Machine Learning Approach for Prediction and Search: Application to Methane Storage in a Metal–Organic Framework

Machine learning is applied to predicting the methane uptake and searching the pore properties and the organic building blocks to determine the maximum uptake. To show the importance of the molecular structure of the building block on the methane uptake, we construct a graph-based kernel function that measures the degree of similarity between two molecular structures. A prediction model is a Gaussian process regression, which is constructed by combining this kernel function and the Gaussian kernel function of the pore properties. The structural relationships of the molecular structure contribute to an improvement in the accuracy of the prediction. After training the prediction model, using a random search, we can determine the candidate pore properties and organic building blocks that will yield an uptake larger than that seen in the training data set

Structures of Hydrocarbon Hydrates during Formation with and without Inhibitors

The formation of hydrates from a methane–ethane-propane mixture is more complex than with single gases. Using nuclear magnetic resonance (NMR) and high-pressure powder X-ray diffraction (PXRD), we have investigated the structural properties of natural gas hydrates crystallized in the presence of kinetic hydrate inhibitors (KHIs), two commercial inhibitors and two biological ice inhibitors, or antifreeze proteins (AFPs). NMR analyses indicated that hydrate cage occupancy was at near saturation for controls and most inhibitor types. Some exceptions were found in systems containing a new commercial KHI (HIW85281) and a recombinant plant AFP, suggesting that these two inhibitors could impact the kinetics of cavity formation. NMR analysis confirmed that the hydrate composition varies during crystal growth by kinetic effects. Strikingly, the coexistence of both structures I (sI) and II (sII) were observed in NMR spectra and PXRD profiles. It is suggested that sI phases may form more readily from liquid water. Real time PXRD monitoring showed that sI hydrates were less stable than sII crystals, and there was a conversion to the stable phase over time. Both commercial KHIs and AFPs had an impact on hydrate metastability, but transient sI PXRD intensity profiles indicated significantly different modes of interaction with the various inhibitors and the natural gas hydrate system

Single THF hydrate crystals.

<p>Single crystals grown in solutions of THF/water (A) and 200 µg/ml GFP (B) show no major changes in morphology. Crystals grown in solutions containing 200 µg/ml (30 µM) Type III AFP-GFP (C), 200 µg/ml (4.9 µM) LpAFP-GFP (D) and 15 µg/ml (2.2 µM) Type III AFP (E) show skeletal growth. Crystals with adsorbed Type III AFP-GFP (100 µg/ml; 3.1 µM) (F) and LpAFP-GFP (100 µg/ml; 2.4 µM) (G) show skeletal growth and fluoresce under UV light. Skeletal crystals were grown in 200 µg/ml (20 µM) PVP (H). Crystals (A–H) were grown at 3°C. Control crystals grown in THF/water at high driving force (0°C) show skeletal growth (I). All experiments were done in triplicate and have 4.5–5 cm crystal diameters.</p

IgM from BALB/c mice enhances germinal center responses.

<p>On day 0, BALB/c mice were immunized i.v. with WT or Cµ13 IgM specific for KLH (50 µg/mouse) or SRBC (0.2 ml of a solution with HA titer 1:32) 30 min before 10 µg KLH (A), 5×10⁵ (B) or 5×10⁶ SRBC (C) were administered via the same route; controls received antigens or specific IgM alone. Spleens were harvested on day 10. Splenocytes from half of each spleen were analyzed by flow cytometry; germinal center B cells were gated as GL7⁺PNA⁺ amongst B220⁺ cells (Figure S1) and the percentages of germinal center B cells were quantified (A-C, upper left panels). The other halves of the spleens were sectioned, stained with anti-B220 (blue), anti-MOMA (green) and PNA (red), and analyzed for number of PNA⁺ germinal centers in B cell follicles by confocal microscopy (A-C, upper right panels); each image is a representative area (1725 µm × 1295 µm) for 2-3 whole sections with original magnification ×10 (A-C, lower panels). Germinal center responses of mice immunized with specific IgM alone were always lower than the responses of mice immunized with antigens alone (not shown). Data are representative of two experiments with each antigen dose. ns = not significant; * = p < 0.05; ** = p < 0.01.</p

IgM from BALB/c and Cμ13 bind equally well to FcμR.

