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

Papers by Bao Nguyen

Chemical purifications are critical processes across many industries, requiring 10 - 15% of human... more Chemical purifications are critical processes across many industries, requiring 10 - 15% of humanity’s global energy budget1,2. Coordination cages are able to catch and release guest molecules based upon their size and shape3,4, providing a new technological basis for achieving chemical separation. Here we show that aqueous solutions of FeII4L6 and CoII4L4 cages can be used as liquid membranes. Selective transport of complex hydrocarbons across these membranes enabled the separation of target compounds from mixtures under ambient conditions. The kinetics of cage-mediated cargo transport are governed by guest binding affinity. Using sequential transport across two consecutive membranes, target compounds were isolated from a mixture in a size-selective fashion. The selectivities of both cages thus enabled a two-stage separation process to isolate a single compound from a mixture of physicochemically similar molecules.

Antioxidants, 2021

Oxidized low-density lipoproteins play an important role in tissue pathology. In this study, we r... more Oxidized low-density lipoproteins play an important role in tissue pathology. In this study, we report a sensitive novel enzyme-linked immunosorbent assay for the detection of malondialdehyde-modified low-density lipoprotein (MDA-LDL), a key component of oxidized LDL. The assay is capable of measuring a variable presence of MDA-LDL within human plasma and serum. We demonstrate the robust nature of the assay on samples stored for over 20 months, as well as high inter-operator reproducibility (r = 0.74, p < 0.0001). The assay was capable of detecting dynamic changes in patient blood samples after coronary artery bypass graft surgery, indicating synthesis or release of MDA-LDL with the oxidative stress of surgery, followed by homeostatic clearance. This robust, sensitive and specific assay for circulating MDA-LDL will serve as a valuable translational tool for the improved detection of oxidative forms of LDL in response to a range of physiological or pathological stimuli, with poten...

Nano Letters, 2021

The toehold-mediated strand displacement reaction (SDR) is a powerful enzyme-free tool for molecu... more The toehold-mediated strand displacement reaction (SDR) is a powerful enzyme-free tool for molecular manipulation, DNA computing, signal amplification, etc. However, precise modulation of SDR kinetics without changing the original design remains a significant challenge. We introduce a new means of modulating SDR kinetics using an external stimulus: a water-soluble Fe II 4 L 4 tetrahedral cage. Our results show that the presence of a flexible phosphate group and a minimum toehold segment length are essential for Fe II 4 L 4 binding to DNA. SDRs mediated by toehold ends in different lengths (3−5) were investigated as a function of cage concentration. Their reaction rates all first increased and then decreased as cage concentration increased. We infer that cage binding on the toehold end slows SDR, whereas the stabilization of intermediates that contain two overhangs accelerates SDR. The tetrahedral cage thus serves as a versatile tool for modulation of SDR kinetics.

Genomics, Proteomics & Bioinformatics, 2005

Classical sorting by reversals uses the unit-cost model, that is, each reversal consumes an equal... more Classical sorting by reversals uses the unit-cost model, that is, each reversal consumes an equal cost. This model limits the biological meaning of sorting by reversal. Bender and his colleagues extended it by assigning a cost function f (l) = l α for all α ≥ 0, where l is the length of the reversed subsequence. In this paper, we extend their results by considering a model in which long reversals are prohibited. Using the same cost function above for permitted reversals, we present tight or nearly tight bounds for the worst-case cost of sorting by reversals. Then we develop algorithms to approximate the optimal cost to sort a given 0/1 sequence as well as a given permutation. Our proposed problems are more biologically meaningful and more algorithmically general and challenging than the problem considered by Bender et al. Furthermore, our bounds are tight and nearly tight, whereas our algorithms provide good approximation ratios compared to the optimal cost to sort 0/1 sequences or permutations by reversals.

