Bone sialoprotein-collagen interaction promotes hydroxyapatite nucleation.

PubMed

Baht, Gurpreet S; Hunter, Graeme K; Goldberg, Harvey A

2008-09-01

In bone, hydroxyapatite (HA) crystals are deposited onto the type I collagen scaffold by a mechanism that has yet to be elucidated. Bone sialoprotein (BSP) is an acidic phosphoprotein that is expressed at high levels in mineralized tissues, capable of binding type I collagen, and nucleating HA. Both bone-extracted and recombinant BSP (rBSP) bind with equal affinity to collagen. The nature of the BSP-collagen interaction and its role in HA nucleation are not known. We have used a solid-phase binding assay and affinity chromatography to characterize the BSP-collagen interaction. rBSP-binding affinities of triple-helical and fibrillar type I collagen were similar (K(D) approximately 13 nM), while that of heat-denatured type I collagen was lower (K(D) approximately 44 nM), indicating the importance of triple-helical structure in binding BSP. Pepsin treatment of collagen had no effect on rBSP binding, demonstrating that the telopeptides of collagen are not involved. The majority of collagen-bound rBSP was eluted by acetonitrile, indicating that hydrophobic interactions are principally responsible for binding. Using an HA-nucleation assay, it was shown that rBSP is ten-fold more potent in reconstituted fibrillar collagen gels than in agarose gels. Nucleating potency of a non-collagen-binding, HA-nucleating peptide [rBSP(134-206)] showed no difference in the two gel systems. The work here shows that optimal binding of rBSP requires collagen to be in a native, triple-helical structure, does not require the telopeptides, and is stabilized by hydrophobic interactions. Upon binding to collagen, rBSP displays an increase in nucleation potency, implying a co-operative effect of BSP and collagen in mineral formation.

Bone sialoprotein stimulates focal adhesion-related signaling pathways: role in migration and survival of breast and prostate cancer cells.

PubMed

Gordon, Jonathan A R; Sodek, Jaro; Hunter, Graeme K; Goldberg, Harvey A

2009-08-15

Bone sialoprotein (BSP) is a secreted glycoprotein found in mineralized tissues however, BSP is aberrantly expressed in a variety of osteotropic tumors. Elevated BSP expression in breast and prostate primary carcinomas is directly correlated with increased bone metastases and tumor progression. In this study, the intracellular signaling pathways responsible for BSP-induced migration and tumor survival were examined in breast and prostate cancer cells (MDA-MB-231, Hs578T and PC3). Additionally, the effects of exogenous TGF-beta1 and EGF, cytokines associated with tumor metastasis and present in high-levels in the bone microenvironment, were examined in BSP-expressing cancer cells. Expression of BSP but not an integrin-binding mutant (BSP-KAE) in tumor cell lines resulted in increased levels of alpha(v)-containing integrins and number of mature focal adhesions. Adhesion of cells to recombinant BSP or the expression of BSP stimulated focal adhesion kinase and ERK phosphorylation, as well as activated AP-1-family proteins. Activation of these pathways by BSP expression increased the expression of the matrix metalloproteinases MMP-2, MMP-9, and MMP-14. The BSP-mediated activation of the FAK-associated pathway resulted in increased cancer cell invasion in a Matrigel-coated Boyden-chamber assay and increased cell survival upon withdrawal of serum. Addition of EGF or TGF-beta1 to the BSP-expressing cell lines significantly increased ERK phosphorylation, AP-1 activation, MMP-2 expression, cell migration and survival compared to untreated cells expressing BSP. This study thus defines the cooperative mechanisms by which BSP can enhance specific factors associated with a metastatic phenotype in tumor cell lines, an effect that is increased by circulating TGF-beta1 and EGF. (c) 2009 Wiley-Liss, Inc.

Brucella Modulates Secretory Trafficking via Multiple Type IV Secretion Effector Proteins

PubMed Central

Myeni, Sebenzile; Child, Robert; Ng, Tony W.; Kupko, John J.; Wehrly, Tara D.; Porcella, Stephen F.; Knodler, Leigh A.; Celli, Jean

