Biomedical subjects

Xiaoming Xu

Publications and source records attributed to Xiaoming Xu.

16 recordsLinked to original sources

PubMed2025

RabbitSketch: a high-performance sketching library for genome analysis.

SUMMARY: We present RabbitSketch, a highly optimized library of sketching algorithms such as MinHash, OrderMinHash, and HyperLogLog that can exploit the power of modern multi-core CPUs. It provides significant speedups compared to existing implementations, ranging from 2.30× to 49.55×, as well as flexible and easy-to-use interfaces for both Python and C++. As a result, the similarity analysis of 455GB genomic data can be completed in only 5 minutes using RabbitSketch with merely 20 lines of Python code. As a case study, we enhanced RabbitTClust by integrating RabbitSketch's Kssd algorithm, resulting in a 1.54× speedup with no loss in accuracy. AVAILABILITY AND IMPLEMENTATION: RabbitSketch is available at https://github.com/RabbitBio/RabbitSketch with an archived version at Zenodo: https://doi.org/10.5281/zenodo.14903962. Detailed API documentation is available at https://rabbitsketch.readthedocs.io/en/latest.

Software↗

PubMed2006

Shear bond strength with increasing light-guide distance from dentin.

BACKGROUND: In Class II composite restorations, the adhesive covering the gingival floor of the deep cavity preparation is 2 to 8 mm from the light guide and may not be adequately cured with a typical 10-second curing time. PURPOSE: The purpose of this study was to evaluate the dentin bond strengths of resin composite when the curing light guide (quartz-tungsten-halogen light) was placed at various distances and to investigate the relationships between radiant exposure, degree of conversion, and shear bond strength. MATERIALS AND METHODS: Single Bond (3M ESPE, St. Paul, MN, USA) was placed onto the dentin following the manufacturer's directions. Four groups of 10 teeth were cured for 20 seconds through a 0, 2.3, 4.6, or 6.9 mm spacer. Two other groups of 10 teeth were cured through a 4.6 mm spacer for 40 seconds and 60 seconds, respectively. Z100 resin composite (3M ESPE) was placed over the cured adhesive and polymerized at the same distance as the adhesive. After 24 hours of storage in water, the shear bond strengths were tested. The irradiance through each spacer was measured using a digital radiometer. The degree of conversion of the adhesive was determined by near infrared spectroscopy. The data were analyzed using analysis of variance and Tukey-B post hoc tests. RESULTS: Dentin shear bond strengths decreased significantly with increasing distance, but they increased significantly when the curing time increased from 20 to 40 or 60 seconds. There is a linear correlation between shear bond strength, degree of conversion, and logarithm (radiant exposure). CONCLUSION: Increasing curing time can compensate for the decreased bond strength owing to a decreased irradiance associated with increased curing distance. CLINICAL SIGNIFICANCE: Under the conditions of this study, when curing the adhesives in deep proximal boxes with a quartz-tungsten-halogen light, the curing time should be increased to 40 to 60 seconds to ensure optimal polymerization.

Analysis of Variance↗

PubMed2006

[Initial detection and analysis of neuro-information from amputee].

By detection and analysis of neuro-information from amputee in experiments, a research on the correlations of three main nerves (median nerve, radial nerve and ulnar nerve), on the patterns for discharging information, and on the mechanics about how neuro-information dominates movements was performed. These researches would contribute to the development of neuroprosthesis.

Adult↗

PubMed2006

[Rhythmic beating cardiomyocytes derived from human embryonic germ (EG) cells in vitro].

