Pathlistings applied to data flow analysis

Summary In this paper the pathlisting mechanism is developed as a new tool useful in performing efficient data flow analysis of programs for a wide variety of problems. An algorithm using this tool for forward flow, code improvement problems is presented. It is shown that for all practical purposes this algorithm is linear in the size of the input which is, generally speaking, a reducible flow graph modeling the given program. Pathlistings generalize the nodelisting approach, introduced by Kennedy, for solving data flow problems. The efficiency of the pathlisting algorithm is due to the reuse of intermediate values and due to the fact that the cycles of a reducible flow graph can be ordered. Other advantages of the approach are also discussed.Work supported by National Science Foundation grant DCR73-00365-AO     

Selective sampling of phosphopeptides for detection by MALDI mass spectrometry

The analysis of phosphopeptides by mass spectrometry (MS) is one of the most challenging tasks in proteomics. This is due to the lower isoelectric point (pI) of phosphopeptides, which leads to inefficient sample ionization in MS, particularly when competing with other peptides. The problem is compounded by the typical low abundance of phosphopeptides in biological samples. We describe here a simple nonsorptive method to isolate phosphopeptides based on their pI. A voltage is applied to selectively migrate the phosphopeptides into a capillary, which are negatively charged at acidic pH. The selectively sampled fraction is directly deposited onto MALDI sample target in nanoliter volumes (7-35 nL) for highly sensitive MS detection. No significant sample loss is evident in this procedure; hence, the MS was able to detect the isolated phosphopeptides at trace quantity. In this case, attomole-level detection limit is achieved for synthetic phosphopeptides (nM concentration and nL volume), from a mixture containing other peptides at up to 1 million times higher in concentration. Selective sampling was also applied to the tryptic digest of beta- and alpha-caseins to reveal the multiple phosphorylated peptides at the low-femtomole level using MALDI MS. Knowledge of pI based on the rejection/injection of peptides was found to be useful in peak assignment. To confirm the sequence of the selectively sampled peptides, fraction collection was performed for offline ESI MS/MS analysis.     

Polymer nanochannels fabricated by thermomechanical deformation for single-molecule analysis

A simple method for fabricating nanoscale channels based on thermomechanical deformation of rigid polymer substrates is demonstrated. Polycarbonate preforms containing microchannels with cross-sectional dimensions on the order of tens of micrometers are controllably deformed to produce submicrometer dimensions. The reduced channel dimensions are achieved by heating the preform while applying a uniaxial tensile force to reduce channel cross sections through the Poisson effect. Nanochannels with circular or elliptical cross sections are defined by varying the channel position and preform geometry prior to deformation. Arrays of parallel nanochannels with critical dimensions down to 400 nm are described. Using the fabrication method, a nanochannel network is fabricated for the detection of single protein molecules via confocal fluorescence microscopy. The chip includes a detection channel with cross-sectional dimensions approaching the confocal volume dimensions of the detection optics and a larger adjacent reference channel used to optimize focusing. Detection of fluorescently labeled bovine serum albumin at 15 and 150 nM concentrations is presented, demonstrating the ability to perform single-molecule fluorescence measurements in polycarbonate chips using visible wavelengths for excitation and detection.     

Image processing based on seeded spontaneous optical pattern formation by optoelectronic feedback

Spontaneous optical pattern formation from an initial seed optical pattern in an optoelectronic system with optical diffractive feedback is investigated experimentally. We demonstrate that the temporal evolution of the spontaneously formed patterns exhibits a contrast enhancement effect, a spatial filtering effect, and filling of vacant space while the surrounding structures are maintained. These effects allow us to perform image processing of natural fringe patterns, i.e., in our experiments, fingerprint patterns. We also demonstrate image processing with defect invariance for fingerprint patterns.     

Production of L-sorbitol from L-fructose by Aureobasidium pullulans LP23 isolated from soy sauce mash

A strain LP23 that can convert L-fructose to L-sorbitol was isolated from soy sauce mash and identified as Aureobasidium pullulans. The cells grown on L-arabinose were found to have relatively high L-fructose to L-sorbitol conversion potential. Addition of erythritol to the reaction mixture considerably accelerated the conversion rate of L-fructose to L-sorbitol. During the conversion reaction, erythritol was added to the reaction mixture at 8-h intervals to maintain the concentration of erythritol at 1.0%. The final conversion ratios were 82.8%, 95.3%, 92.4%, and 42.6% using washed cells when the concentrations of L-fructose were 1.0%, 2.0%, 5.0% and 10.0%, respectively. The product from L-fructose was identified as L-sorbitol by HPLC analysis, infrared spectroscopy, optical rotation and melting point measurements.     

Important role of blood rheology in atherosclerosis of patients with hemodialysis

Concerning a role of blood rheology for atherosclerosis in patients with hemodialysis (HD), little data are available. It may be due to the fact that the method for evaluating rheologic properties of circulating blood has been limited. We examined blood rheology in 118 HD patients by using microchannel array flow analyzer that makes it possible to directly observe the flow of blood cell elements through the microchannel. Transit time (T(B)) of heparinized whole blood through slit pores (7 x 30 microm) was used as an index of rheology and related with various inflammatory biomarkers such as high-sensitive CRP (hsCRP), monocyte chemotactic protein-1, osteopontin, or fibrinogen (Fg). Moreover, as a surrogate marker of atherosclerosis, carotid intima-media thickness (IMT) and aortic stiffness evaluated by brachial-ankle pulse-wave velocity (baPWV) were studied. In HD patients, T(B) had strong positive correlations with hsCRP (r = 0.427; p < 0.00001), Fg (r = 0.452; p < 0.00001), and osteopontin (r = 0.227; p < 0.0134). Further, T(B) was significantly well correlated with IMT (r = 0.400; p < 0.0001) and PWV (r = 0.470; p < 0.0001). Multivariate regression analysis showed that baPWV, IMT, Fg, hematocrit, white blood cell count, and CRP were chosen as significant explanatory factors for T(B.) These results suggest that blood rheology may play an important role for atherosclerosis in patients with HD.     

The inhibitive action of bound water in the passive film of stainless steel against chloride corrosion

The stability of passivated 304 stainless steel specimens in the presence of chloride ions was investigated in relation to the amount of bound water in the passive film. As a measure of the stability the induction period for pit initiation and number of the anodic fluctuation prior to pit initiation were used. The amount of bound water was controlled by varying of passivation potentials, passivation times and passivation temperatures. Two kinds of bound water with different inhibitive action against corrosion by chloride ions were found in the passive film.