2013-01-01

The intracellular pathogenic bacterium Brucella generates a replicative vacuole (rBCV) derived from the endoplasmic reticulum via subversion of the host cell secretory pathway. rBCV biogenesis requires the expression of the Type IV secretion system (T4SS) VirB, which is thought to translocate effector proteins that modulate membrane trafficking along the endocytic and secretory pathways. To date, only a few T4SS substrates have been identified, whose molecular functions remain unknown. Here, we used an in silico screen to identify putative T4SS effector candidate proteins using criteria such as limited homology in other bacterial genera, the presence of features similar to known VirB T4SS effectors, GC content and presence of eukaryotic-like motifs. Using β-lactamase and CyaA adenylate cyclase reporter assays, we identified eleven proteins translocated into host cells by Brucella, five in a VirB T4SS-dependent manner, namely BAB1_0678 (BspA), BAB1_0712 (BspB), BAB1_0847 (BspC), BAB1_1671 (BspE) and BAB1_1948 (BspF). A subset of the translocated proteins targeted secretory pathway compartments when ectopically expressed in HeLa cells, and the VirB effectors BspA, BspB and BspF inhibited protein secretion. Brucella infection also impaired host protein secretion in a process requiring BspA, BspB and BspF. Single or combined deletions of bspA, bspB and bspF affected Brucella ability to replicate in macrophages and persist in the liver of infected mice. Taken together, these findings demonstrate that Brucella modulates secretory trafficking via multiple T4SS effector proteins that likely act coordinately to promote Brucella pathogenesis. PMID:23950720

In vivo functional analysis of polyglutamic acid domains in recombinant bone sialoprotein.

PubMed

Wazen, Rima M; Tye, Coralee E; Goldberg, Harvey A; Hunter, Graeme K; Smith, Charles E; Nanci, Antonio

2007-01-01

Bone sialoprotein (BSP) is an anionic phosphoprotein expressed in mineralizing connective tissues that binds to hydroxyapatite and nucleates its formation in vitro. Two polyglutamic acid regions (poly [E]) are believed to participate in these activities. The aim of this study was to evaluate the contribution of these acidic regions to the binding of prokaryote recombinant BSP (prBSP(E)) within an actual in vivo environment. Full-length prBSP(E) and prBSP(E) in which the poly [E] domains were replaced by polyalanine (prBSP(A)) were tagged with dinitrophenol (DNP). Tagged preparations comprised intact molecules and some fragmented forms. They were infused through a surgically created hole in the bone of rat hemimandibles and detected using immunogold labeling with anti-DNP antibodies. prBSP(E)-DNP was consistently immunodetected along exposed mineralized bone surfaces and osteocyte canaliculi at the surgical site. Few gold particles were observed on these surfaces when prBSP(A)-DNP was infused. Quantitative analyses showed significant differences in labeling between prBSP(E)-DNP (5.04 +/- 0.73 particles/micro m2) and prBSP(A)-DNP (1.37 +/- 0.35 particles/micro m2). These results indicate that poly [E] domains influence binding of prBSP(E) to surfaces presenting a mixture of mineral and proteins bathed by tissue fluids and suggest that they may similarly mediate the interaction of native BSP in the bone environment.

Efficient Boundary Extraction of BSP Solids Based on Clipping Operations.

PubMed

Wang, Charlie C L; Manocha, Dinesh

2013-01-01

We present an efficient algorithm to extract the manifold surface that approximates the boundary of a solid represented by a Binary Space Partition (BSP) tree. Our polygonization algorithm repeatedly performs clipping operations on volumetric cells that correspond to a spatial convex partition and computes the boundary by traversing the connected cells. We use point-based representations along with finite-precision arithmetic to improve the efficiency and generate the B-rep approximation of a BSP solid. The core of our polygonization method is a novel clipping algorithm that uses a set of logical operations to make it resistant to degeneracies resulting from limited precision of floating-point arithmetic. The overall BSP to B-rep conversion algorithm can accurately generate boundaries with sharp and small features, and is faster than prior methods. At the end of this paper, we use this algorithm for a few geometric processing applications including Boolean operations, model repair, and mesh reconstruction.

Transcriptional regulation of bone sialoprotein gene expression by Osx.

