Free-flow isoelectric focusing of proteins remaining in cell fragments following sonication of thyroid carcinoma cells

The method of preparing protein mixtures for electrophoretic analysis of membrane-associated cell proteins was improved. By sonication, about one-half of the proteins of thyroid cells were released into the supernatant, while the other half preferentially comprising membrane proteins still remained in cell fragments, which could be sedimented by centrifugation. After sonication, even those proteins which remained in cell fragments, could completely be dissolved by free-flow isoelectric focusing media. They migrated through the free-flow electrophoresis chamber without forming precipitates. Because of these improvements, it was possible to show that the two thyroid cancer cell lines ML-1 and ONCO-DG1 express cytokeratin 8 at similar rates, but cytokeratins 7 and 18 differently. In addition, the presence of inorganic pyrophosphatase, tubulin-beta-5, and tubulin-beta-1 chains in human thyroid cells was proved for the first time.     

Cut sharing for multistage stochastic linear programs with interstage dependency

Multistage stochastic programs with interstage independent random parameters have recourse functions that do not depend on the state of the system. Decomposition-based algorithms can exploit this structure by sharing cuts (outer-linearizations of the recourse function) among different scenario subproblems at the same stage. The ability to share cuts is necessary in practical implementations of algorithms that incorporate Monte Carlo sampling within the decomposition scheme. In this paper, we provide methodology for sharing cuts in decomposition algorithms for stochastic programs that satisfy certain interstage dependency models. These techniques enable sampling-based algorithms to handle a richer class of multistage problems, and may also be used to accelerate the convergence of exact decomposition algorithms. Research leading to this work was partially supported by the Department of Energy Contract DE-FG03-92ER25116-A002; the Office of Naval Research Contract N00014-89-J-1659; the National Science Foundation Grants ECS-8906260, DMS-8913089; and the Electric Power Research Institute Contract RP 8010-09, CSA-4O05335. This author's work was supported in part by the National Research Council under a Research Associateship at the Naval Postgraduate School, Monterey, California.     

N-H···π hydrogen-bonding and large-amplitude tipping vibrations in jet-cooled pyrrole-benzene

The N-H···π hydrogen bond is an important intermolecular interaction in many biological systems. We have investigated the infrared (IR) and ultraviolet (UV) spectra of the supersonic-jet cooled complex of pyrrole with benzene and benzene-d(6) (Pyr·Bz, Pyr·Bz-d(6)). DFT-D density functional, SCS-MP2 and SCS-CC2 calculations predict a T-shaped and (almost) C(s) symmetric structure with an N-H···π hydrogen bond to the benzene ring. The pyrrole is tipped by ω(S(0)) = ±13° relative to the surface normal of Bz. The N···ring distance is 3.13 ?. In the S(1) excited state, SCS-CC2 calculations predict an increased tipping angle ω(S(1)) = ±21°. The IR depletion spectra support the T-shaped geometry: The NH stretch is redshifted by -59 cm(-1), relative to the "free" NH stretch of pyrrole at 3531 cm(-1), indicating a moderately strong N-H···π interaction. The interaction is weaker than in the (Pyr)(2) dimer, where the NH donor shift is -87 cm(-1) [Dauster et al., Phys. Chem. Chem. Phys., 2008, 10, 2827]. The IR C-H stretch frequencies and intensities of the Bz subunit are very similar to those of the acceptor in the (Bz)(2) dimer, confirming that Bz acts as the acceptor. While the S(1)←S(0) electronic origin of Bz is forbidden and is not observable in the gas-phase, the UV spectrum of Pyr·Bz in the same region exhibits a weak 0 band that is red-shifted by 58 cm(-1) relative to that of Bz (38?086 cm(-1)). The origin appears due to symmetry-breaking of the π-electron system of Bz by the asymmetric pyrrole NH···π hydrogen bond. This contrasts with (Bz)(2), which does not exhibit a 0 band. The Bz moiety in Pyr·Bz exhibits a 6a band at 0 + 518 cm(-1) that is about 20× more intense than the origin band. The symmetry breaking by the NH···π hydrogen bond splits the degeneracy of the ν(6)(e(2g)) vibration, giving rise to 6a' and 6b' sub-bands that are spaced by ～6 cm(-1). Both the 0 and 6 bands of Pyr·Bz carry a progression in the low-frequency (10 cm(-1)) excited-state tipping vibration ω', in agreement with the change of the ω tipping angle predicted by SCS-MP2 and SCS-CC2 calculations.     

