novel hybrid material containing graphene and an inorganic semiconducting material, cadmium sulfide quantum dots (CdS QDs), is demonstrated for the first time. First, amino-functionalized CdS QDs were prepared by modifications of the kinetic trapping method. Then, pristine graphite was oxidized and exfoliated to obtain graphene oxide nanosheets (GONS), which were then acylated with thionyl chloride to introduce acyl chloride groups on their surface. Subsequently, immobilization of the CdS QDs on the GONS surface was achieved through an amidation reaction between the amino groups located on the CdS QDs surface and the acyl chloride groups bound to the GONS surface. Fourier transform infrared spectroscopy (FT-IR), (1)H nuclear magnetic resonance ((1)H-NMR), x-ray diffraction (XRD), x-ray photoelectron spectroscopy (XPS), and energy dispersive x-ray (EDX) spectroscopy were employed to investigate the changes in the surface functionalities, while high resolution transmission electron microscopy (HR-TEM) and field emission scanning electronic microscopy (FE-SEM) were used to study the morphologies and distribution of the CdS QDs on the GONS surface. Thermogravimetric analysis (TGA) was employed to characterize the weight loss of the samples on heating. Photoluminescence (PL) measurements were used to study the optical properties of the prepared CdS QDs and the CdS-graphene hybrid material.

Academic Emergency Medicine, 2008

Introduction: Improving patient identification (ID), by using two identifiers, is a Joint Commiss... more Introduction: Improving patient identification (ID), by using two identifiers, is a Joint Commission safety goal. Appropriate identifiers include name, date of birth (DOB), or medical record number (MRN).

The synthesis of biocompatible magnetic nanoparticles is one of the important topics in nanoscien... more The synthesis of biocompatible magnetic nanoparticles is one of the important topics in nanoscience because such materials have potential biomedical applications. Herein, we report a facile approach for surface functionalization of magnetic nanoparticles (MNPs) with boronic acid and their ...

… Transactions of the …, 1997

A multiwavelength, high bandwidth (1 GHz) frequency-domain photon migration (FDPM) instrument has... more A multiwavelength, high bandwidth (1 GHz) frequency-domain photon migration (FDPM) instrument has been developed for quantitative, non-invasive measurements of tissue optical and physiological properties. The instrument produces 300 kHz to 1 GHz photon density waves (PDWs) in optically turbid media using a network analyser, an avalanche photodiode detector and four amplitude-modulated diode lasers (674 nm, 811 nm, 849 nm, and 956 nm). The frequency of PDW phase and amplitude is measured and compared to analytically derived model functions in order to calculate absorption, mu a, and reduced scattering, mu s, parameters. The wavelength-dependence of absorption is used to determine tissue haemoglobin concentration (total, oxy- and deoxy- forms), oxygen saturation and water concentration. We present preliminary results of non-invasive FDPM measurements obtained from normal and tumour-containing human breast tissue. Our data clearly demonstrate that physiological changes caused by the presence of small (about 1 cm diameter) palpable lesions can be detected using a handheld FDPM probe.

Journal of medicinal chemistry, Jan 5, 2006

Surflex-Dock employs an empirically derived scoring function to rank putative protein-ligand inte... more Surflex-Dock employs an empirically derived scoring function to rank putative protein-ligand interactions by flexible docking of small molecules to proteins of known structure. The scoring function employed by Surflex was developed purely on the basis of positive data, comprising noncovalent protein-ligand complexes with known binding affinities. Consequently, scoring function terms for improper interactions received little weight in parameter estimation, and an ad hoc scheme for avoiding protein-ligand interpenetration was adopted. We present a generalized method for incorporating synthetically generated negative training data, which allows for rigorous estimation of all scoring function parameters. Geometric docking accuracy remained excellent under the new parametrization. In addition, a test of screening utility covering a diverse set of 29 proteins and corresponding ligand sets showed improved performance. Maximal enrichment of true ligands over nonligands exceeded 20-fold in over 80% of cases, with enrichment of greater than 100-fold in over 50% of cases.

Chemical Communications, 2007

A novel negative, inorganic polymer photoresist was demonstrated to be suitable for simple and di... more A novel negative, inorganic polymer photoresist was demonstrated to be suitable for simple and direct fabrication of tribological SiCN-based ceramic microstructures via UV photolithography and subsequent pyrolysis at 800 degrees C.