<p>BW5147 cells expressing mFcμR-IRES-GFP (right panel) or GFP alone (middle panel), as well as virus-nontransduced BW5147 (left panel) cells were analyzed for binding to SRBC-specific WT IgM (red) or Cμ13 IgM (blue) antibodies. The unstained BW5147 (black) and BW5147 stained with biotinylated anti-IgM and SA-PE (grey) are shown as controls.</p

Purification of recombinant proteins.

<p>Typical 12% SDS-PAGE analysis of recombinant His-tagged bioreactor-produced proteins including LpAFP-GFP (A), Type III AFP-GFP (B), GFP (C) and Type III AFP (D), purified using Co²⁺-agarose affinity chromatography. Average TH values are shown below.</p

Levels of AFP adsorbed into THF hydrate.

<p>Differences in the average µmoles of protein adsorbed per gram of THF hydrate crystal (µmoles/g-crystal) between LpAFP-GFP (horizontal lines), Type III AFP-GFP (vertical lines) and GFP (solid) are plotted as a function of protein concentration (µM). Bars indicate standard deviation. Statistical significance between each data group is indicated by letters A–C, where identical letters indicate no statistical difference.</p

IgM from Cμ13 mice cannot enhance antibody responses.

<p>BALB/c mice were immunized i.v. with WT or Cµ13 IgM anti-KLH (50 µg/mouse) or anti-SRBC (0.2 ml of a solution with HA titer 1:8). Thirty minutes later, 10 µg KLH, 5×10⁵ or 5×10⁶ SRBC were administered. Mice immunized with only antigen or IgM were used as controls. All groups were bled at indicated time points and sera were screened for IgG anti-KLH (A) or IgG anti-SRBC (B, C). Antibody responses of mice immunized with specific IgM only were much lower than that of mice immunized with antigens alone (data not shown). Data represent three (A, B) or two (C) experiments. Statistical comparison is shown between mice given antigen alone and mice given antigen together with WT IgM (above) or Cµ13 IgM (below). ns = not significant; * = p < 0.05; ** = p < 0.01; *** = p < 0.001.</p

Adsorption of AFPs on THF hydrate.

<p>Representative THF hydrate polycrystals fluoresce green under UV light after being grown in solutions containing Type III AFP-GFP (left) and LpAFP-GFP (center). THF hydrate crystals grown in GFP control solutions (right) displayed no fluorescence. Sample diameters were 3–3.5 cm.</p

<i>Bifidobacterium longum</i> Alleviates Dextran Sulfate Sodium-Induced Colitis by Suppressing IL-17A Response: Involvement of Intestinal Epithelial Costimulatory Molecules

<div><p>Although some bacterial strains show potential to prevent colitis, their mechanisms are not fully understood. Here, we investigated the anti-colitic mechanisms of <i>Bifidobacterium longum</i> subsp. <i>infantis</i> JCM 1222^T, focusing on the relationship between interleukin (IL)-17A secreting CD4⁺ T cells and intestinal epithelial costimulatory molecules in mice. Oral administration of JCM 1222^T to mice alleviated dextran sulfate sodium (DSS)-induced acute colitis. The expression of type 1 helper T (Th1)- and IL-17 producing helper T (Th17)-specific cytokines and transcriptional factors was suppressed by JCM 1222^T treatment. Intestinal epithelial cells (IECs) from colitic mice induced IL-17A production from CD4⁺ T cells in a cell-cell contact-dependent manner, and this was suppressed by oral treatment with JCM 1222^T. Using blocking antibodies for costimulatory molecules, we revealed that epithelial costimulatory molecules including CD80 and CD40, which were highly expressed in IECs from colitic mice, were involved in IEC-induced IL-17A response. Treatment of mice and intestinal epithelial cell line Colon-26 cells with JCM 1222^T decreased the expression of CD80 and CD40. Collectively, these data indicate that JCM 1222^T negatively regulate epithelial costimulatory molecules, and this effect might be attributed, at least in part, to suppression of IL-17A in DSS-induced colitis.</p> </div