UNLABELLED: Embryonic germ (EG) cells are pluripotent cells derived from primordial germ cells (PGCs) of gonads, gonadal ridges and mesenteries, analogies of fetuses,with the ability to undergo both highly self-renewal and multiple differentiation. These cells in vitro can differentiate into derivatives of all three embryonic germ layers when transferred to an in vitro environment and have the ability to form any fully differentiated cells of the body. The aim of this study is to investigate the potentiality of human EG cells differentiation into cardiomyocytes. Inducing human EG cells with the method of murine ES cells differentiation into cardiomyocytes, supplemented with 0.75%-1% DMSO, 20% NBS, 10(-7) mM RA and 20% cardiomyocytes conditioned medium. RESULTS: 20 heart-like (rhythmic beating cell masses were observed in vitro culture and delayed human EG cells, which beat spontaneously from 20-120 times per minute and maintained beating for 2-15 days, periodic acid's staining (PAS), Myoglobin and a-actin immunological histology positive were all positive and reacted with K+, Ca2+ and adrenalin. Relatively unorganized myofibrillar bundles or more organized sarcomeres, z-bands or a gap junction, the presence of desmosomes in a few cells of the cell masses was observed with transmision electron microscope, which initially demonstrated that these cells were cardiomyocytes. We could not get rhythmly beating cardiomyocytes with 0.75%-1% DMSO, 10-7 mM RA and 20% cardiomyocytes conditioned medium,but in which the percentage of cardiac alpha-actin immunostaining positive cells were increased. The results first demonstrated that human EG cells can differentiate into rhythmic beating cardiomyocytes in vitro and suggests that human EG cells may represent a new potent resource for cardiomyocytes transplantation therapy for myocardium infarction.

Cell Culture Techniques↗

PubMed2005

Formulation and characterization of a novel fluoride-releasing dental composite.

OBJECTIVES: The aims of this study were to formulate a novel fluoride-releasing dental composite and to evaluate its mechanical properties, fluoride release and recharge capabilities, water sorption and solubility. METHODS: A fluoride-releasing dimethacrylate monomer containing a ternary zirconium fluoride chelate was synthesized. Three experimental fluoride-releasing composites were fabricated with different monomer formulas (wt.%)-(1) Control A: 40 BisGMA/40 TEDMA/20 UEDMA; (2) EXPERIMENTAL: 20 F-releasing monomer/20 BisGMA/40 TEDMA/20 UEDMA; (3) Control B: the same formula as Control A except that it contained 10 wt.% (of total monomer) tetrabutylammonium fluoride (TBAF), which had a fluoride content equivalent to EXPERIMENTAL. All three materials had the same filler content: 55 wt.% silanized fluoroaluminosilicate particles (0.8 microm) and 10 wt.% silanized fumed silica (14 nm). All materials contained 0.17 wt.% camphorquinone (CQ) as a photoinitiator and 0.69 wt.% ethyl-4-dimethylaminobenzoate (4EDMAB) as an accelerator. The materials were tested for fluoride release (for 184 days), fluoride recharge, compressive and flexure strength, water sorption and solubility. The data were analyzed using ANOVA and Tukey-HSD tests, and Kruskal-Wallis test. RESULTS: The experimental composite had significantly higher fluoride release and fluoride recharge capabilities than both Control composites. It had significantly better physical and mechanical properties than Control B. SIGNIFICANCE: The combined use of the fluoride-releasing dimethacrylate monomer and fluoride-releasing filler can provide sustained high fluoride release and recharge as well as acceptable mechanical and physical properties. Simply adding organic fluoride salt in the monomer yields composites with poor mechanical and physical properties.

4-Aminobenzoic Acid↗

PubMed2005

Gene therapy with iNOS provides long-term protection against myocardial infarction without adverse functional consequences.

Previous studies have shown that gene therapy with inducible nitric oxide synthase (iNOS) protects against myocardial infarction at 3 days after gene transfer. However, the long-term effects of iNOS gene therapy on myocardial ischemic injury and cardiac function are unknown. To address this issue, we used a recombinant adenovirus 5 (Ad5) vector (Av3) with deletions of the E1, E2a, and E3 regions, which enables long-lasting recombinant gene expression for at least 2 mo due to lack of inflammation. Mice received intramyocardial injections in the left ventricular (LV) anterior wall of Av3/LacZ (LacZ group) or Av3/iNOS (iNOS group); 1 or 2 mo later, they were subjected to myocardial infarction (30-min coronary occlusion followed by 4 h of reperfusion). Cardiac iNOS gene expression was confirmed by immunoblotting and activity assays at 1 and 2 mo after gene transfer. In the iNOS group, infarct size (percentage of risk region) was significantly reduced (P < 0.05) both at 1 mo (24.2 +/- 3.4%, n = 6, vs. 48.0 +/- 3.6%, n = 8, in the LacZ group) and at 2 mo (23.4 +/- 3.1%, n = 8, vs. 36.6 +/- 2.4%, n = 7). The infarct-sparing effects of iNOS gene therapy were as powerful as those observed 24 h after ischemic preconditioning (23.1 +/- 3.4%, n = 10). iNOS gene transfer had no effect on LV function or dimensions up to 8 wk later (echocardiography). These data demonstrate that iNOS gene therapy mediated by the Av3 vector affords long-term (2 mo) cardioprotection without inflammation or adverse functional consequences, a finding that provides a rationale for further preclinical testing of this therapy.

