Showing papers by "Qingming Luo published in 2006"
TL;DR: It is demonstrated that LSTCA can significantly suppress the influence of the laser speckle from the stationary structure, such as the skull, and thus reveal the blood flow and morphology of blood vessels through the laser Speckle images recorded from the intact rat skull.
Abstract: We discovered that laser speckle temporal contrast analysis (LSTCA) is able to access the two-dimensional (2D) cerebral blood flow velocity and vessel structure through the intact rat skull. It is demonstrated that LSTCA can significantly suppress the influence of the laser speckle from the stationary structure, such as the skull, and thus reveal the blood flow and morphology of blood vessels through the laser speckle images recorded from the intact rat skull.
237 citations
TL;DR: In this paper, the magnetic entropy changes compare favorably with that of Gd and are slightly larger than that of the known crystalline magnetic refrigerant compound Gd5Si2Ge1.9Fe0.1.
Abstract: Magnetocaloric effect and refrigerant capacity of Gd-based Gd53Al24Co20Zr3 and Gd33Er22Al25Co20 bulk metallic glasses are investigated. It is found that the magnetic entropy changes compare favorably with that of Gd and are slightly larger than that of the known crystalline magnetic refrigerant compound Gd5Si2Ge1.9Fe0.1. Their good refrigerant efficiency combining with high electrical resistivity, high thermal stability, outstanding mechanical properties, tunable nature, and sufficiently soft magnetic property make them an attractive candidate for magnetic refrigerants in the temperature range of 10–100K.
191 citations
TL;DR: In this paper, the photoluminescence of water-soluble CdSe/ZnS core/shell quantum dots is found to be temperature-dependent: as temperature arising from 280-K to 351-K, the emission peak shifts towards the red at a rate of ∼ 0.11-nm−K −1.
94 citations
TL;DR: Two-photon fluorescence microscopy used the compensated 2D AOD scanner to image a fluorescent microsphere, which improves signal intensity -15-fold compared with the uncompensated scanner.
Abstract: The dispersive nature of the acousto-optical deflector (AOD) presents a challenge to applications of two sequential orthogonal AODs (a two-dimensional AOD) as XY scanners in multiphoton microscopy. Introducing a prism before the two-dimensional (2D) AOD allows both temporal and spatial dispersion to be compensated for simultaneously. A 90fs laser pulse was broadened to 572fs without compensation, and 143fs with compensation. The ratio of long axis to short axis of the exiting laser beam spot was 3.50 without compensation and 1.14 with compensation. The insertion loss was 37%. Two-photon fluorescence microscopy used the compensated 2D AOD scanner to image a fluorescent microsphere, which improves signal intensity ~15-fold compared with the uncompensated scanner.
91 citations
TL;DR: Recent advances in OMI are reviewed extensively, such as the development of molecular probes that make imaging brighter, more stable and more informative, and applications for measuring biological events from molecule to organism level, including gene expression, protein and subcellular compartment localization, protein activation and interaction, and low-mass molecule dynamics.
Abstract: The development of highly efficient analytical methods capable of probing biological systems at system level is an important task that is required in order to meet the requirements of the emerging field of systems biology. Optical molecular imaging (OMI) is a very powerful tool for studying the temporal and spatial dynamics of specific biomolecules and their interactions in real time in vivo. In this article, recent advances in OMI are reviewed extensively, such as the development of molecular probes that make imaging brighter, more stable and more informative (e.g., FPs and semiconductor nanocrystals, also referred to as quantum dots), the development of imaging approaches that provide higher resolution and greater tissue penetration, and applications for measuring biological events from molecule to organism level, including gene expression, protein and subcellular compartment localization, protein activation and interaction, and low-mass molecule dynamics. These advances are of great significance in the field of biological science and could also be applied to disease diagnosis and pharmaceutical screening. Further developments in OMI for systems biology are also proposed.
67 citations
TL;DR: The results suggest that the systemic states of metabolic networks do not always remain optimal, but may become suboptimal when a transient perturbation occurs, which supports the relevance of the hypothesis of original minimization of metabolic adjustment.
