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X Song

Publications and source records attributed to X Song.

At least 19 recordsLinked to original sources
PubMed2006

Experimental and theoretical investigations of solvation dynamics of ionic fluids: appropriateness of dielectric theory and the role of DC conductivity.

An analysis is provided of the subnanosecond dynamic solvation of ionic liquids in particular and ionic solutions in general. It is our hypothesis that solvation relaxation in ionic fluids, in the nonglassy and nonsupercooled regimes, can be understood rather simply in terms of the dielectric spectra of the solvent. This idea is suggested by the comparison of imidazolium ionic liquids with their pure organic counterpart, butylimidazole (J. Phys. Chem. B 2004, 108, 10245-10255). It is borne out by a calculation of the solvation correlation time from frequency dependent dielectric data for the ionic liquid, ethylammonium nitrate, and for the electrolyte solution of methanol and sodium perchlorate. Very good agreement is obtained between these theoretically calculated solvation relaxation functions and those obtained from fluorescence upconversion spectroscopy. Our comparisons suggest that translational motion of ions may not be the predominant factor in short-time solvation of ionic fluids and that many tools and ideas about solvation dynamics in polar solvents can be adapted to ionic fluids.

Journal Article↗
PubMed2006

AHNP-streptavidin: a tetrameric bacterially produced antibody surrogate fusion protein against p185her2/neu.

The anti-p185(her2/neu) peptidomimetic (AHNP) is a small exo-cyclic peptide derived from the anti-p185(her2/neu) rhumAb 4D5 (h4D5). AHNP mimics many but not all of the antitumor characteristics exhibited by h4D5. However, the pharmacokinetic profiles of AHNP are less than optimal for therapeutic or diagnostic purposes. To improve the binding affinity to p185(her2/neu) and the antitumor efficacy, we have engineered a fusion protein containing AHNP and a nonimmunoglobulin protein scaffold, streptavidin (SA). The recombinant protein, AHNP-SA (ASA) bound to p185(her2/neu) with high affinity, inhibited the proliferation of p185(her2/neu)-overexpressing cells, and reduced tumor growth induced by p185(her2/neu)-transformed cells. These data suggest that the bacterially produced tetrameric ASA can be used as an antibody-surrogate molecule. This class of molecule will play a role in the diagnosis and treatment of p185(her2/neu)-related tumors. Our studies establish a general principle by which a small biologically active synthetic exo-cyclic peptide can be engineered to enhance functional aspects by structured oligomerization and can be produced recombinantly using bacterial expression.

Animals↗
PubMed2006

Genotypic relatedness of yeasts in thrush and denture stomatitis.

BACKGROUND/AIM: Candida is an opportunistic pathogen. Understanding its genetic characters might increase our understanding of the pathogenesis of candidosis. We examined the genetic relationships of yeasts from the most common forms of oral candidosis: thrush and denture stomatitis. METHODS: Yeasts were sampled from palate, buccal mucosa, gingival sulci/periodontal pockets and/or denture fitting surface of 19 thrush patients and 22 denture stomatitis patients. Random amplified polymorphic DNA and the Dendron computer-assisted program were used to determine the genotypic relatedness of the yeasts. RESULTS: A dendrogram generated from 105 thrush isolates had similarity coefficients (S(AB)) ranging from 0.58 to 1 with four clusters derived at S(AB) 68%. Another dendrogram was generated from 91 isolates from denture stomatitis, with S(AB) ranging from 0.59 to 1. Three clusters were established at S(AB) 71%. In a composite dendrogram incorporating the thrush and denture stomatitis data and orally healthy data compiled from a previous study, five genotypic clusters were generated at S(AB) 68%. Cluster II, the most dominant, comprised isolates from thrush, denture stomatitis and healthy conditions, while clusters III and IV contained yeasts mainly from thrush. CONCLUSIONS: Palatal yeast carriage was significantly increased in thrush and denture stomatitis, also after radiation, chemotherapy and denture wearing. The buccal mucosa was favorable for yeast colonization regardless of oral condition. Yeasts in thrush were more diverse than in conditions of oral health. The common clone (II) of infecting yeasts and commensals suggested that commensals could induce thrush and denture stomatitis, whereas the unique clones in thrush (III, IV) might have been established through strain replacement or maintenance with minor genetic variation.

