A parallel scheme for accelerating parameter sweep applications on a GPU

This paper proposes a parallel scheme for accelerating parameter sweep applications on a graphics processing unit. By using hundreds of cores on the graphics processing unit, we found that our scheme simultaneously processes multiple parameters rather than a single parameter. The simultaneous sweeps exploit the similarity of computing behaviors shared by different parameters, thus allowing memory accesses to be coalesced into a single access if similar irregularities appear among the parameters’ computational tasks. In addition, our scheme reduces the amount of off‐chip memory access by unifying the data that are commonly referenced by multiple parameters and by placing the unified data in the fast on‐chip memory. In several experiments, we applied our scheme to practical applications and found that our scheme can perform up to 8.5 times faster than a naive scheme that processes a single parameter at a time. We also include a discussion on application characteristics that are required for our scheme to outperform the naive scheme. Copyright © 2013 John Wiley & Sons, Ltd.     

Large-scale preparation and glycan characterization of sialylglycopeptide from bovine milk glycomacropeptide and its bifidogenic properties

Bovine glycomacropeptide (GMP) is a 7,000-Da glycopolypeptide released from κ-casein during cheese making. The O-glycan chains linked to GMP have many biological activities, but their utilization for nutraceutical products is limited due to their low content. To concentrate the functional glycan chains of GMP, we prepared sialylglycopeptide concentrate (SGC) from GMP-containing whey protein concentrate via proteolytic digestion of peptide chains and concentration of sialylglycopeptide by ultrafiltration using membranes with a molecular weight cut-off of 1,000 Da. The abundant saccharides detected in the prepared SGC were N-acetylneuraminic acid (Neu5Ac: 32.3% wt/wt), N-acetylgalactosamine (11.3%), and galactose (10.2%), which constitute O-glycans attached to GMP. The Neu5Ac content in SGC was found concentrated at approximately 4.8-fold of its content in GMP-containing whey protein concentrate (6.8%). Structural analysis of O-glycopeptides by liquid chromatography tandem mass spectrometry identified 88 O-glycopeptides. Moreover, O-acetylated or O-diacetylated Neu5Ac was detected in addition to the previously characterized O-glycans of GMP. Quantitative analysis of O-glycan in SGC by fluorescence labeling of chemically released O-glycan revealed that a disialylated tetrasaccharide was the most abundant glycan (76.6% of the total O-glycan). We further examined bifidogenic properties of SGC in vitro, which revealed that SGC served as a more potent carbon source than GMP and contributes to the growth-promoting effects on certain species of bifidobacteria. Overall, our study findings indicate that SGC contains abundant O-glycans and has a bifidogenic activity. Moreover, the protocol for the preparation of SGC described herein is relatively simple, providing a high yield of glycan, and can be used for large-scale preparation.     

Contrast Improvement Method for Monochrome Images Based on the Ratio of Local Variances of Gray levels

When the contrast of a captured image is not good, a method for contrast improvement may be useful. Especially, liner transform (LT) of gray levels and the histogram equalization (HE) method are well known as general methods. However, an effective contrast improvement does not always work, or an unnatural output is often generated by these methods. This paper proposes a method for contrast improvement to generate an image with medium contrast between those obtained by LT and HE. An input image is separated into an object area and a background area by every pixel. The variance of gray levels in the local area is used for measuring the local contrast. The ratio of the variances of gray levels in these areas is evaluated to determine the relative weights of LT and HE. The experimental results show that output images with higher contrast than that by LT and with less saturation of brightness and less noise than those by HE were generated by the proposed method. Copyright © 2008 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.     

Observation and quantitative analysis of rat bone marrow stromal cells cultured in vitro on newly formed transparent β-tricalcium phosphate

To observe living cell morphology on ceramics by light microscopy, we fabricated a new material—transparent β - tricalcium phosphate (t-β TCP) ceramic—for the purpose of serving as a tissue culture substrate. Bone marrow stromal cells (BMSCs) were obtained from rat femora and cultured on both t-β TCP ceramic disks and culture grade polystyrene (PS) dishes in an osteogenic medium. After 1 day of culture, cell attachment and spreading on both the t-β TCP and PS substrata were equally and clearly detected by ordinary light microscopy. After 14 days of culture, extensive cell growth, alkaline phosphatase (ALP) staining, and bone mineral deposition could be detected on both substrata. In addition, quantitative biochemical analyses revealed high DNA content, ALP activity, and osteocalcin content of these cultures. This experiment is significant in that all of the results were similarly observed on both the t-β TCP and PS substrata, indicating the excellent properties of β TCP ceramics for BMSCs culture towards osteogenic differentiation.     

