Inversion using a new low-dimensional representation of complex binary geological media based on a deep neural network

Efficient and high-fidelity prior sampling and inversion for complex geological media is still a largely unsolved challenge. Here, we use a deep neural network of the variational autoencoder type to construct a parametric low-dimensional base model parameterization of complex binary geological media. For inversion purposes, it has the attractive feature that random draws from an uncorrelated standard normal distribution yield model realizations with spatial characteristics that are in agreement with the training set. In comparison with the most commonly used parametric representations in probabilistic inversion, we find that our dimensionality reduction (DR) approach outperforms principle component analysis (PCA), optimization-PCA (OPCA) and discrete cosine transform (DCT) DR techniques for unconditional geostatistical simulation of a channelized prior model. For the considered examples, important compression ratios (200 - 500) are achieved. Given that the construction of our parameterization requires a training set of several tens of thousands of prior model realizations, our DR approach is more suited for probabilistic (or deterministic) inversion than for unconditional (or point-conditioned) geostatistical simulation. Probabilistic inversions of 2D steady-state and 3D transient hydraulic tomography data are used to demonstrate the DR-based inversion. For the 2D case study, the performance is superior compared to current state-of-the-art multiple-point statistics inversion by sequential geostatistical resampling (SGR). Inversion results for the 3D application are also encouraging

Isoprene Polymerization with Iminophosphonamide Rare-Earth-Metal Alkyl Complexes: Influence of Metal Size on the Regio- and Stereoselectivity

The protonolysis reaction of β-iminophosphonamine ligand (NPN^dipp = Ph₂P­(NC₆H₃^<i>i</i>Pr₂-2,6)₂) with one equivalent of rare-earth-metal tris­(alkyl)­s afforded the corresponding bis­(alkyl) complexes NPN^dippLn­(CH₂SiMe₃)₂(THF) (Ln = Sc (<b>1</b>), Lu (<b>2</b>), Y (<b>3</b>), Er (<b>4</b>)). The bis­(4-methylbenzyl) complexes NPN^dippLn­(CH₂Ph-4-Me)₂(THF) (Ln = Nd (<b>5</b>), La (<b>6</b>)) were prepared by treatment of the tris­(4-methylbenzyl) compounds Ln­(CH₂Ph-4-Me)₃(THF)₃ with β-iminophosphonamine ligand. The small-size rare-earth-metal-based complexes <b>1</b>–<b>4</b> upon activation with Al^<i>i</i>Bu₃ and [Ph₃C]­[B­(C₆F₅)₄] showed high 3,4-selectivities up to 98.1% for isoprene polymerization. When the larger size rare-earth-metal-based 4-methylbenzyl complexes <b>5</b> and <b>6</b> were employed instead, moderate 3,4-selectivities were obtained since the opening coordination environment facilitated the 1,4-enchainment (Nd³⁺: 76.1%; La³⁺: 62.9%). Replacing Al^<i>i</i>Bu₃ by AlEt₃, the <b>5</b> and <b>6</b> systems exhibited high activity and excellent <i>trans</i>-1,4 selectivity for both isoprene (96.5%, 0 °C) and butadiene (92.8%, 20 °C) polymerizations

CD8β mRNA is absent in purified liver cCD8α⁺DC.

<p>HMNC were pooled from livers of <i>Pb</i>γ-spz-fully immunized mice 6 days after the 3° immunization and were incubated with a cocktail of biotinylated microbeads to deplete T cells, B cells, NK cells, granulocytes and macrophages as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005075#s4" target="_blank">Materials and Methods</a>. cCD8α⁺DC were further isolated from the enriched CD11c⁺NK1.1⁻ population by positive magnetic selection as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005075#s4" target="_blank">Materials and Methods</a>. Staining with anti-CD8α, CD3, CD8b and CD11c was performed on permeabilized cells to reveal both the surface and the intracellular presence of these markers. (A) Dot plot show the relative % of T cells (red) and cCD8α⁺DC (blue) within the purified cCD8α⁺DC population. (B) Two-step quantitative real-time PCR was performed on RNA isolated from magnetic-bead purified liver cCD8α⁺DC (described in A). Ratio of CD8β/CD8α gene expression was calculated using standard curves for each gene. Measurements were done in duplicates in wells containing 1000, 1, 0.1 cells/well, or non-template control (NTC). Representative results of one out of two experiments are shown. (C) Histogram plots show expression of DEC 205, I-A^b and costimulatory molecules on the cCD8α⁺DC population (black lines). Grey lines represent staining of the isotype controls.</p

CD11c⁺NK1.1⁻ DC are constitutively present in the spleens of naïve mice but do not substantially increase following immunization.