Abstract: To better understand the dynamic regulation of optimality in metabolic networks under perturbed conditions, we reconstruct the energetic-metabolic network in mammalian myocardia using dynamic flux balance analysis (DFBA). Additionally, we modified the optimal objective from the maximization of ATP production to the minimal fluctuation of the profile of metabolite concentration under ischemic conditions, extending the hypothesis of original minimization of metabolic adjustment to create a composite modeling approach called M-DFBA. The simulation results are more consistent with experimental data than are those of the DFBA model, particularly the retentive predominant contribution of fatty acid to oxidative ATP synthesis, the exact mechanism of which has not been elucidated and seems to be unpredictable by the DFBA model. These results suggest that the systemic states of metabolic networks do not always remain optimal, but may become suboptimal when a transient perturbation occurs. This finding supports the relevance of our hypothesis and could contribute to the further exploration of the underlying mechanism of dynamic regulation in metabolic networks.
62 citations
TL;DR: A new algorithm capturing both expression pattern similarities and biological function similarities is developed, and it is shown that this method has advantages in both the quality of clusters and the precision of biological annotations.
60 citations
TL;DR: DNA probe hybridization experiments indicated that the coding signal and target signal can be detected simultaneously and that the assays based on these probe-conjugated silica/QD/polystyrene beads have good specificity and sensitivity that can detect a concentration as low as 0.01 microg/ml target DNA in denatured calf thymus DNA solution, indicating that it is feasible to use this kind of bead for multiplex analysis.
56 citations
TL;DR: In this review, systems biology-oriented micro-separation technologies are introduced for comprehensive profiling of genome, proteome and metabolome, characterization of biomolecules interaction and single cell analysis, and their multidimensional combinations, parallel integrations, microfabricated formats, and nano technology involvement.
41 citations
TL;DR: The results suggest that the propagation patterns of a series of SD waves are time-varying in different regions of rat cortex, and the variation is related to the interval between SD waves.
40 citations
TL;DR: The prediction results show that the SVM can detect operon genes in target genomes efficiently and offers a satisfactory balance between sensitivity and specificity.
TL;DR: In this article, a boron-doped polycrystalline diamond thick film was prepared by a hot filament chemical vapor deposition (HFCVD) method and the morphology and structure of the diamond were evaluated by scanning electron microscopy (SEM), X-ray diffraction (XRD) and micro-Raman spectroscopy.
TL;DR: In this paper, a multiphoton laser scanning microscope based on a dual-axis acousto-optic deflector (AOD) is described, which has a high random addressing and data-acquisition rate of 10μspixel.
Abstract: The construction of a multiphoton laser scanning microscope based on a dual-axis acousto-optic deflector (AOD) is described. Without mechanical inertia and physical movement of the scanner, this system has a high random-addressing and data-acquisition rate of 10μspixel. By proper compensation of the dispersion of the AODs, the spatial resolution of the system is 0.5μm for lateral direction and 1.5μm for axial direction. Fluorescence images are acquired to demonstrate these imaging performances.
TL;DR: A fluorescence resonance energy transfer probe was developed to image the activation of caspase-3 and the related apoptotic pathway in TRAIL-treated cells in real time, which suggests that rest apoptosis is preceded by casp enzyme-3-independent pathways, as CE has the ability to quantitatively detect caspasesase-dependent apoptosis.
TL;DR: A family of holmium-based bulk metallic glasses (BMGs) with high glass-forming ability is obtained in this paper, where Ho-based BMGs exhibit much larger elastic moduli and high thermal stability in contrast to other known rare-earth (RE)-based BMGs.
Abstract: A family of holmium-based bulk metallic glasses (BMGs) with high glass-forming ability is obtained. The Ho-based BMGs exhibit much larger elastic moduli and high thermal stability in contrast to other known rare-earth (RE)-based BMGs. In particular, the BMGs show a large value of fragility. It is expected that the hard RE-based glasses with high glass-forming ability and fragile behaviors make them the appropriate candidate for glass transition study.
TL;DR: Optical reflectance imaging at 550 +/- 10-nm wavelength using a charge-coupled device (CCD) camera, called optical intrinsic signal imaging (OISI) in the neuroscience community, provides high resolution imaging of SD waves based on changes in blood perfusion.
Abstract: Spreading depression SD waves occur in focal cerebral ischemia of the brain. Optical reflectance imaging at 550±10-nm wavelength using a charge-coupled device CCD camera, called op- tical intrinsic signal imaging OISI in the neuroscience community, provides high resolution imaging of SD waves based on changes in blood perfusion. We present optical images of SD waves in normal rat brain induced by a pinprick, and the spontaneous SD waves that fol- low middle cerebral artery occlusion MCAO. The images of change in reflectance are calculated as A=IIo/Io, where I is pixel intensity as some timepoint and Io is the initial intensity just prior to an SD wave. Difference images B=IiIi1/Io, where Ii is the image at time i and Ii1 is the previous image at time i1 a 6.4-s inter- val, significantly sharpen the boundaries between leading and trailing edges of the SD wave. Maximum rate-of-change images C=maxB display the maximum pixel value of B within the duration of a single SD wave, and provide an image that visualizes the entire penumbra. The penumbra appear bright due to a rapid drop in perfusion, while the normal brain and infarct area appear dark. © 2006 Society of Photo-
TL;DR: It is found that during cisplatin-induced apoptosis, caspase-2 activation occurred more slowly than did activation of casp enzyme-3 and was initiated much earlier than that of cospase-3.
