Descriptive Anatomy and Three-Dimensional Reconstruction of the Skull of the Early Tetrapod Acanthostega gunnari Jarvik, 1952

The early tetrapod Acanthostega gunnari is an iconic fossil taxon exhibiting skeletal morphology reflecting the transition of vertebrates from water onto land. Computed tomography data of two Acanthostega skulls was segmented using visualization software to digitally separate bone from matrix and individual bones of the skull from each other. A revised description of cranial and lower jaw anatomy in this taxon based on CT data includes new details of sutural morphology, the previously undescribed quadrate and articular bones, and the mandibular symphysis. Sutural morphology is used to infer loading regime in the skull during feeding, and suggests Acanthostega used its anterior jaws to initially seize prey while smaller posterior teeth were used to restrain struggling prey during ingestion. Novel methods were used to repair and retrodeform the skull, resulting in a three-dimensional digital reconstruction that features a longer postorbital region and more strongly hooked anterior lower jaw than previous attempts while supporting the presence of a midline gap between the nasals and median rostrals

Inhibition of prostate cancer cell growth by human secreted PDZ domain-containing protein 2, a potential autocrine prostate tumor suppressor

A possible role of the PDZ domain-containing protein 2 (PDZD2) in prostate tumorigenesis has been suggested. Besides, PDZD2 is posttranslationally cleaved by a caspase-dependent mechanism to form a secreted PDZ domain-containing protein 2 (sPDZD2) with unknown functions in humans. In this study, we demonstrate the endogenous expression of PDZD2 and secretion of sPDZD2 in cancerous DU145, PC-3, 22Rv1, LNCaP, and immortalized RWPE-1 prostate epithelial cells. Inhibition of endogenous sPDZD2 production and secretion by DU145, PC-3, 22Rv1, and RWPE-1 cells via the caspase-3 inhibitor Z-DEVD-FMK resulted in increased cell proliferation, which was abrogated by treatment with exogenous recombinant sPDZD2. Whereas sPDZD2-induced antiproliferation in DU145, PC-3, and 22Rv1 cells, it induced apoptosis in LNCaP cells. The data suggest that endogenous sPDZD2, produced by caspase-3-mediated cleavage from PDZD2, may function as a novel autocrine growth suppressor for human prostate cancer cells. The antiproliferative effect of sPDZD2 was apparently mediated through slowing the entry of DU145, PC-3, and 22Rv1 cells into the S phase of the cell cycle. In DU145 cells, this can be attributed to stimulated p53 and p21 CIP1/WAF1 expression by sPDZD2. On the other hand, the apoptotic effect of sPDZD2 on LNCaP cells was apparently mediated via p53-independent Bad stimulation. Together our results indicate the presence of p53-dependent and p53-independent PDZD2/sPDZD2 autocrine growth suppressive signaling pathways in human prostate cancer cells and suggest a novel therapeutic approach of harnessing the latent tumor-suppressive potential of an endogenous autocrine signaling protein like sPDZD2 to inhibit prostate cancer growth. Copyright © 2006 by The Endocrine Society.postprin

Non-Negative Local Sparse Coding for Subspace Clustering

Subspace sparse coding (SSC) algorithms have proven to be beneficial to clustering problems. They provide an alternative data representation in which the underlying structure of the clusters can be better captured. However, most of the research in this area is mainly focused on enhancing the sparse coding part of the problem. In contrast, we introduce a novel objective term in our proposed SSC framework which focuses on the separability of data points in the coding space. We also provide mathematical insights into how this local-separability term improves the clustering result of the SSC framework. Our proposed non-linear local SSC algorithm (NLSSC) also benefits from the efficient choice of its sparsity terms and constraints. The NLSSC algorithm is also formulated in the kernel-based framework (NLKSSC) which can represent the nonlinear structure of data. In addition, we address the possibility of having redundancies in sparse coding results and its negative effect on graph-based clustering problems. We introduce the link-restore post-processing step to improve the representation graph of non-negative SSC algorithms such as ours. Empirical evaluations on well-known clustering benchmarks show that our proposed NLSSC framework results in better clusterings compared to the state-of-the-art baselines and demonstrate the effectiveness of the link-restore post-processing in improving the clustering accuracy via correcting the broken links of the representation graph.Comment: 15 pages, IDA 2018 conferenc