PubMed

Yang, Ya; Huang, Yehong; Zhang, Li; Zhang, Chi

2016-08-05

Osteoporosis is the most common metabolic bone disease characterized by decreased bone mass, decreased bone strength, and increased risk of fracture. It is due to unbalance between bone formation and bone resorption. Bone formation is a complex process which involves the differentiation of mesenchymal stem cells to osteoblasts. Osteoblasts produce a characteristic extracellular collagenous matrix that subsequently becomes mineralized. Osterix (Osx) is an osteoblast-specific transcription factor required for osteoblast differentiation. Bone sialoprotein (Bsp) is a member of the SIBLING gene family. Expression of Bsp correlates with the differentiation of osteoblasts and the onset of mineralization. Our preliminary data showed that Bsp was abolished in Osx-null mice; however, the detailed mechanism of Osx regulation on Bsp is not fully understood. In this study, regulation of Bsp expression by Osx was further characterized. It was shown that overexpression of Osx led to Bsp upregulation. Inhibition of Osx by small interfering RNA resulted in Bsp downregulation in osteoblast. Transfection assay demonstrated that Osx was able to activate Bsp promoter reporter in a dose-dependent manner. To define minimal region of Bsp promoter activated by Osx, a series of deletion mutants of Bsp promoter were generated, and the minimal region was narrowed down to the proximal 100 bp. Point-mutagenesis studies showed that one GC-rich site was required for Bsp promoter activation by Osx. ChIP assays demonstrated that endogenous Osx associated with native Bsp promoter in primary osteoblasts. Our observations provide evidence that Osx targets Bsp expression directly. Copyright © 2016 Elsevier Inc. All rights reserved.

Milk proteins interact with goat Binder of SPerm (BSP) proteins and decrease their binding to sperm.

PubMed

de Menezes, Erika Bezerra; van Tilburg, Mauricio; Plante, Geneviève; de Oliveira, Rodrigo V; Moura, Arlindo A; Manjunath, Puttaswamy

2016-11-01

Seminal plasma Binder of SPerm (BSP) proteins bind to sperm at ejaculation and promote capacitation. When in excess, however, BSP proteins damage the sperm membrane. It has been suggested that milk components of semen extenders associate with BSP proteins, potentially protecting sperm. Thus, this study was conducted to investigate if milk proteins interact with BSP proteins and reduce BSP binding to goat sperm. Using gel filtration chromatography, milk was incubated with goat seminal plasma proteins and loaded onto columns with and without calcium. Milk was also fractionated into parts containing mostly whey proteins or mostly caseins, incubated with seminal plasma proteins and subjected to gel filtration. Eluted fractions were evaluated by immunoblot using anti-goat BSP antibodies, confirming milk protein-BSP protein interactions. As determined by ELISA, milk proteins coated on polystyrene wells bound to increasing of goat BSP proteins. Far-western dot blots confirmed that BSP proteins bound to caseins and β-lactoglobulin in a concentration-dependent manner. Then, cauda epididymal sperm from five goats was incubated with seminal plasma; seminal plasma followed by milk; and milk followed by seminal plasma. Sperm membrane proteins were extracted and evaluated by immunoblotting. The pattern of BSP binding to sperm membrane proteins was reduced by 59.3 % when epididymal sperm were incubated with seminal plasma and then with skimmed milk (p < 0.05). When epididymal sperm were treated with milk followed by seminal plasma, coating of sperm with BSP proteins was not significantly reduced (57.6 %; p > 0.05). In conclusion, goat BSP proteins have an affinity for caseins and whey proteins. Milk reduces BSP binding to goat sperm, depending whether or not sperm had been previously exposed to seminal plasma. Such events may explain the protective effect of milk during goat sperm preservation.

Predictive significance of bone sialoprotein and osteopontin for bone metastases in resected Chinese non-small-cell lung cancer patients: a large cohort retrospective study.

PubMed

Zhang, Li; Hou, Xue; Lu, Shun; Rao, Huilan; Hou, Jinghui; Luo, Rongzhen; Huang, He; Zhao, Hongyun; Jian, Hong; Chen, Zhiwei; Liao, Meilin; Wang, Xin

2010-01-01

Bone is one of the most common sites of metastasis in patients with non-small-cell lung cancer (NSCLC). Over-expression of bone sialoprotein (BSP) and osteopontin (OPN) in tumour samples has shown prognostic significance in bone metastasis (BM) of breast and prostate cancer, respectively. However, their importance in BM of NSCLC has not been verified. Therefore, we planned a large cohort retrospective study to investigate the relationship between the expression of these two biomarkers (BSP and OPN) and BM in surgically resected NSCLC patients. 180 completely resected NSCLC patients were included in this study. 40 patients subsequently developed BM. Paraffin-embedded primary tumour tissues of patients were supplied to produce a tissue microarray, and immunohistochemistry method was used for evaluation of the expression of BSP and OPN. Different expressions of these two biomarkers among BM group and non-BM group were estimated by chi(2) test. BM-free survival was analyzed by Kaplan-Meier method. The prognostic impact of clinicopathologic variables and biomarker expression was evaluated by Cox proportional hazards model. BSP expression was associated with BM (p=0.007), whereas OPN expression did not reach statistical significance (p=0.245). Univariate analysis showed that expression of BSP (p=0.010) and N staging (p<0.005) was associated with BM-free survival. Multivariate analyses showed BSP expression (HR=3.322, p=0.003), N staging (HR=1.879, p=0.001), and T staging (HR=1.618, p=0.024) were independent prognostic factors for BM. BSP protein expression in the primary resected NSCLC is strongly associated with BM and could be used to identify high-risk patients. Correlation of OPN protein expression and BM needs further investigation.