Abstract: Caspase-2 is important for the mitochondrial apoptotic pathway, however, the mechanism by which caspase-2 executes apoptosis remains obscure. We carry out the first measurements of the dynamics of caspase-2 activation in a single living cell by a FRET (fluorescence resonance energy transfer) probe. Two FRET probes are constructed that each encoded a CRS (caspase-2 or caspase-3 recognition site) fused with a cyan fluorescent protein (CFP) and a red fluorescent protein (DsRed) (CFP-CRS-DsRed). Using these probes, we found that during cisplatin-induced apoptosis, caspase-2 activation occurred more slowly than did activation of caspase-3; additionally, caspase-2 activation was initiated much earlier than that of caspase-3.
TL;DR: KDE Bioscience is a java-based software platform that collects a variety of bioinformatics tools and provides a workflow mechanism to integrate them and makes an ideal integrated informatics environment for future bioinformics or systems biology research.
TL;DR: Multi-electrode arrays (MEA) are used to record the spontaneous electrophysiological activities of cultured rat hippocampal neuronal network for a long time and a transition from single spike to burst is observed in several networks.
Abstract: Many neural networks in mammalian central nervous system (CNS) fire single spike and complex spike burst. In fact, the conditions for triggering burst are not well understood. In the paper multi-electrode arrays (MEA) are used to record the spontaneous electrophysiological activities of cultured rat hippocampal neuronal network for a long time. After about 3 weeks culture, a transition from single spike to burst is observed in several networks. All of these spikes fire quickly before burst begins. The firing rate during the burst is lower than that just before the burst, but differences of inter-spike intervals (ISIs) between two firing patterns are not clear. Moreover, the electrical activities on neighboring electrodes show strong synchrony during the burst activities. In a word, the generation of the burst requires that network should have a sufficient level of excitation as well as a balance of synaptic inhibition.
TL;DR: Investigations on CW-MPE fluorescence detection with diode laser for capillary zone electrophoresis and micellar electrokinetic chromatography separations of fluorescein isothiocyanate labeled amino acids indicated good prospect of this detection approach in various micro or nano-column liquid phase separation technologies.
TL;DR: The availability of a high‐resolution atlas of the adult rat is reported, constructed using serial cryosection‐milling techniques and segmented, labelled and reconstructed into three‐dimensional (3D) computerized models.
Abstract: This paper reports the availability of a high-resolution atlas of the adult rat. The atlas is composed of 9475 cryosectional images captured in 4600 × 2580 × 24-bit TIFF format, constructed using serial cryosection-milling techniques. Cryosection images were segmented, labelled and reconstructed into three-dimensional (3D) computerized models. These images, 3D models, technical details, relevant software and further information are available at our website, http://vchibp.vicp.net/vch/mice/.
TL;DR: In this article, the aging behavior and the stability of a Ce68Al10Cu20Fe2 bulk metallic glass (BMG) with low glass transition temperature Tg have been investigated upon isothermal annealing near Tg.
Abstract: The aging behavior and the stability of a Ce68Al10Cu20Fe2 bulk metallic glass (BMG) with low glass transition temperature Tg have been investigated upon isothermal annealing near Tg. The annealing time-dependent acoustic velocities, density, elastic constants, and thermodynamic parameters are determined to monitor the structural and properties changes upon aging, and the structural relaxation progress is monitored by the change of enthalpy recovery after annealing. It is found that BMG with Tg near room temperature has high thermal and property stabilities. Stable BMG provides an ideal system to investigate relaxation and supercooled liquid state in alloys.
TL;DR: In this article, a two-photon spectrofluoroelectrochemical system has been established for the first time through combining twophoton-excited fluorescence and electrochemical methods.
TL;DR: A novel multiplex analysis technology based on quantum dot (QD) optical encoded beads was studied and shows that the QDs and target signals can be obviously identified from a single-bead-level spectrum.