Antioxidant properties of herbal extracts selected from screening for potent scavenging activity against superoxide anions

BACKGROUND: In a previous study with the electron spin resonance (ESR) spin‐trapping method on large‐scale screening with ethanol extracts of approximately 1000 kinds of herbs, four herbal extracts with prominently potent ability to scavenge superoxide anions were chosen, namely the extracts from Punica granatum (peel), Syzygium aromaticum (bud), Mangifera indica (kernel) and Phyllanthus emblica (fruit)). In the present study, these extracts were further examined to determine if they also scavenge hydroxyl radicals, by applying the ESR spin‐trapping method, and if they have heat resistance as a desirable characteristic feature. RESULTS: Experiments with the Fenton reaction and UV irradiation of hydrogen peroxide, both of which generate hydroxyl radicals, showed that all four extracts had potent ability to directly scavenge hydroxyl radicals. Each extract exerted more potent hydroxyl radical‐scavenging activity than mannitol and salicylic acid. Furthermore, the scavenging activities against superoxide anions and hydroxyl radicals of the extracts of P. granatum (peel), M. indica (kernel) and P. emblica (fruit) proved to be heat‐resistant. CONCLUSION: The four herbal extracts chosen from extensive screening possess desirable antioxidant properties. In particular, three of them are expected to be suitable for food processing in which thermal devices are used, because of their heat resistance. Copyright © 2008 Society of Chemical Industry     

Luminosity monitor for the venus detector at TRISTAN

We constructed a luminosity monitor of the lead-scintillator sandwich type for the VENUS detector at the e⁺e⁻ collider TRISTAN. Photomultiplier tubes with transmissive mesh dynodes could be operated fairly well in a high magnetic field and hence the readout optics system was considerably simplified. We present the performance of the luminosity monitor for e⁺e⁻ collisions at √s = 50 and 52 GeV.     

Interfacial properties of polyelectrolyte–cellulose systems. III. Theoretical model for the electrokinetic behavior of cellulose fibers with adsorbed monolayers of cationic polyelectrolyte

A theoretical model is proposed to account for the experimental results in part II. The basic assumption is that the total surface charge of the monolayer-formed DP fibers stems from (i) fixed ionized groups on the surface and (ii) adsorbed ions on the surface from surrounding solutions. The fixed ionized groups are the carboxyl groups of the fibers and quaternary ammonium groups of the polymer. The proposed model correlates the amount of adsorbed polymer with the zeta potential of the monolayer-formed DP fibers. Calculations made on the proposed model using the experimental data in part II suggest that a comparison of the charge calculated from zeta potential with that from the amount of adsorbed polymer yields ca. 0.04% of the fixed ionizable groups as effective charged sites, i.e., electrokinetically detectable. This finding is due to the binding of counterions to the fixed ionized sites on the surface. Zeta potentials of the DP with adsorbed monolayers largely stem from the fixed ionized groups with only a minor contribution from the adsorbed ions. The zeta potentials are nearly proportional to the difference between the number of cationic and anionic groups on the surface.     

Starvation induces the formation of giant mitochondria in gastric parietal cells of guinea pigs

Mitochondria occasionally increase in size in response to metabolic injury. Numerous studies have reported giant mitochondria in patients with various diseases and animals with metabolic injuries, but there are few reports on giant mitochondria in normal cells under physiological conditions. Here, we report giant mitochondria in normal gastric parietal cells. Stomachs of guinea pigs fed freely, fasted or fasted and then injected with histamine were processed for electron microscopy. Giant mitochondria >2 microm in the diameter of their major axis were observed in resting-type parietal cells in the gastric glands of animals fasted for 60-72 h, whereas acid-secreting-type parietal cells found in those fed ad libitum did not contain giant mitochondria. Giant mitochondria showed unusual structures, especially in their cristae: they contained closely packed, tubular and concentric cristae as well as amorphous and pleomorphic inclusion bodies in their matrix. We observed giant mitochondria consisting of several segments, suggesting the fusion of several normal-sized mitochondria. Histamine injection decreased in a frequency of giant mitochondria in accordance with a decrease in a frequency of resting-type parietal cells. This is the first report of giant mitochondria in gastric parietal cells under physiological or near physiological conditions. Gastric parietal cells might be a good model for examining mitochondrial fusion and fission in a physiological state accompanied by the morphological change of the cells in the membrane system from an acid-secreting to resting type.     

Rational Design of a Ratiometric Fluorescent Probe Based on Arene–Metal‐Ion Contact for Endogenous Hydrogen Sulfide Detection in Living Cells

We report the design and development of a fluorescent Cd^II ion complex that is capable of the ratiometric detection of H₂S in living cells. This probe exploits the metal‐ion‐induced emission red shift resulting from direct contact between the aromatic ring of a fluorophore and a metal ion (i.e., arene–metal‐ion or “AM” contact). The Cd^II complex displays a large emission blue shift upon interaction with H₂S as the Cd^II‐free ligand is released by the formation of cadmium sulfide. Screening of potential ligands and fluorophores led to the discovery of a pyronine‐type probe, 6? Cd^II, that generated a sensitive and rapid ratio value change upon interaction with H₂S, without interference from the glutathione that is abundant in the cell. The membrane‐impermeable 6? Cd^II was successfully translocated into live cells by using an oligo‐arginine peptide and pyrenebutylate as carriers. As such, 6? Cd^II was successfully applied to the ratiometric detection of both exogenous and endogenous H₂S produced by the enzymes in living cells, thus demonstrating the utility of 6? Cd^II in biological fluorescence analysis.