Trichomonas vaginalis vast BspA-like gene family: evidence for functional diversity from structural organisation and transcriptomics

PubMed Central

2010-01-01

Background Trichomonas vaginalis is the most common non-viral human sexually transmitted pathogen and importantly, contributes to facilitating the spread of HIV. Yet very little is known about its surface and secreted proteins mediating interactions with, and permitting the invasion and colonisation of, the host mucosa. Initial annotations of T. vaginalis genome identified a plethora of candidate extracellular proteins. Results Data mining of the T. vaginalis genome identified 911 BspA-like entries (TvBspA) sharing TpLRR-like leucine-rich repeats, which represent the largest gene family encoding potential extracellular proteins for the pathogen. A broad range of microorganisms encoding BspA-like proteins was identified and these are mainly known to live on mucosal surfaces, among these T. vaginalis is endowed with the largest gene family. Over 190 TvBspA proteins with inferred transmembrane domains were characterised by a considerable structural diversity between their TpLRR and other types of repetitive sequences and two subfamilies possessed distinct classic sorting signal motifs for endocytosis. One TvBspA subfamily also shared a glycine-rich protein domain with proteins from Clostridium difficile pathogenic strains and C. difficile phages. Consistent with the hypothesis that TvBspA protein structural diversity implies diverse roles, we demonstrated for several TvBspA genes differential expression at the transcript level in different growth conditions. Identified variants of repetitive segments between several TvBspA paralogues and orthologues from two clinical isolates were also consistent with TpLRR and other repetitive sequences to be functionally important. For one TvBspA protein cell surface expression and antibody responses by both female and male T. vaginalis infected patients were also demonstrated. Conclusions The biased mucosal habitat for microbial species encoding BspA-like proteins, the characterisation of a vast structural diversity for the TvBspA proteins, differential expression of a subset of TvBspA genes and the cellular localisation and immunological data for one TvBspA; all point to the importance of the TvBspA proteins to various aspects of T. vaginalis pathobiology at the host-pathogen interface. PMID:20144183

Overlapping functions of bone sialoprotein and pyrophosphate regulators in directing cementogenesis.

PubMed

Ao, M; Chavez, M B; Chu, E Y; Hemstreet, K C; Yin, Y; Yadav, M C; Millán, J L; Fisher, L W; Goldberg, H A; Somerman, M J; Foster, B L

2017-12-01

Although acellular cementum is essential for tooth attachment, factors directing its development and regeneration remain poorly understood. Inorganic pyrophosphate (PP i ), a mineralization inhibitor, is a key regulator of cementum formation: tissue-nonspecific alkaline phosphatase (Alpl/TNAP) null mice (increased PP i ) feature deficient cementum, while progressive ankylosis protein (Ank/ANK) null mice (decreased PP i ) feature increased cementum. Bone sialoprotein (Bsp/BSP) and osteopontin (Spp1/OPN) are multifunctional extracellular matrix components of cementum proposed to have direct and indirect effects on cell activities and mineralization. Studies on dentoalveolar development of Bsp knockout (Bsp -/- ) mice revealed severely reduced acellular cementum, however underlying mechanisms remain unclear. The similarity in defective cementum phenotypes between Bsp -/- mice and Alpl -/- mice (the latter featuring elevated PP i and OPN), prompted us to examine whether BSP is operating by modulating PP i -associated genes. Genetic ablation of Bsp caused a 2-fold increase in circulating PP i , altered mRNA expression of Alpl, Spp1, and Ank, and increased OPN protein in the periodontia. Generation of a Bsp knock-out (KO) cementoblast cell line revealed significantly decreased mineralization capacity, 50% increased PP i in culture media, and increased Spp1 and Ank mRNA expression. While addition of 2μg/ml recombinant BSP altered Spp1, Ank, and Enpp1 expression in cementoblasts, changes resulting from this dose were not dependent on the integrin-binding RGD motif or MAPK/ERK signaling pathway. Decreasing PP i by genetic ablation of Ank on the Bsp -/- mouse background reestablished cementum formation, allowing >3-fold increased acellular cementum volume compared to wild-type (WT). However, deleting Ank did not fully compensate for the absence of BSP. Bsp -/- ; Ank -/- double-deficient mice exhibited mean 20-27% reduced cementum thickness and volume compared to Ank -/- mice. From these data, we conclude that the perturbations in PP i metabolism are not solely driving the cementum pathology in Bsp -/- mice, and that PP i is more potent than BSP as a cementum regulator, as shown by the ability to override loss of BSP by lowering PP i . We propose that BSP and PP i work in concert to direct mineralization in cementum and likely other mineralized tissues. Copyright © 2017 Elsevier Inc. All rights reserved.