Abstract: A novel multiplex analysis technology based on quantum dot (QD) optical encoded beads was studied. Carboxyl functionalized polystyrene beads, about 100 µm in size, were precisely encoded by the various ratios of two types of QDs whose emission wavelengths are 576 and 628 nm, respectively. Then the different encoded beads were covalently immobilized with different probes in the existing of sulfo-NHS and 1-[3-(Dimethylamino) propyl]-3-ethylcarbodiimide methiodide, and the probe density could reach to 3.1 mmol/g. These probe-linked encoded beads were used to detect the target DNA sequences in complex DNA solution by hybridization. Hybridization was visualized using fluorescein isothiocynate–labeled DNA sequences. The results show that the QDs and target signals can be obviously identified from a single-bead-level spectrum. This technology can detect DNA targets effectively with a detection limit of 0.2 µg/mL in complex solution.
TL;DR: In this paper, the conical diamond tip arrays are formed on a freestanding diamond film via focused ion beam (FIB) milling technology and hot-filament chemical vapor deposition (CVD) method.
TL;DR: The origin site of CSD was easily determined using OISI with the benefit of high resolution in rats under alpha-chloralose/urethane anesthesia and the migration of the origin sites implied a growth of the infarcted area.
TL;DR: Capillary electrophoresis (CE) was demonstrated as a novel means to monitor the activation of proteinase during cell apoptosis by engineering a unique fluorescent probe that fused a specific amino acid sequence DEVD with two fluorescent proteins enhanced cyan fluorescent protein and red fluorescent protein.
TL;DR: An in silico platform for metabolic modeling and analyses based on stoichiometry has been developed as a publicly available tool for systems biology research and has been applied to rebuild a metabolic network in mammalian mitochondria, producing meaningful results.
Abstract: Stoichiometry-based analyses of metabolic networks have aroused significant interest of systems biology researchers in recent years. It is necessary to develop a more convenient modeling platform on which users can reconstruct their network models using completely graphical operations, and explore them with powerful analyzing modules to get a better understanding of the properties of metabolic systems. Herein, an in silico platform, FluxExplorer, for metabolic modeling and analyses based on stoichiometry has been developed as a publicly available tool for systems biology research. This platform integrates various analytic approaches, including flux balance analysis, minimization of metabolic adjustment, extreme pathways analysis, shadow prices analysis, and singular value decomposition, providing a thorough characterization of the metabolic system. Using a graphic modeling process, metabolic networks can be reconstructed and modified intuitively and conveniently. The inconsistencies of a model with respect to the FBA principles can be proved automatically. In addition, this platform supports systems biology markup language (SBML). FluxExplorer has been applied to rebuild a metabolic network in mammalian mitochondria, producing meaningful results. Generally, it is a powerful and very convenient tool for metabolic network modeling and analysis.
TL;DR: In this mini-review, the concept of single cell proteomics (SCP) is clarified and recent advancement on strategy and methodology of SCP is reviewed, with emphasis on micro-separation technique improvement such as ultra-thin layer gel electrophoresis, multidimensional micro liquid chromatography and capillary electrophoreis, and microfluidic chip.
Abstract: At present, proteomics that promises deep understanding of genomic functions is developing rapidly. Proteomics at single cell level represents new challenges that greatly call for technique innovation in current analytical chemistry. In this mini-review, the concept of single cell proteomics (SCP) is clarified. Recent advancement on strategy and methodology of SCP is reviewed, with emphasis on micro-separation technique improvement such as ultra-thin layer gel electrophoresis, multidimensional micro liquid chromatography and capillary electrophoresis, and microfluidic chip as well. Future development on SCP is also suggested.
TL;DR: This work compared the result clusters of two clustering algorithms based on graph structure constituted by biological knowledge in terms of the homogeneity of clusters and coherence of annotation and matching ratio and showed that the clusters of knowledge-guided analysis seem much more applicable than GO-Cluster in a larger dataset.
Abstract: Although many numerical clustering algorithms have been applied to gene expression data analysis, the essential step is still biological interpretation by manual inspection. The correlation between genetic co-regulation and affiliation to a common biological process is what biologists expect. Here, we introduce some clustering algorithms that are based on graph structure constituted by biological knowledge. After applying a widely used dataset, we compared the result clusters of two of these algorithms in terms of the homogeneity of clusters and coherence of annotation and matching ratio. The results show that the clusters of knowledge-guided analysis are the kernel parts of the clusters of Gene Ontology (GO)-Cluster software, which contains the genes that are most expression correlative and most consistent with biological functions. Moreover, knowledge-guided analysis seems much more applicable than GO-Cluster in a larger dataset.