Superparamagnetic iron oxide nanoparticles (SPIONs) are currently unavailable as MRI contrast age... more Superparamagnetic iron oxide nanoparticles (SPIONs) are currently unavailable as MRI contrast agents for detecting atherosclerosis in the clinical setting because of either low signal enhancement or safety concerns. Therefore, a new generation of SPIONs with increased circulation time, enhanced image contrast, and less cytotoxicity is essential. In this study, monodisperse SPIONs were synthesized and coated with polyethylene glycol (PEG) of varying molecular weights. The resulting PEGylated SPIONs were characterized, and their interactions with vascular smooth muscle cells (VSMCs) were examined. SPIONs were tested at different concentrations (100 and 500 ppm Fe) for stability, T 2 contrast, cytotoxicity, and cellular uptake to determine an optimal formulation for in vivo use. We found that at 100 ppm Fe, the PEG 2K SPIONs showed adequate stability and magnetic contrast, and exhibited the least cytotoxicity and nonspecific cellular uptake. An increase in cell viability was observed when the SPION-treated cells were washed with PBS after 1 h incubation compared to 5 and 24 h incubation without washing. Our investigation provides insight into the potential safe application of SPIONs in the clinic.

Proceedings of 2012 UKACC International Conference on Control, 2012

The emergence of RFID applications has huge influence to become pervasive in modern life. However... more The emergence of RFID applications has huge influence to become pervasive in modern life. However the vulnerability of the transmission through the air and the unique identification number of RFID tag are the drawbacks that impact the popularity of RFID technology. In this paper, a mutual authentication protocol is proposed based on the challengeresponse model. The Advanced Encryption Standard (AES) is used as a cryptographic primitive to secure the data. The experimental works are carried out to validate the protocol in term of security and privacy. The timing analysis is also presented and applied to a case study of conveyor belt system.

Mycobiology, 2011

Spores of Aspergillus sp. SU14 were treated repeatedly and sequentially with Co(60) γ-rays, ultra... more Spores of Aspergillus sp. SU14 were treated repeatedly and sequentially with Co(60) γ-rays, ultraviolet irradiation, and N-methyl-N'-nitro-N-nitrosoguanidine. One selected mutant strain, Aspergillus sp. SU14-M15, produced cellulase in a yield 2.2-fold exceeding that of the wild type. Optimal conditions for the production of cellulase by the mutant fungal strain using solid-state fermentation were examined. The medium consisted of wheat-bran supplemented with 1% (w/w) urea or NH(4)Cl, 1% (w/w) rice starch, 2.5 mM MgCl(2), and 0.05% (v/w) Tween 80. Optimal moisture content and initial pH was 50% (v/w) and 3.5, respectively, and optimal aeration area was 3/100 (inoculated wheat bran/container). The medium was inoculated with 25% 48 hr seeding culture and fermented at 35℃ for 3 days. The resulting cellulase yield was 8.5-fold more than that of the wild type strain grown on the basal wheat bran medium.

Advances in Intelligent Systems and Computing, 2014

Phishing is a real threat on the Internet nowadays. According to a report released by an American... more Phishing is a real threat on the Internet nowadays. According to a report released by an American security firm, RSA, there have been approximately 33,000 phishing attacks globally each month in 2012, leading to a loss of $687 million. Therefore, fighting against phishing attacks is of great importance. One popular and widely-deployed solution with browsers is to integrate a blacklist sites into them. However, this solution, which is unable to detect new attacks if the database is out of date, appears to be not effective when there are a lager number of phishing attacks created very day. In this paper, we propose a solution to this problem by applying Genetic Programming to phishing detection problem. We conducted the experiments on a data set including both phishing and legitimate sites collected from the Internet. We compared the performance of Genetic Programming with a number of other machine learning techniques and the results showed that Genetic Programming produced the best solutions to phishing detection problem.

Synthetic Metals, 2010

Natural graphite powder was oxidized by Hummers' method and graphite oxide was prepared . After u... more Natural graphite powder was oxidized by Hummers' method and graphite oxide was prepared . After ultrasonication was expanded, in order to exfoliate single or/and few layered graphene oxide sheets (GO). Although, the quite low solubility of GO, which is a very important factor in organic photovoltaics, blocks the formation of stable suspensions, as well as solutions, for the exploitation of its unique mechanical properties. In this study, we report our recent results on the covalent functionalization of graphene oxide via a chemical and photochemical method; the addition of an aliphatic amine group linked with a small molecule is demonstrated to increase the dispersability of chemically and photochemically functionalized graphene oxide in organic solvents, so that to synthesize new electron acceptors, appropriate for organic photovoltaics, based on heterostructure polymer-graphene composite layers. In particular, the carboxyl groups of GO are activated using thionyl chloride (SOCl 2 ) and finally are coupled with 3,5-dinitrobenzoyl chloride (DNBC) by using 1,4-ethylenediamine as ligament. The above coupling reaction was performed by chemical, as well as by photochemical way, yielded GO-EDNB and LGO-EDNB, respectively. The photochemical method for the simultaneous functionalization of GO was held through pulsed UV laser irradiation of GO in liquid precursor media . Using this technique we have successfully synthesized GO-ethylene dinitrobenzoyl (EDNB) at room temperature in less than 2 hours, compared to 3 days required upon using a conventional chemical route . GO-EDNB and LGO-EDNB derivatives were used as the electron acceptor materials in poly-(3hexylthiophene) (P3HT) bulk heterojunction photovoltaic devices to significantly enhance the performance, yielding a power conversion efficiency improvement of two orders and one order of magnitude compared with the pristine P3HT and the P3HT-GO devices respectively.