Effect of bone sialoprotein on proliferation and osteodifferentiation of human bone marrow-derived mesenchymal stem cells in vitro.

PubMed

Xia, Bing; Wang, Jie; Guo, Lida; Jiang, Zujun

2011-07-01

We performed this study to investigate the effects of recombinant human bone sialoprotein (BSP) on the proliferation and osteodifferentiation of human BMSCs(hBMSCs). The hBMSC cultures were divided into 4 groups: control group, 10(-10) M BSP group (BSP group), osteogenic medium group (10 nM dexamethasone, 10 mM β-glycerophosphate, and 50 mg/L ascorbic acid, OM group) and BSP + OM group (OM plus10(-10) M BSP). Compared with the control group, cell growth of the other three groups slowed down, while fluorescence at the G(0)/G(1) phase increased. After 28 days, in the OM group and the BSP + OM group, the proportion of STRO-1-positive cells decreased by 22.7% and 38.4% and ALP activity increased by 50% and 71.43%, respectively. CD271 mRNA expression decreased while Cbfa1, osteocalcin and osterix mRNA levels increased in the OM and BSP + OM groups, and the mRNA level change was greater in the BSP + OM group. After 28 days, the number of nodules in the BSP + OM group was 112.5% more than that in the OM group, but nodules did not formed in the control or BSP group. We conclude that BSP is capable of inhibiting hBMSCs proliferation and enhancing their osteogenic differentiation and mineralization in the presence of OM. Copyright © 2011 The International Alliance for Biologicals. Published by Elsevier Ltd. All rights reserved.

Effects of bone sialoprotein on pancreatic cancer cell growth, invasion and metastasis.

PubMed

Kayed, Hany; Kleeff, Jörg; Keleg, Shereen; Felix, Klaus; Giese, Thomas; Berger, Martin R; Büchler, Markus W; Friess, Helmut

2007-01-08

Bone sialoprotein (BSP) is an acidic glycoprotein that plays an important role in cancer cell growth, migration and invasion. The expression, localization and possible function of BSP in chronic pancreatitis (CP) and pancreatic ductal adenocarcinoma (PDAC) were analyzed by QRT-PCR, laser capture microdissection, DNA microarray analysis, immunoblotting, radioimmunoassays and immunohistochemistry as well as cell growth, invasion, scattering, and adhesion assays. BSP mRNA was detected in 40.7% of normal, in 80% of CP and in 86.4% of PDAC samples. The median BSP mRNA levels were 6.1 and 0.9copies/microl cDNA in PDAC and CP tissues, respectively, and zero copies/microl cDNA in normal pancreatic tissues. BSP was weakly present in the cytoplasm of islet cells and ductal cells in 20% of normal pancreatic tissues. BSP was localized in the tubular complexes of both CP and PDAC, as well as in pancreatic cancer cells. Five out of 8 pancreatic cancer cell lines expressed BSP mRNA. Recombinant BSP (rBSP) inhibited Capan-1 and SU8686 pancreatic cancer cell growth, with a maximal effect of -46.4+/-12.0% in Capan-1 cells and -45.7+/-14.5% in SU8686 cells. rBSP decreased the invasion of SU8686 cells by -59.1+/-11.2% and of Capan-1 cells by -13.3+/-3.8% (P<0.05), whereas it did not affect scattering or adhesion of both cell lines. In conclusion, endogenous BSP expression levels in pancreatic cancer cells and low to absent BSP expression in the surrounding stromal tissue elements may indirectly act to enhance the proliferation and invasion of pancreatic cancer cells.

Loss of bone sialoprotein leads to impaired endochondral bone development and mineralization.