The Annals of thoracic surgery, Jan 18, 2015

Coronary artery bypass grafting (CABG) with conventional cardiopulmonary bypass (CPB) induces sys... more Coronary artery bypass grafting (CABG) with conventional cardiopulmonary bypass (CPB) induces systemic inflammation. Miniaturized CPB may attenuate systemic inflammatory activation. The intracellular signaling pathways promoting inflammation in cardiac operations and the relative effects of CPB on these processes are uncertain. In this study, induction of reactive oxygen species (ROS) and activation of nuclear factor (NF)-κB, p38 mitogen-activated protein kinase (MAPK) within leukocytes, and leukocyte accumulation in cantharidin-induced blisters was compared in patients exposed to miniaturized CPB (mCPB) and those who underwent conventional CPB (cCPB). Patients undergoing CABG were randomized to receive either cCPB (n = 13) or mCPB (n = 13). Blood samples were collected preoperatively and 5 times after initiating CPB (up to 5 hours) and analyzed by flow cytometry for intracellular markers of activation (ROS, p38-MAPK, and NF-κB phosphorylation). ROS in lymphocytes were elevated in c...

Lecture Notes in Computer Science

ABSTRACT Nowadays Smart Home seems to be getting popular. An essential element of Smart Home is i... more ABSTRACT Nowadays Smart Home seems to be getting popular. An essential element of Smart Home is its sensor network to convey environment information to the control station. There have been many communication protocols for this sensor network. A problem from previous protocols is unbalanced energy consumption among sensor nodes. Even though they tried to overcome unbalanced energy consumption, they could not solve this problem completely yet. In this paper, we found that the basic reason for this unbalanced energy consumption is that there is normally one base node. Because of this architectural problem, the nodes around this sink node lose their energy more easily in relevance to other nodes. So, we propose the sensor network model with 2 and only 2 base stations with simulations, and its corresponding communication protocol.

2007 IFIP International Conference on Network and Parallel Computing Workshops (NPC 2007), 2007

Abstract Smart home is getting popular. An essential element of smart home is sensor network to c... more Abstract Smart home is getting popular. An essential element of smart home is sensor network to convey environment information to the control station. There have been many communication protocols for this sensor network. One problem of previous protocols is ...

7th IEEE International Conference on Computer and Information Technology (CIT 2007), 2007

Abstract Nowadays Smart Home seems to be getting popular. An essential element of Smart Home is i... more Abstract Nowadays Smart Home seems to be getting popular. An essential element of Smart Home is its sensor network to convey environment information to the control station. There have been many communication protocols for this sensor network. A problem from ...

Molecular and cellular biochemistry, 2014

Myocardial ischemic stress and early reperfusion injury in patients undergoing coronary artery by... more Myocardial ischemic stress and early reperfusion injury in patients undergoing coronary artery bypass grafting (CABG) operated on using intermittent cross-clamp fibrillation (ICCF) are not presently known. The role of mini-cardiopulmonary bypass (mCPB) versus conventional CPB (cCPB) during ICCF has not been investigated. These issues have been addressed as secondary objective of randomised controlled trial (ISRCTN30610605) comparing cCPB and mCPB. Twenty-six patients undergoing primary elective CABG using ICCF were randomised to either cCPB or mCPB. Paired left ventricular biopsies collected from 21 patients at the beginning and at the end of CPB were used to measure intracellular substrates (ATP and related compounds). Cardiac troponin T (cTnT) and CK-MB levels were measured in plasma collected from all patients preoperatively and after 1, 30, 60, 120, and 300 min after institution of CPB. ICCF was associated with significant ischemic stress as seen by fall in energy-rich phosphate...