Flavor SU(3) symmetry and QCD factorization in B→PPB \to PP and PVPV decays

Using flavor SU(3) symmetry, we perform a model-independent analysis of charmless $\bar B_{u,d} (\bar B_s) \to PP, ~PV$ decays. All the relevant topological diagrams, including the presumably subleading diagrams, such as the QCD- and EW-penguin exchange diagrams and flavor-singlet weak annihilation ones, are introduced. Indeed, the QCD-penguin exchange diagram turns out to be important in understanding the data for penguin-dominated decay modes. In this work we make efforts to bridge the (model-independent but less quantitative) topological diagram or flavor SU(3) approach and the (quantitative but somewhat model-dependent) QCD factorization (QCDF) approach in these decays, by explicitly showing how to translate each flavor SU(3) amplitude into the corresponding terms in the QCDF framework. After estimating each flavor SU(3) amplitude numerically using QCDF, we discuss various physical consequences, including SU(3) breaking effects and some useful SU(3) relations among decay amplitudes of $\bar B_s \to PV$ and $\bar B_d \to PV$.Comment: 47 pages, 3 figures, 28 table

C-terminal truncated hepatitis B virus X protein promotes hepatocellular carcinogenesis through induction of cancer and stem cell-like properties

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In‐situ microbially induced Ca2+‐alginate polymeric sealant for seepage control in porous materials

This paper presents a novel approach of using in-situ microbially induced Ca2+-alginate polymeric sealant for seepage control in porous materials. This process comprises two steps: (i) generation of insoluble calcium carbonate inside the pores of porous materials (such as sand) through a microbially induced carbonate precipitation (MICP) process in-situ and (ii) injection of sodium alginate for in-situ gelation via reaction between alginate and Ca2+ions. The experimental results showed that the hydraulic conductivity/permeability of sand decreased with the increase in alginate concentration. When 5% alginate was used with a CaCO3concentration of 0.18 g g-1sand, the permeability of the alginate-treated sand reduced from 5.0 × 10-4to 2.2 × 10-9 m s-1. The scanning electron microscopy images revealed that a film-type coating was formed around sand particles with spherical round crystals embedded. Furthermore, the in-situ formed Ca-alginate polymeric sealant can also be used for the removal of Cu2+ion and suspended particles from contaminated water by more than 90%. Built on the current research, the envisioned practical application of the proposed method may include clogging fractured rock, reducing seepage and prevent piping through dams, excavation dewatering, and forming barriers for remediating specific contaminants

A Schwarz lemma for K\"ahler affine metrics and the canonical potential of a proper convex cone

This is an account of some aspects of the geometry of K\"ahler affine metrics based on considering them as smooth metric measure spaces and applying the comparison geometry of Bakry-Emery Ricci tensors. Such techniques yield a version for K\"ahler affine metrics of Yau's Schwarz lemma for volume forms. By a theorem of Cheng and Yau there is a canonical K\"ahler affine Einstein metric on a proper convex domain, and the Schwarz lemma gives a direct proof of its uniqueness up to homothety. The potential for this metric is a function canonically associated to the cone, characterized by the property that its level sets are hyperbolic affine spheres foliating the cone. It is shown that for an $n$-dimensional cone a rescaling of the canonical potential is an $n$-normal barrier function in the sense of interior point methods for conic programming. It is explained also how to construct from the canonical potential Monge-Amp\`ere metrics of both Riemannian and Lorentzian signatures, and a mean curvature zero conical Lagrangian submanifold of the flat para-K\"ahler space.Comment: Minor corrections. References adde

Surface Percolation for Soil Improvement by Biocementation Utilizing In Situ Enriched Indigenous Aerobic and Anaerobic Ureolytic Soil Microorganisms

The use of biocementation via microbially induced carbonate precipitation (MICP) for improving the mechanical properties of weak soils in the laboratory has gained increased attention in recent years. This study proposes an approach for applying biocementation in situ, by combining the surface percolation of nutrients and cementation solution (urea/CaCl2) with in situ cultivation of indigenous soil urease positive microorganisms under non-sterile conditions. The enrichment of indigenous ureolytic soil bacteria was firstly tested in batch reactors. Using selective conditions (i.e., pH of 10 and urea concentrations of 0.17 M), highly active ureolytic microorganisms were enriched from four diverse soil samples under both oxygen-limited (anoxic) and oxygen-free (strictly anaerobic) conditions, providing final urease activities of more than 10 and 5 U/mL, respectively. The enrichment of indigenous ureolytic soil microorganisms was secondly tested in pure silica sand columns (300 and 1000 mm) for biocementation applications using the surface percolation approach. By applying the same selective conditions, the indigenous ureolytic soil microorganisms with high urease activity were also successfully enriched for both the fine and coarse sand columns. However, the in situ enriched urease activity was highly related to the dissolved oxygen of the percolated growth medium. The results showed that the in situ cultivated urease activity may produce non-clogging cementation over the entire 1000-mm columns, with unconfined compressive strength varying between 850–1560 kPa (for coarse sand) and 150–700 kPa (for fine sand), after 10 subsequent applications of cementation solution. The typically observed loss of ureolytic activity during the repeated application of the cementation solution was recovered by providing more growth medium under selective enrichment conditions, enabling the in situ enriched ureolytic microorganisms to increase in numbers and urease activity in such a way that continued cementation was possible