Journal of Biotechnology, 2010

Endo ␤-1,4-mannanases (␤-mannanases, EC 3.2.1.78), belonging to CAZy GH5 and GH26 families, catal... more Endo ␤-1,4-mannanases (␤-mannanases, EC 3.2.1.78), belonging to CAZy GH5 and GH26 families, catalyze the hydrolysis of structurally different mannans. In this study, the mannanase encoding gene of Aspergillus aculeatus VN was expressed in Aspergillus niger D15#26 using pAN 52-4 vector, under the control of PgpdA promoter and TtrpC terminator. In order to improve the hydrolytic capacity of this GH5 on lignocellulosic substrate, the family 1 carbohydrate-binding module (CBM1) of Aspergillus niger cellobiohydrolase B was artificially fused at the C-terminal end of this enzyme with a natural linker. Both mannanase and mannanase-CBM genes were successfully expressed in A. niger D15#26, producing proteins with molecular masses of 54 and 79 kDa, respectively. The Michaelis-Menten constants, pH activity profiles and temperature optima of three enzymes (wild-type mannanase, recombinant mannanase and recombinant mannanase-CBM) were similar, but the fused mannanase-CBM enzyme was more thermostable. Cross-comparison of the three enzymes for softwood hydrolysis in association with Trichoderma reesei enzymatic cocktail showed that mannanase-CBM improved the glucose yield compared to wild-type and recombinant mannanases.

Current Microbiology, 2011

Transformation is an indispensable method for the manipulation of Saccharomyces cerevisiae cell. ... more Transformation is an indispensable method for the manipulation of Saccharomyces cerevisiae cell. The spf1 cell, in which the gene encoding an endoplasmic reticulum-located P-type ATPase is deleted, has been known to show the high-transformation phenotype. In this study, fluorescent microscopic observation of transformation process of S. cerevisiae using plasmid DNA labelled with fluorescent DNA probe, YOYO-1, suggested that the spf1 cell absorbed more plasmid DNA on cellular surface than did the wild-type cell and the unwashed cell did more plasmid DNA than the washed cell. The amounts of the absorbed DNA correlated with the transformation efficiency (number of transformants per μg plasmid DNA) and frequency (transformation efficiency per viable cell number). The high-transformation phenotype of spf1 cell and the effect of heat shock, which effectively induces the transformation of intact cell, disappeared upon cell wall digestion. Electron microscopic observation of the transformation process using negatively charged Nanogold as a mimic of plasmid DNA supported the result obtained using YOYO-1 and implied that plasmid DNA enters into cell together with membrane structure. These data strongly suggest that during the transformation of intact cell, plasmid DNA is initially absorbed on the cell wall, passes through the cell wall with the aid of heat shock, reaches to the membrane, and enters into the cell together with the membrane structure and that the capacity of the cell wall to absorb DNA is at least one of the determinants of transformation efficiency and frequency.

Current Genetics, 2011

Transformation is an indispensable method for the genetic manipulation of cells. Saccharomyces ce... more Transformation is an indispensable method for the genetic manipulation of cells. Saccharomyces cerevisiae can be transformed by incubating intact cells and plasmid DNA in the presence of polyethylene glycol alone. Lithium acetate (LiAc) and single-stranded carrier DNA (ssDNA) enhance the transformation efficiency, but the mechanism underlying this enhancement has remained elusive. In this study, we first confirmed that LiAc and ssDNA synergistically improve the transformation efficiency of S. cerevisiae intact cells. We then used transmission electron microscopy to observe the cell walls of yeast incubated with both LiAc and ssDNA in the presence of negatively charged Nanogold (in this context, a mimic of DNA). Under these conditions, the cell walls exhibited protruded, loose, and porous structures. The Nanogold was observed within the cell wall, rather than on the surface. We also made observations using YOYO-1, a fluorescent DNA probe. Based on the transmission electron microscopy and fluorescence data, we speculated that ssDNA covers the whole cell and enters, at least partially, into the cell wall structure, causing the cell wall to become protruded, loose, and porous; meanwhile, LiAc produces effect on the cell wall. Together, the two compounds synergistically enhance the transformation efficiency and frequency.