<p>(A) CD11c⁺NK1.1⁻DC in <i>Pb</i>γ−spz-immune splenic MNC were identified according to the procedure described for HMNC in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005075#pone-0005075-g001" target="_blank">Fig 1</a>. After exclusion of T cells, CD11c⁺ cells were segregated into CD11c⁺NK1.1⁺ and CD11c⁺NK1.1⁻ populations. Splenic mononuclear cells were isolated from individual mice before and after prime and boost immunizations with <i>Pb</i>γ−spz or uninfected mosquito debris (sham). Cells were stained with a cocktail of mAbs and NK1.1⁻ DC and CD8⁺ T_EM cells were identified by flow cytometry. (B) Panels show representative contour plots of DC in the spleens of naïve mice and in spleens of mice 6 days after either the 1°, 2° and 3° immunizations and in sham-immunized mice 6 days after the 3° immunization. The percentages of the CD11c⁺NK1.1⁻ DC in relation to the total SMNC/spleen for each representative mouse are indicated in each panel. (C) The results show the mean percentage ±SD of CD11c⁺NK1.1⁻ DC in total spleens of naïve mice, <i>Pb</i> γ−spz-immunized mice at day 6 after each immunization and in sham-immunized mice at day 6 after the 3° immunization. (D) Panels show representative contour plots of CD8⁺ T_CM cells and CD8⁺ T_EM cells in the spleens of naïve mice as well as of <i>Pb</i> γ−spz-immunized mice and sham-immunized mice at the same time-points described in (B). The numbers indicate the percentages of the T_CM and T_EM cells in the gated splenic CD3⁺CD8⁺ T cell population. (E) The results show the mean percentage ±SD of CD8⁺T_EM in the gated splenic CD3⁺CD8⁺ T cell population of naïve and immunized mice at day 6 after each immunization. Contour plots and bar graphs are representative of three individual mice per group in three independent experiments.</p

Hepatic cCD8α⁺ DC from <i>Pb</i>γ-spz-immunized and challenged mice mediate <i>in vitro</i> activation of naïve CD8⁺ T cells.

<p>HMNC were pooled from livers of <i>Pb</i>γ-spz-fully immunized and challenged mice (n = 18) and were incubated with a cocktail of biotinylated microbeads to deplete T cells, B cells, NK cells, granulocytes and macrophages as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005075#s4" target="_blank">Materials and Methods</a>. DC subpopulations were further isolated from the enriched CD11c⁺NK1.1⁻ population by positive magnetic selection for cCD8α⁺DC and pDC and by negative selection for CD8α⁻DC, as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005075#s4" target="_blank">Materials and Methods</a>. (A) Dot plots show the relative % of T cells and NK1.1 cells within the purified cCD8α⁺DC population. (B) CD8⁺ T cells were isolated from the spleens of naïve mice using magnetic beads and labeled with 2 µM CFSE. Dot plots show the gating scheme for the analysis of CFSE-labeled CD3⁺CD8⁺T cells for expression of the CD45RB^loCD44^hi phenotype. (C) cCD8α⁺ DC, cCD8α⁻ DC and pDC were purified from CD11c⁺NK1.1⁻ DC isolated from pooled livers 3 days after the challenge of <i>Pb</i>γ-spz-immunized mice. Liver DC subpopulations and CFSE-labeled splenic CD8⁺ T cells were co-cultured at a ratio of 1 DC : 2 CD8⁺T cells for 4 days. Cells were harvested, stained with a cocktail of mAbs and the % of CD3⁺CD8⁺CD45RB^loCD44^hi cells (CD8⁺ T_EM) was analyzed by flow cytometry. Results show contour plots of CD8⁺T cells co-cultured with cDC and pDC subpopulations. (D) Bar graphs show the percentage of CD8⁺ T_EM in the gated CD3⁺CD8⁺ T cell population after co-culture with cCD8α⁺ DC, cCD8α⁻ DC and pDC each isolated from <i>Pb</i>γ-spz-immunized-challenged mice.</p

Numbers of splenic CD11c⁺NK1.1⁻ DC and cCD8α⁺DC in naïve and <i>Pb</i>γ-spz-immunized mice^a

a<p>SMNC were isolated from individual C57BL/6 mice before and after prime and boost immunizations with <i>Pb</i> γ−spz. Cells were stained with a cocktail of mAbs for identification of CD11c⁺NK1.1⁻ DC and cCD8α⁺DC as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005075#s4" target="_blank">Materials and Methods</a> and analyzed by flow cytometry. Data represent the mean±SD of the number of cells of three mice per group and are representative of three independent experiments.</p

Liver CD11c⁺NK1.1⁻ cells from <i>Pb</i>γ-spz-immunized mice induce protection against infectious sporozoites.