Adolescent↗
PubMed2006

A vascular risk factor index in relation to mortality and incident dementia.

To develop a method for quantifying risks of death and dementia in relation to vascular risk factors the Gothenburg H-70 1901-02 birth cohort was studied (n=380, was followed over 20 years, with 103 incident dementia cases). Separate vascular risk factor indices were calculated using 23 vascular risk factors to predict: (i) dementia-free-survival, and (ii) incident dementia derived from post hoc optimal separation of affected and unaffected cases. Classification of adverse outcomes (dementia/non-dementia; alive/dead) was assessed using receiver-operator characteristic (ROC) curves, and the area under the curve (AUC). Each index showed high separation between affected and unaffected cases. For dementia/non-dementia, the AUC was 0.74+/-0.02 for 10 year and 0.67+/-0.02 for 20 year; for death/survival, the AUC was 0.75+/-0.02 for 10 years and 0.79+/-0.03 for 20 years. Of note, few items were important in both indexes, and most showed reciprocal effects (e.g. decreased the risk of death but increased the risk of dementia). Our results suggest that vascular risk factor indexes can give robust estimates of dementia and life span prognoses in elderly people, but death and dementia have different risk profiles. This may be because of death being a competing risk for incident late-onset dementia.

Dementia↗
PubMed2006

A frequent partial AZFc deletion does not render an increased risk of spermatogenic impairment in East Asians.

The gene families in the AZFc region of the Y chromosome have been shown to be functionally important in human spermatogenesis. The gr/gr deletion, a partial AZFc deletion that reduces the copy numbers of all the AZFc gene families, was identified as a significant risk factor for spermatogenic impairment in Dutch, Spanish and Italians. However, the presence of this deletion in healthy French and Germans questioned its importance in male infertility. In this study, we have shown that the gr/gr deletion does not render an increased risk in Han Chinese. In fact, the gr/gr deletion is frequent (about 8%) in our survey of 886 East Asians from 8 ethnic groups. Furthermore, the DAZ1/DAZ2 deletion has been detected as the primary subtype of the gr/gr deletion in East Asians, though this doublet has been considered as crucial for normal spermatogenesis in Europeans. The different spermatogenic effects of various types of the partial AZFc deletion suggest that the functional difference between AZFc gene copies is a likely cause of inconsistent associations of the gr/gr deletion with spermatogenic impairment across populations.

Base Sequence↗
PubMed2005

Delimitation of the rice wide compatibility gene S5 ( n ) to a 40-kb DNA fragment.

Wide compatibility varieties (WCVs) are a special class of rice (Oryza sativa L.) germplasm that produces hybrids with normal pollen and spikelet fertility when crossed with both indica and japonica subspecies. The wide compatibility gene S5 ( n ) has been used extensively in inter-subspecific hybrid breeding programs. We previously mapped the S5 locus to a 2.2-cM genomic region between RM253 and R2349 on chromosome 6, using a population of 356 F(1) plants derived from the three-way cross 02428/Nanjing11//Balilla. In this study, a chromosome walking strategy was employed to construct a physical map covering this genomic region using these two closest markers as the starting points. A physical map consisting of six overlapping BAC clones was formed, spanning a genomic region of 540-kb in length. By analyzing recombination events from a population of 8,000 F(1) plants derived from a three-way cross based on near isogenic lines of the S5 locus, the S5 locus was localized to a DNA fragment of 40-kb in length, flanked by two shotgun subclones, 7B1 and 15D2. Sequence analysis of this fragment predicted five open reading frames, encoding xyloglucan fucosyltransferases, dnak-type molecular chaperone BiP, a putative eukaryotic aspartyl protease, and a hypothetical protein. This result will be very useful in molecular cloning of the S5 ( n ) allele and marker-assisted transferring of the wide compatibility gene in rice breeding programs.