2012 38th Annual Northeast Bioengineering Conference (NEBEC), 2012

ABSTRACT Bone marrow biopsy is a commonly practiced procedure in hospitals used for a number of p... more ABSTRACT Bone marrow biopsy is a commonly practiced procedure in hospitals used for a number of purposes, such as diagnosing blood diseases and gauging a patient's response to chemotherapy, etc. The procedure is relatively simple, but crude. The physician uses a specially designed needle to penetrate the tissue and the bone. Currently, the method by which a physician determines whether or not the needle is in the marrow is by his or her judgment/feeling from a slight reduction in pressure while the needle advances from bone to the bone marrow region. We present a re-design of a bone marrow biopsy needle that will increase the efficiency and success rate of the procedure. The design incorporates a dual-fiber optic cable system into a needle in order to achieve the purpose. Low power laser light (5 mW) is transmitted down one fiber optic cable through the needle and the reflected light is caught by the second fiber optic cable and is analyzed as the needle tip moves through the tissue. A distinct difference in reflectivity exists between the bone and marrow that can be detected and used to send a signal alerting the user of the exact needle tip location. This in turn will increase the probability of obtaining an adequate marrow sample, as well as simplifying the procedure, reducing patient discomfort, and preventing the need to use more than one needle biopsy due to procedural errors.

Lecture Notes in Computer Science, 2005

Reticulation events occur frequently in many types of species. Therefore, to develop accurate met... more Reticulation events occur frequently in many types of species. Therefore, to develop accurate methods for reconstructing phylogenetic networks in order to describe evolutionary history in the presence of reticulation events is important. Previous work has suggested that constructing phylogenetic networks by merging gene trees is a biologically meaningful approach. This paper presents two new efficient algorithms for inferring a phylogenetic network from a set T of gene trees of arbitrary degrees. The first algorithm solves the open problem of constructing a refining galled network for T (if one exists) with no restriction on the number of hybrid nodes; in fact, it outputs the smallest possible solution. In comparison, the previously best method (SpNet) can only construct networks having a single hybrid node. For cases where there exists no refining galled network for T , our second algorithm identifies a minimum subset of the species set to be removed so that the resulting trees can be combined into a galled network. Based on our two algorithms, we propose two general methods named RGNet and RGNet+. Through simulations, we show that our methods outperform the other existing methods neighbor-joining, NeighborNet, and SpNet.

SIAM Journal on Computing, 2006

This paper considers the problem of determining whether a given set T of rooted triplets can be m... more This paper considers the problem of determining whether a given set T of rooted triplets can be merged without conflicts into a galled phylogenetic network and, if so, constructing such a network. When the input T is dense, we solve the problem in O(|T |) time, which is optimal since the size of the input is Θ(|T |). In comparison, the previously fastest algorithm for this problem runs in O(|T | 2) time. We also develop an optimal O(|T |)-time algorithm for enumerating all simple phylogenetic networks leaf-labeled by L that are consistent with T , where L is the set of leaf labels in T , which is used by our main algorithm. Next, we prove that the problem becomes NP-hard if extended to nondense inputs, even for the special case of simple phylogenetic networks. We also show that for every positive integer n, there exists some set T of rooted triplets on n leaves such that any galled network can be consistent with at most 0.4883 • |T | of the rooted triplets in T. On the other hand, we provide a polynomial-time approximation algorithm that always outputs a galled network consistent with at least a factor of 5 12 (> 0.4166) of the rooted triplets in T .

Proceedings of the National Academy of Sciences, 2003

FCP1 [transcription factor II F (TFIIF)-associated c arboxyl-terminal domain (CTD) p hosphatase] ... more FCP1 [transcription factor II F (TFIIF)-associated c arboxyl-terminal domain (CTD) p hosphatase] is the only identified phosphatase specific for the phosphorylated CTD of RNA polymerase II (RNAP II). The phosphatase activity of FCP1 is enhanced in the presence of the large subunit of TFIIF (RAP74 in humans). It has been demonstrated that the CTD of RAP74 (cterRAP74; residues 436–517) directly interacts with the highly acidic CTD of FCP1 (cterFCP; residues 879–961 in human). In this manuscript, we have determined a high-resolution solution structure of a cterRAP74/cterFCP complex by NMR spectroscopy. Interestingly, the cterFCP protein is completely disordered in the unbound state, but forms an α-helix (H1′; E945–M961) in the complex. The cterRAP74/cterFCP binding interface relies extensively on van der Waals contacts between hydrophobic residues from the H2 and H3 helices of cterRAP74 and hydrophobic residues from the H1′ helix of cterFCP. The binding interface also contains two crit...