Multi-stage stochastic linear programs for portfolio optimization

The paper demonstrates how multi-period portfolio optimization problems can be efficiently solved as multi-stage stochastic linear programs. A scheme based on a blending of classical Benders decomposition techniques and a special technique, called importance sampling, is used to solve this general class of multi-stochastic linear programs. We discuss the case where stochastic parameters are dependent within a period as well as between periods. Initial computational results are presented.Research and reproduction of this report were partially supported by the Office of Naval Research Contract N00014-89-J-1659; the National Science Foundation Grants ECS-8906260, DMS-8913089, the Electric Power Research Institute Contract RP-8010-09, CSA-4O05335, and the Austrian Science Foundation, Fonds zur Förderung der wissenschaftlichen Forschung, Grant J0323-Phy. Any opinions, findings, and conclusions or recommendations expressed in this publication are those of the authors and do NOT necessarily reflect the views of the above sponsors. The comments of anonymous referees are gratefully acknowledged.     

The use of sigmoid pH gradients in free-flow isoelectric focusing of human endothelial cell proteins

Prefractionation of proteins enhances the resolution of proteome analysis of whole cells. Free-flow electrophoresis (FFE) provides a useful step in various prefractionation protocols, since matrix-free isoelectric focusing (FF-IEF) performed in this machine enables the enrichment of large, easily absorbable, sensitive proteins. The impact of the FFE on the success of a proteome analysis depends on the quality of the FF-IEF separation procedure. Therefore, attempts are continuously being made to improve FF-IEF. Here, we applied sigmoid pH gradients to the prefractionation of endothelial cell proteins. Small steps of pH incline between neighboring FFE fractions were established in pH ranges, in which the proteins of interest have their pIs. With the help of this advanced technology, we separated vimentin and cytoplasmic actin as well as triosephosphate isomerase and glyceraldehyde phosphate dehydrogenase preparatively, and found a pI of 5.9 ± 0.2 for nonmuscle myosin.     

Modelling history-dependent parameters in the SMPS format for stochastic programming

G. Infanger Management Science and Engineering, Stanford University, Stanford, CA Email: Horand.Gassmann{at}dal.ca Received on 1 October 2004. Accepted on 31 January 2007. This paper proposes two extensions to the SMPS format for stochasticprograms to permit modelling of autoregressive-moving average(ARMA) processes. Sampling-based algorithms can thus proceedindependently of any underlying modelling system, increasingefficiency. An illustrative example demonstrates the power ofthe new constructs.     

Simulation-based confidence bounds for two-stage stochastic programs

This paper provides a rigorous asymptotic analysis and justification of upper and lower confidence bounds proposed by Dantzig and Infanger (A probabilistic lower bound for two-stage stochastic programs, Stanford University, CA, 1995) for an iterative sampling-based decomposition algorithm, introduced by Dantzig and Glynn (Ann. Oper. Res. 22:1–21, 1990) and Infanger (Ann. Oper. Res. 39:41–67, 1992), for solving two-stage stochastic programs. The paper provides confidence bounds in the presence of both independent sampling across iterations, and when common samples are used across different iterations. Confidence bounds for sample-average approximation then follow as a special case. Extensions of the theory to cover use of variance reduction and the dropping of cuts are also presented. An extensive empirical investigation of the performance of these bounds establishes that the bounds perform reasonably on realistic problems.

     

Lipoprotein Subclasses Independently Contribute to Subclinical Variance of Microvascular and Macrovascular Health

Lipoproteins are important cardiovascular (CV) risk biomarkers. This study aimed to investigate the associations of lipoprotein subclasses with micro- and macrovascular biomarkers to better understand how these subclasses relate to atherosclerotic CV diseases. One hundred and fifty-eight serum samples from the EXAMIN AGE study, consisting of healthy individuals and CV risk patients, were analysed with nuclear magnetic resonance (NMR) spectroscopy to quantify lipoprotein subclasses. Microvascular health was quantified by measuring retinal arteriolar and venular diameters. Macrovascular health was quantified by measuring carotid-to-femoral pulse wave velocity (PWV). Nineteen lipoprotein subclasses showed statistically significant associations with retinal vessel diameters and nine with PWV. These lipoprotein subclasses together explained up to 26% of variation (R² = 0.26, F(29,121) = 2.80, p < 0.001) in micro- and 12% (R² = 0.12, F(29,124) = 1.70, p = 0.025) of variation in macrovascular health. High-density (HDL-C) and low-density lipoprotein cholesterol (LDL-C) as well as triglycerides together explained up to 13% (R² = 0.13, F(3143) = 8.42, p < 0.001) of micro- and 8% (R² = 0.08, F(3145) = 5.46, p = 0.001) of macrovascular variation. Lipoprotein subclasses seem to reflect micro- and macrovascular end organ damage more precisely as compared to only measuring HDL-C, LDL-C and triglycerides. Further studies are needed to analyse how the additional quantification of lipoprotein subclasses can improve CV risk stratification and CV disease prediction.