Aspartic Acid Endopeptidases↗
PubMed2005

Fast modelling of the collimator-detector response in Monte Carlo simulation of SPECT imaging using the angular response function.

Interactions of incident photons with the collimator and detector, including septal penetration, scatter and x-ray fluorescence, are significant sources of image degradation in applications of SPECT including dual isotope imaging and imaging using radioisotopes that emit high- or medium-energy photons. Modelling these interactions using full Monte Carlo (MC) simulations is computationally very demanding. We present a new method based on the use of angular response functions (ARFs). The ARF is a function of the incident photon's direction and energy and represents the probability that a photon will either interact with or pass through the collimator, and be detected at the intersection of the photon's direction vector and the detection plane in an energy window of interest. The ARFs were pre-computed using full MC simulations of point sources that include propagation through the collimator-detector system. We have implemented the ARF method for use in conjunction with the SimSET/PHG MC code to provide fast modelling of both interactions in the patient and in the collimator-detector system. Validation results in the three cases studied show that there was good agreement between the projections generated using the ARF method and those from previously validated full MC simulations, but with hundred to thousand fold reductions in simulation time.

Algorithms↗
PubMed2005

Latent membrane protein 1 encoded by Epstein-Barr virus modulates directly and synchronously cyclin D1 and p16 by newly forming a c-Jun/Jun B heterodimer in nasopharyngeal carcinoma cell line.

Recently we confirmed that latent membrane protein 1 (LMP1) encoded by Epstein-Barr virus (EBV) accelerates a newly forming active c-Jun/Jun B heterodimer, a transcription factor, but little is known about the target gene regulated by it. In this paper, results indicated that a c-Jun/Jun B heterodimer induced by LMP1 upregulated cyclin D1 promoters activity and expression, on the contrary, downregulated p16, and maladjustment of cyclin D1 and p16 expression accelerated progression of cell cycle. Firstly, we found a c-Jun/Jun B heterodimer regulated synchronously and directly cyclin D1 and p16 in the Tet-on-LMP1-HNE2 cell line, in which LMP1 expression is regulated by Tet-on system. This paper investigated in depth function of the newly forming active c-Jun/Jun B heterodimer, and built new connection between environmental pathogenic factor, signal transduction and cell cycle.

Carcinoma↗
PubMed2004

The complex of apomyoglobin with the fluorescent dye coumarin 153.

Understanding a protein's dielectric response requires both a theoretical model and a well-defined experimental system. The former has already been proposed by Song (J. Chem. Phys. 116, 9359 [2002]). We suggest that the latter is provided by the complex of coumarin 153 (C153) with apomyoglobin (ApoMb). C153 has been exhaustively studied and has proven to be an excellent probe of the solvation dynamics of polar solvents. Myoglobin is one of the most thoroughly studied proteins. Myoglobins from a wide range of species have been subject to X-ray structural analysis and site-directed mutagenesis. Here, we demonstrate the existence of a robust C153-apomyglobin system by means of molecular dynamics simulations, equilibrium binding studies using a Job's plot and capillary electrophoresis, circular dichroism and time-resolved fluorescence. The reorganization energy of C153 bound to ApoMb is compared with that of C153 in bulk solvent using the method of Jordanides et al. (J. Phys. Chem. B 103, 7995 [1999]).

Apoproteins↗
PubMed2004

Biological nitrogen removal in SBR bypassing nitrate generation accomplished by chlorination and aeration time control.