<p>(A) 1×10⁶ CD11c⁺NK1.1⁻ cells, isolated from the livers of <i>Pb</i>γ-spz-fully-immunized mice 6 days after the 3° immunization, were adoptively transferred (i.v.) into naïve recipients. Seven days later the adoptively transferred recipients (n = 3) as well as naïve infectivity control mice (n = 3) were challenged with 10K infectious sporozoites. The results show the level of parasitemia assessed in each individual mouse and expressed as the mean of parasitemia per mice/group at 4, 7 and 10 days following challenge. (B) 1×10⁶ hepatic CD11c⁺NK1.1⁻ cells, purified as described in (A) were isolated from <i>Pb</i>γ-spz-immunized-challenged mice and from naïve-challenged mice and adoptively transferred into naïve syngeneic recipients (n = 13) that were challenged 7 days later with either 250 (n = 6) or 1000 (n = 7) infectious sporozoites. The protected group (250 sporozoites) were re-challenged 60 days later along with another group of naïve infectivity control mice (n = 3). <i>Pb</i> γ-spz-immunized mice (n = 3), used as positive controls, were sterily protected at challenge and re-challenge. Parasitemia and survival were evaluated from day 2 post-challenge.</p

Liver cCD8α⁺ DC are more efficient than splenic cCD8α⁺ DC in inducing differentiation of and IFN-γ production by CD8⁺ T cells.

<p>Differentiation and induction of CD8⁺ T cell function is MHC class I- and IL-12 dependent. HMNC or splenic MNC were prepared after the 3° immunization as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005075#pone-0005075-g003" target="_blank">Fig. 3</a>. CD8α⁺ DC were purified as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005075#pone-0005075-g001" target="_blank">Figs 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005075#pone-0005075-g003" target="_blank">3</a>. Splenic (A and C) or hepatic (B and D) cCD8α⁺ DC were co-cultured for 4 days either alone or with purified CD8⁺ T cells from the livers (open bars) or spleen (filled bars) of naïve mice. Cells were harvested, stained with the appropriate mAb and analyzed by flow cytometry. Culture supernatants were analyzed for IFNγ by ELISA. (A and B) Results show the mean % of CD8⁺ T_EM in the gated CD3⁺CD8⁺ T cell population and (C and D) the amount of IFNγ in the culture supernatant. Data are representative of two individual experiments. (E and F) Liver cCD8α⁺ DC were co-cultured with naïve splenic CD8⁺ T cells in the presence or absence of anti-IL-12 (clone C17.1) and/or anti-MHC class I (clone 28-8-6) mAbs for 4 days. (E) Results show the mean % of CD8⁺ T_EM in the gated CD3⁺CD8⁺ T cell population and (F).the amount of IFNγ. Data is representative of two individual experiments.</p

Numbers of hepatic CD11c⁺NK1.1⁻ DC and cCD8α⁺DC in naïve and <i>Pb</i>γ-spz-immunized mice^a

a<p>IHMNC were isolated from individual C57BL/6 mice before and after prime and boost immunizations with <i>Pb</i> γ−spz. Cells were stained with a cocktail of mAbs for identification of CD11c⁺NK1.1⁻ DC and cCD8α⁺DC as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005075#s4" target="_blank">Materials and Methods</a> and analyzed by flow cytometry. Data represent the mean±SD of the number of cells of three mice per group and are representative of three independent experiments.</p

cCD8α⁺ DC, relatively absent in the livers of naïve mice, are induced after prime-boost immunizations with <i>Pb</i>γ-spz.

<p>(A) Hepatic CD11c⁺NK1.1⁻ DC (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005075#pone-0005075-g001" target="_blank">Fig. 1</a>) were stained with Abs specific for B220 and CD8α and analyzed by flow cytometry to reveal 3 subpopulations of DC . (B) HMNC isolated from livers of <i>Pb</i>γ-spz-fully immunized mice 6 days after the 3° immunization were incubated with a cocktail of biotinylated microbeads to deplete T cells, B cells, NK cells, granulocytes and macrophages as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005075#s4" target="_blank">Materials and Methods</a>. DC subpopulations were further isolated from the enriched CD11c⁺NK1.1⁻ population by positive magnetic selection for cCD8α⁺DC and pDC and by negative selection for CD8α⁻DC, as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005075#s4" target="_blank">Materials and Methods</a>. Panels show photographs at 100× of Giemsa stained cytospins of cCD8α⁺DC, cCD8α⁻DC and pDC. (C and E) HMNC and (D and F) splenic MNC were isolated from individual naïve mice and from individual mice at 6 days after 1°, 2° and 3° immunizations with <i>Pb</i> γ−spz and after 3° immunizations with uninfected mosquito debris (sham). Cells were stained with a cocktail of mAbs for identification of DC subpopulations as described in (A). Bar graphs show the mean % ± SD of the cCD8α⁺DC (C and D) and cCD8α⁻DC (E and F) in the gated CD11c⁺NK1.1⁻ cells. Data are representative of three individual mice per group at each time-point in two independent experiments.</p