Animals↗

PubMed2005

Structure-based design of cycloamide-urethane-derived novel inhibitors of human brain memapsin 2 (beta-secretase).

A series of novel macrocyclic amide-urethanes was designed and synthesized based upon the X-ray crystal structure of our lead inhibitor (1, OM99-2 with eight residues) bound to memapsin 2. Ring size and substituent effects have been investigated. Cycloamide-urethanes containing 14- to 16-membered rings exhibited low nanomolar inhibitory potencies against human brain memapsin 2 (beta-secretase).

Amides↗

PubMed2004

Assignment of absolute stereochemistry and total synthesis of (-)-spongidepsin.

[structure: see text] An enantioselective total synthesis of (-)-spongidepsin (2) and elucidation of the absolute stereochemistry of its four stereocenters are described. Spongidepsin (2), a 13-membered depsipeptide isolated from the Vanuatu marine sponge Spongia sp., has shown potent antitumor properties against a variety of NCI tumor cell lines. Our synthesis is convergent, and the absolute stereochemistry of four of the five chiral centers was assigned through synthesis.

Animals↗

PubMed2003

Comparison of several well-known controllers used in process control.

In this paper, several well-known design methods, PID control, Smith predictor, inferential control, internal model control, Dahlin controller, deadbeat control, and predictive control, are studied. A suboptimal Smith predictor is derived. The relationship among these methods is investigated. It is shown that these methods are equivalent to each other on certain premises. This explains why they are widely used in process control and provides insight into the work of bringing these techniques together to control system design. Examples are given to illustrate the result.

Journal Article↗

PubMed2003

Compressive strength, fluoride release and recharge of fluoride-releasing materials.

The compressive strength, fluoride releases and recharge profiles of 15 commercial fluoride-releasing restorative materials have been studied. The materials include glass ionomers (Fuji IX, Ketac Molar, Ketac Silver, and Miracle Mix), resin-modified glass ionomers (Fuji II LC Improved, Photac-Fil, and Vitremer), compomers (Compoglass, Dyract AP, F2000, and Hytac) and composite resins (Ariston pHc, Solitaire, Surefil and Tetric Ceram). A negative linear correlation was found between the compressive strength and fluoride release (r(2)=0.7741), i.e., restorative materials with high fluoride release have lower mechanical properties. The fluoride-releasing ability can be partially regenerated or recharged by using a topical fluoride agent. In general, materials with higher initial fluoride release have higher recharge capability (r(2)=0.7088). Five equations have been used in curve fitting to describe the cumulative fluoride release from different materials. The equation [F](c)=[F](I)(1-e(-bt))+betat best describes the cumulative fluoride release for most glass ionomers, resin-modified glass ionomers, and some high fluoride-releasing compomers and composites, whereas [F](c)=[F](I)/(t(1/2)+t)+alphat best describes the cumulative fluoride release for most compomers and composite resins. The clinic applications of different fluoride-releasing materials have also been discussed.

Cariostatic Agents↗

PubMed2002

H(infinity) PID controller design for runaway processes with time delay.

This paper presents an efficient method for designing proportional-integra-derivative (PID) controllers for runaway processes with time delay. The method is developed based on the H(infinity) control theory in frequency domain. The constraints imposed by the internal stability and asymptotic properties of the closed-loop system are first investigated, a new procedure is then developed for analytically designing the controller, and simple design formulas are obtained. It is shown that the new controller can be designed to meet specified time domain performances. Typical design examples are provided to illustrate the proposed method.

Computer Simulation↗

PubMed2002

A new two-degree-of-freedom level control scheme.