A novel control strategy for biological nitrogen removal with high nitrite built-up through chlorine dosage was studied. In the biological nitrogen removal process operated in a bench-scale sequencing batch reactor, dose of chlorine of 0.2 mg/l in the form of sodium hypochlorite was applied after the COD was depleted. The aerobic phase switched to an anoxic phase shortly after the ammonium was completely biotically oxidized. Nitrite accumulation was stably achieved which was attributed to the chlorination and the lag-time of nitrification. With the time control, stable 100% conversion of nitrite could also be sustained even under the absence of chlorine for at least 20 days. The nitrite oxidizer should have been killed rather than been suppressed in this study. For engineering applications, the advantages of the nitrification/denitrification via nitrite can compensate the cost of chlorine dosage. Combined with the aeration time control, it is feasible to apply chlorination in a biological nitrogen removal process in SBRs.

Bioreactors↗
PubMed2003

Syntheses of cyclic prodrugs of RGD peptidomimetics with various macrocyclic ring sizes: evaluation of physicochemical, transport and antithrombic properties.

The objective of this work was to synthesize cyclic prodrugs 1a-d of RGD peptidomimetics 2a-d with various ring sizes (n[CH2] = 1, 3, 5 and 7) and to evaluate the effect of ring size on their transport, physicochemical, enzymatic stability, and antithrombic properties. The syntheses of cyclic prodrugs 1a-d were achieved by converging two key intermediates, Boc-Phe-O-CH2-OCO-OpNP (5) and H2N-(CH2)n-CO-Asp(OBzl)-OTce (8a-d), to give linear precursors Boc-Phe-O-CH2-OCO-HN-(CH2)n-CO-Asp(OBzl)-OTce (9a-d). The N- and C-terminus protecting groups were removed from 9a-d to give 10a-d. Linear precursors 10a-d were cyclized, and the remaining Bzl-protecting group was removed to produce cyclic prodrugs 1a-d in around 20% overall yield. The linear RGD peptidomimetics (2a-d) were synthesized using standard Boc-amino acid chemistry by solution-phase method. Increasing the ring size by adding methylene groups also increases the hydrophobicity of the cyclic prodrugs and parent RGD peptidomimetics. The transport properties of cyclic prodrugs 1c and 1d were 2.6- and 4.4-fold better than those of parent compounds 2c and 2d, respectively. These results suggest that increasing the hydrophobicity of the cyclic prodrugs and parent RGD peptidomimetics enhanced their transport properties. The hydrodynamic radii of the cyclic prodrugs were also smaller than those of their respective parent compounds, suggesting that the change in size may contribute to their transport properties. The chemical stability of the cyclic prodrugs was affected by the ring size, and the cyclic prodrug with the larger ring size (i.e. 1d) was more stable than the smaller one (i.e. 1a). All the cyclic prodrugs were more stable at pH 4 than at pH 7 and 10. Prodrug-to-drug conversion could be induced by isolated esterase as well as esterase found in human plasma. An increase in the length of methylene group (n[CH2] = 1, 3, 5, 7) enhanced the antithrombic activity of the prodrugs and the parent compounds. In summary, the ring size of cyclic prodrugs affected their transport, physicochemical, and antithrombic properties.

Biological Transport↗
PubMed2003

Effects of sex, gonadectomy, and oestrogen substitution on ischaemic preconditioning and ischaemia-reperfusion injury in mice.

AIM: Ischaemic preconditioning (IPC) has been demonstrated to protect heart function and viability, but has been predominantly studied in male animals. METHODS: We studied a possible influence of sex and oestrogen for protection in IPC. Infarct size and heart function after 40 min global ischaemia and 60 min reperfusion with or without preceding classic IPC was investigated in Langendorff-perfused hearts. Hearts were harvested from 10-week-old male and female C57BL6 mice with or without gonadectomy 6 weeks earlier, or gonadectomy and substitution with 17 beta-oestradiol for 4 weeks (n = 104). RESULTS: Classic IPC reduced depression of left ventricular developed pressure (P < 0.01), attenuated the increase of end-diastolic pressure (P < 0.01), and reduced infarct size (P < 0.01) in hearts of untreated male mice, but failed to protect untreated females which had improved functional recovery and smaller infarctions than untreated males. After gonadectomy of female mice, developed pressure was reduced (P < 0.01) and infarct size increased (P < 0.01) compared with normal females, with no protection of preconditioning. The changes were not reversed by 17 beta-oestradiol substitution. In hearts of gonadectomized males, the post-ischaemic increase of end-diastolic pressure was attenuated (P < 0.01), and enhanced after substitution with 17 beta-oestradiol (P < 0.01). The preconditioning effect disappeared after gonadectomy and gonadectomy with substitution in male mice. CONCLUSION: There is a sex difference in evoking preconditioning in male and female mice which is only partially dependent on sex hormones.