Journal of the American Chemical Society, 2006

This supporting information includes (1) the full author list for reference 13; (2) the C source ... more This supporting information includes (1) the full author list for reference 13; (2) the C source code for the HSQC pulse sequence employed; (3) the shape files for the broadband inversion pulses used in the pulse sequence; (4) details of the biochemistry for expressing, purifying, and concentrating SUMO-1 for NMR; (5) values for delays, gradient strengths and other pulse sequence parameters for the pulse sequence in Figure 1; and (6) 15 N-1 H 2D spectra with more increments, to compare with the FDM and lowresolution FT data shown in the Communication.

Journal of Magnetic Resonance, 2007

Excitation sculpting, a general method to suppress unwanted magnetization while controlling the p... more Excitation sculpting, a general method to suppress unwanted magnetization while controlling the phase of the retained signal [T.L. Hwang, A.J. Shaka, Water suppression that works. Excitation sculpting using arbitrary waveforms and pulsed field gradients, J. Magn. Reson. Ser. A 112 (1995) 275-279] is a highly effective method of water suppression for both biological and small molecule NMR spectroscopy. In excitation sculpting, a double pulsed field gradient spin echo forms the core of the sequence and pairing a low-power soft 180°(Àx) pulse with a high-power 180°(x) all resonances except the water are flipped and retained, while the water peak is attenuated. By replacing the hard 180°pulse in the double echo with a new phase-alternating composite pulse, broadband and adjustable excitation of large bandwidths with simultaneous high water suppression is obtained. This ''Solvent-Optimized Gradient-Gradient Spectroscopy'' (SOGGY) sequence is a reliable workhorse method for a wide range of practical situations in NMR spectroscopy, optimizing both solute sensitivity and water suppression.

Journal of Biomolecular NMR, 2005

WSEAS Transactions on …, 2006

Abstract:—Smart Home is getting popular. An essential element of smart home is sensor network to ... more Abstract:—Smart Home is getting popular. An essential element of smart home is sensor network to convey environment information to the control station. There have been many communication protocols for this sensor network. One problem of previous protocols is ...

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2007

The small parsimony problem is studied for reconstructing recombination networks from sequence da... more The small parsimony problem is studied for reconstructing recombination networks from sequence data. The small parsimony problem is polynomial-time solvable for phylogenetic trees. However, the problem is proven NP-hard even for galled recombination networks. A dynamic programming algorithm is also developed to solve the small parsimony problem. It takes Oðdn2 3h Þ time on an input recombination network over length-d sequences in which there are h recombination and n À h tree nodes.

Discrete Optimization, 2006

We study the problem of finding a length-constrained maximum-density path in a tree with weight a... more We study the problem of finding a length-constrained maximum-density path in a tree with weight and length on each edge. This problem was proposed in [R.R. Lin, W.H. Kuo, K.M. Chao, Finding a length-constrained maximum-density path in a tree, Journal of Combinatorial Optimization 9 (2005) 147-156] and solved in O(nU) time when the edge lengths are positive integers, where n is the number of nodes in the tree and U is the length upper bound of the path. We present an algorithm that runs in O(n log 2 n) time for the generalized case when the edge lengths are positive real numbers, which indicates an improvement when U = Ω (log 2 n). The complexity is reduced to O(n log n) when edge lengths are uniform. In addition, we study the generalized problems of finding a length-constrained maximum-sum or maximum-density subtree in a given tree or graph, providing algorithmic and complexity results.