In this paper, a two-degree-of-freedom level control scheme for delay free processes is analyzed. The nominal performance and robustness are examined. And sufficient and necessary conditions for robust stability are derived. An alternative level control scheme is developed for processes with dead time and suboptimal controllers that can produce smooth response are derived analytically based on the internal model control. The scheme has an important feature in that it is simple and transparent in design and in the corporation of performance and robust stability issues. Numerical examples are provided to compare the proposed scheme with those developed.

Equipment Design↗

PubMed2002

Design PID controllers for desired time-domain or frequency-domain response.

Practical requirements on the design of control systems, especially process control systems, are usually specified in terms of time-domain response, such as overshoot and rise time, or frequency-domain response, such as resonance peak and stability margin. Although numerous methods have been developed for the design of the proportional-integral-derivative (PID) controller, little work has been done in relation to the quantitative time-domain and frequency-domain responses. In this paper, we study the following problem: Given a nominal stable process with time delay, we design a suboptimal PID controller to achieve the required time-domain response or frequency-domain response for the nominal system or the uncertain system. An H(infinity) PID controller is developed based on optimal control theory and the parameters are derived analytically. Its properties are investigated and compared with that of two developed suboptimal controllers: an H2 PID controller and a Maclaurin PID controller. It is shown that all three controllers can provide the quantitative time-domain and frequency-domain responses.

Computer Simulation↗

PubMed2002

Optimal solution, quantitative performance estimation, and robust tuning of the simplifying controller.

Recently, a simplifying controller has been proposed based on the principal of simplification of the control system transfer functions, which offers improved control for processes with a large time delay. It is the purpose of this complementary paper to give a comprehensive analysis on the scheme. First, the relationship among the simplifying controller, the Smith predictor, and the internal model control are discussed. Second, an analytical design procedure is developed based on internal model control (IMC) and optimal solution is derived. Third, the problem of estimating the time domain performance of the closed loop system, quantitatively, is discussed. Fourth, a simple robust tuning procedure is presented. Numerical examples are provided to illustrate the proposed method.

Computer Simulation↗

PubMed2002

In vitro evaluation of the retention of composite fiber and stainless steel posts.

PURPOSE: This study compared the tensile retentive strength of composite fiber-reinforced dowels luted with a resin cement to stainless steel dowels luted with zinc phosphate cement. MATERIALS AND METHODS: The crowns of 40 extracted human mandibular premolars were removed with a separating disc 1-mm coronal to the cementoenamel junction. The teeth were randomly divided into 4 groups (n = 10). A post space was prepared in each specimen to a depth of 9 mm, using the drill supplied by the respective manufacturer. For the stainless steel post group, 1.25-mm-diameter posts were cemented with zinc phosphate cement. For the composite fiber reinforced groups, posts with diameters of 1.00, 1.25, and 1.50 mm were luted with a Bisphenol A-Glycidyl Methacrylate (BIS-GMA) resin bonding system (Jeneric/Pentron, Wallingford, CT) according to manufacturer specifications. The specimens were stored in a sealed container with a moist environment for 24 hours, placed in a fixture in an 801 Materials Test Systems (MTS) machine (MTS Systems Corp, Minneapolis, MN), and loaded in tension at a rate of 5.0 mm/min until failure. Differences among the 4 groups were determined using a one-way analysis of variance and Tukey-B post-hoc tests (alpha = 0.05). RESULTS: The mean loads to failure ranged from 43.9 +/- 10.4 kg for the stainless steel dowel group to 19.9 +/- 5.7 kg for the composite fiber-reinforced 1.00-mm-diameter group. The stainless steel post luted with zinc phosphate cement provided significantly greater tensile resistance than all composite fiber dowel groups. The retention of the 1.00-mm composite fiber-reinforced post was significantly less than the remaining groups. CONCLUSIONS: Under the conditions of this study, the stainless steel dowel luted with zinc phosphate cement provided significantly greater retention.

Analysis of Variance↗

PubMed2002

[Research on signal sources for prosthetic limb control].

Proper signal sources for prosthetic limb control are the premises in designing upper extremities with high effectiveness and multi-degree of freedom(DOF). With an overview of input sources adopted in prosthetic design, this paper reviews comprehensively on characters of signals available for arm control.

Artificial Limbs↗