Animals↗
PubMed2003

Specimen processing and concentration of Chlamydia trachomatis added can influence false-negative rates in the LCx assay but not in the APTIMA Combo 2 assay when testing for inhibitors.

Inhibitors in clinical specimens can be detected by adding the target of nucleic acid amplification to the sample. Introduction of a Chlamydia trachomatis L2 434 preparation containing 12 elementary bodies (EBs) into first-void urine (FVU) from 225 nonpregnant women and 190 pregnant women before specimen processing by the assays produced false-negative rates of 0.48% (2 of 415 specimens) and 13% (44 of 338 specimens) by the APTIMA Combo 2 and the Chlamydia LCx tests, respectively. Reducing the amount of C. trachomatis added to one EB, a concentration closer to the APTIMA Combo 2 test cutoff, for a subset of 244 FVU specimens increased the number of specimens with false-negative results by the APTIMA Combo 2 assay to 7 (2.9%), suggesting that the strength of the input C. trachomatis per specimen has an influence on the number of specimens with false-negative results. Repeat testing after overnight storage and dilution decreased the APTIMA Combo 2 test false-negative rates to 0% (0 of 415 specimens) with the stronger inoculum and 0.8% (2 of 244 specimens) with the weaker inoculum; the false-negative rate of the LCx assay was reduced to 5.4% (18 of 334 specimens). When an additional 70 FVU specimens from women to which 12 EBs were added before specimen processing were tested by the LCx assay, 34 specimens had false-negative results, whereas 21 specimens had false-negative results when the C. trachomatis EBs were introduced after processing. Nine of the 21 specimens to which EBs were added after processing and all of the 34 urine specimens to which the target was added before processing remained falsely negative on repeat testing at a 1:2 dilution, suggesting that input C. trachomatis DNA was lost during processing by the LCx assay. In contrast, the APTIMA Combo 2 assay appears to have a higher sensitivity and either lost little nucleic acid during processing or demonstrated few problems with inhibitors of transcription-mediated amplification.

Adult↗
PubMed2003

Design of a continuous flow centrifugal pediatric ventricular assist device.

Thousands of pediatric patients suffering from cardiomyopathy or single ventricular physiologies secondary to debilitating heart defects may benefit from long-term mechanical circulatory support due to the limited number of donor hearts available. This article presents the initial design of a fully implantable centrifugal pediatric ventricular assist device (PVAD) for 2 to 12 year olds. Conventional pump design equations, including a nondimensional scaling approach, enabled performance estimations of smaller scale versions (25 mm and 35 mm impeller diameters) of our adult support VAD. Based on this estimated performance, a computational model of the PVAD with a 35 mm impeller diameter was generated. Employing computational fluid dynamics (CFD) software, the flow paths through the PVAD and overall performance were analyzed for steady state flow conditions. The numerical simulations involved flow rates of 2 to 5 LPM for rotational speeds of 2750 to 3250 RPM and incorporated a k-epsilon fluid turbulence model with a logarithmic wall function to characterize near-wall flow conditions. The CFD results indicated best efficiency points ranging from 25% to 28%, which correlate well with typical values of blood pumps. The results further demonstrated that the pump could deliver 2 to 5 LPM at 70 to 95 mmHg for desired physiologic conditions in resting 2 to 12 year olds. Scalar stress levels remained below 300 Pa, thereby signifying potentially low levels of hemolysis. Several flow regions in the pump exhibited signs of vortices, retrograde flow, and stagnation points, which require optimization and further study. This CFD model represents a reasonable starting point for future model enhancements, leading to prototype manufacturing and experimental validation.