Journal of computer-aided molecular design, 2008

Empirical scoring functions used in proteinligand docking calculations are typically trained on a... more Empirical scoring functions used in proteinligand docking calculations are typically trained on a dataset of complexes with known affinities with the aim of generalizing across different docking applications. We report a novel method of scoring-function optimization that supports the use of additional information to constrain scoring function parameters, which can be used to focus a scoring function's training towards a particular application, such as screening enrichment. The approach combines multiple instance learning, positive data in the form of ligands of protein binding sites of known and unknown affinity and binding geometry, and negative (decoy) data of ligands thought not to bind particular protein binding sites or known not to bind in particular geometries. Performance of the method for the Surflex-Dock scoring function is shown in cross-validation studies and in eight blind test cases. Tuned functions optimized with a sufficient amount of data exhibited either improved or undiminished screening performance relative to the original function across all eight complexes. Analysis of the changes to the scoring function suggest that modifications can be learned that are related to protein-specific features such as active-site mobility.

Biochemical and Biophysical Research Communications, 2004

Understanding of the molecular system for DNA delivery into eucaryotic cells, a key to human DNA ... more Understanding of the molecular system for DNA delivery into eucaryotic cells, a key to human DNA therapy, remains obscure. To understand this system, we undertook a study using the Saccharomyces cerevisiae model into which DNA delivery is easily assessed through competence (transformability) and for which all nonessential gene mutants (about 5000 strains) are available. We analyzed the competence of each of these mutants and identified three low-competence mutants, i.e., sin3D, she4D, and arc18D, and three high-competence mutants, i.e., pde2D, spf1D, and pmr1D. Through further studies using the six mutants, we concluded that the Arp2/3 activation machinery involving the Myo3/5p, Vrp1p, Las17p, Pan1p, and Arp2/3 complex is crucial to delivery (competence), and that high cAMP enhances competence via protein kinase A installing Tpk3p. We also propose that DNA is taken up via an endocytosis-like event, being at least partially different from well-known endocytosis.

Annals of Emergency Medicine, 2010

The study included prospective, simulated patient scenarios with an eye-tracking device that show... more The study included prospective, simulated patient scenarios with an eye-tracking device that showed where the health care workers looked. Simulations involved nurses administering an intravenous medication, technicians labeling a blood specimen, and clerks applying an identity band. Participants were asked to perform their assigned task on 3 simulated patients, and the third patient had a different date of birth and medical record number than the identity information on the artifact label specific to the health care workers' task. Health care workers were unaware that the focus of the study was patient identity.

Nanotechnology, 2010

A facile approach for the preparation of a novel hybrid material containing graphene and an inorg... more A facile approach for the preparation of a novel hybrid material containing graphene and an inorganic semiconducting material, cadmium sulfide quantum dots (CdS QDs), is demonstrated for the first time. First, amino-functionalized CdS QDs were prepared by modifications of the kinetic trapping method. Then, pristine graphite was oxidized and exfoliated to obtain graphene oxide nanosheets (GONS), which were then acylated with thionyl chloride to introduce acyl chloride groups on their surface. Subsequently, immobilization of the CdS QDs on the GONS surface was achieved through an amidation reaction between the amino groups located on the CdS QDs surface and the acyl chloride groups bound to the GONS surface. Fourier transform infrared spectroscopy (FT-IR), (1)H nuclear magnetic resonance ((1)H-NMR), x-ray diffraction (XRD), x-ray photoelectron spectroscopy (XPS), and energy dispersive x-ray (EDX) spectroscopy were employed to investigate the changes in the surface functionalities, while high resolution transmission electron microscopy (HR-TEM) and field emission scanning electronic microscopy (FE-SEM) were used to study the morphologies and distribution of the CdS QDs on the GONS surface. Thermogravimetric analysis (TGA) was employed to characterize the weight loss of the samples on heating. Photoluminescence (PL) measurements were used to study the optical properties of the prepared CdS QDs and the CdS-graphene hybrid material.

Academic Emergency Medicine, 2008

Introduction: Improving patient identification (ID), by using two identifiers, is a Joint Commiss... more Introduction: Improving patient identification (ID), by using two identifiers, is a Joint Commission safety goal. Appropriate identifiers include name, date of birth (DOB), or medical record number (MRN).

The synthesis of biocompatible magnetic nanoparticles is one of the important topics in nanoscien... more The synthesis of biocompatible magnetic nanoparticles is one of the important topics in nanoscience because such materials have potential biomedical applications. Herein, we report a facile approach for surface functionalization of magnetic nanoparticles (MNPs) with boronic acid and their ...