Child↗
PubMed2002

The application of quantitative oil streaking to the HeartQuest left ventricular assist device.

Methods of flow visualization using oil streaking are established techniques for investigating surface shear and near wall flow patterns. Recent studies have used an array of oil dots on a surface which form streaks when exposed to shear forces. This method is generally qualitative, but it is possible to make quantitative measurements of the shear if the oil streaks have been calibrated. This paper presents the application of a quantitative oil streak method to the HeartQuest left ventricular assist device (LVAD). An array of dots was applied to the top housing of the pump, yielding quantitative values for the shear and qualitative patterns of the near wall flow in that region. The results were used to locate regions likely to promote thrombosis, such as stagnation points or recirculation regions. Regions of high shear, where hemolysis might occur, also can be identified with this method. In addition to being an important design technique, quantitative oil streaking assisted in the verification of computational fluid dynamics results within the HeartQuest LVAD.

Cardiovascular Diseases↗
PubMed2001

Structural analysis of regulatory protein domains using GST-fusion proteins.

The glutathione S-transferase (GST) fusion protein expression system has been used extensively to generate a large quantity of proteins for structural studies. To avoid the inter-domain flexibility introduced by the GST segment, GST-fusion proteins are normally cleaved with proteases to release the GST moiety prior to crystallization. Recently, several reports have shown that GST-fusion proteins can also be used as a vehicle to determine the crystal structures of the attached small peptides and biological regulatory domains. In comparison with the standard method, GST-fusion proteins are more easily crystallized under similar conditions. In addition, the structure of the desired protein or peptide can be determined using the molecular replacement method with the help of the GST structure. Thus, GST-fusion proteins can be used as a new technique for structural determination of small regulatory domains, especially of small peptides. Here, we review the recent progress on this technique, known as GST-driven crystallization. We have summarized and compared different methods of protein preparation and crystallization used by different groups. We have also compared the three-dimensional structures, especially those of the fused peptide segments. Finally, we have discussed the potential effects of the crystal packing on the crystal structure.

Crystallization↗
PubMed2001

Activation of the Akt-related cytokine-independent survival kinase requires interaction of its phox domain with endosomal phosphatidylinositol 3-phosphate.

Protein kinases of the Akt and related serum- and glucocorticoid-regulated kinase (SGK) families are major downstream mediators of phosphatidylinositol (PI) 3-kinase signaling to many cellular processes including metabolic flux, membrane trafficking, and apoptosis. Activation of these kinases is thought to occur at the plasma membrane through their serine and threonine phosphorylation by the phosphoinositide-dependent kinase 1 (PDK1) protein kinase, which interacts with membrane 3'-polyphosphoinositides through its pleckstrin homology (PH) domain. Here, we demonstrate that the SGK family member cytokine-independent survival kinase (CISK) binds strongly and selectively to the monophosphoinositide PI(3)P through its phox homology (PX) domain. Comparing native green fluorescent protein-CISK (EGFP-CISK) to a mutant EGFP-CISK (Y51A) that displays attenuated binding to PI(3)P reveals that this interaction is both necessary and sufficient for its localization to early endosome antigen (EEA1)-positive endosomes. Furthermore, early endosome association of expressed epitope-tagged CISK in COS cells directed by binding of its PX domain to PI(3)P is required for activation of the CISK protein kinase by both insulin-like growth factor-1 and epidermal growth factor. Taken together, these results reveal a critical role of endosomal PI(3)P in the signal transmission mechanism whereby this survival kinase is activated in response to PI3-kinase stimulation by growth factors.

Animals↗