PubMed

Holm, Erik; Aubin, Jane E; Hunter, Graeme K; Beier, Frank; Goldberg, Harvey A

2015-02-01

Bone sialoprotein (BSP) is an anionic phosphoprotein in the extracellular matrix of mineralized tissues, and a promoter of biomineralization and osteoblast development. Previous studies on the Bsp-deficient mouse (Bsp(-/-)) have demonstrated a significant bone and periodontal tissue phenotype in adulthood. However, the role of BSP during early long bone development is not known. To address this, early endochondral ossification in the Bsp(-/-) mouse was studied. Embryonic day 15.5 (E15.5) wild-type (WT) tibiae showed early stages of ossification that were absent in Bsp(-/-) mice. At E16.5, mineralization had commenced in the Bsp(-/-) mice, but staining for mineral was less intense and more dispersed compared with that in WT controls. Tibiae from Bsp(-/-) mice also demonstrated decreased mineralization and shortened length at postnatal day 0.5 (P0.5) compared to WT bones. There was no detectable difference in the number of tartrate-resistant acid phosphatase-positive foci at P0.5, although the P0.5 Bsp(-/-) tibiae had decreased Vegfα expression compared with WT tissue. Due to the shortened tibiae the growth plates were examined and determined to be of normal overall length. However, the length of the resting zone was increased in P0.5 Bsp(-/-) tibiae whereas that of the proliferative zone was decreased, with no change in the hypertrophic zone length of Bsp(-/-) mice. A reduction in cells positive for Ki-67, an S-phase cell-cycle marker, was noted in the proliferative zone. Decreased numbers of TUNEL-positive hypertrophic chondrocytes were also apparent in the Bsp(-/-) tibial growth plates, suggesting decreased apoptosis. Expression of the osteogenic markers Alp1, Col1a1, Sp7, Runx2, and Bglap was reduced in the endochondral bone of the neonatal Bsp(-/-) compared to WT tibiae. These results suggest that BSP is an important and multifaceted protein that regulates both chondrocyte proliferation and apoptosis as well as transition from cartilage to bone during development of endochondral bone. Copyright © 2014 Elsevier Inc. All rights reserved.

The role of the SIBLING, Bone Sialoprotein in skeletal biology - Contribution of mouse experimental genetics.

PubMed

Bouleftour, Wafa; Juignet, Laura; Bouet, Guenaelle; Granito, Renata Neves; Vanden-Bossche, Arnaud; Laroche, Norbert; Aubin, Jane E; Lafage-Proust, Marie-Hélène; Vico, Laurence; Malaval, Luc

2016-01-01

Bone Sialoprotein (BSP) is a member of the "Small Integrin-Binding Ligand N-linked Glycoproteins" (SIBLING) extracellular matrix protein family of mineralized tissues. BSP has been less studied than other SIBLING proteins such as Osteopontin (OPN), which is coexpressed with it in several skeletal cell types. Here we review the contribution of genetically engineered mice (BSP gene knockout and overexpression) to the understanding of the role of BSP in the bone organ. The studies made so far highlight the role of BSP in skeletal mineralization, as well as its importance for proper osteoblast and osteoclast differentiation and activity, most prominently in primary/repair bone. The absence of BSP also affects the local environment of the bone tissue, in particular hematopoiesis and vascularization. Interestingly, lack of BSP induces an overexpression of OPN, and the cognate protein could be responsible for some aspects of the BSP gene knockout skeletal phenotype, while replacing BSP for some of its functions. Such interplay between the partly overlapping functions of SIBLING proteins, as well as the network of cross-regulations in which they are involved should now be the focus of further work. Copyright © 2016 International Society of Matrix Biology. Published by Elsevier B.V. All rights reserved.

The Bordetella pertussis Type III Secretion System Tip Complex Protein Bsp22 Is Not a Protective Antigen and Fails To Elicit Serum Antibody Responses during Infection of Humans and Mice

PubMed Central

Villarino Romero, Rodrigo; Bibova, Ilona; Cerny, Ondrej; Vecerek, Branislav; Wald, Tomas; Benada, Oldrich; Zavadilova, Jana; Sebo, Peter

2013-01-01

The type III secretion system (T3SS) of pathogenic bordetellae employs a self-associating tip complex protein Bsp22. This protein is immunogenic during infections by Bordetella bronchiseptica and could be used as a protective antigen to immunize mice against B. bronchiseptica challenge. Since low-passage clinical isolates of the human pathogen Bordetella pertussis produce a highly homologous Bsp22 protein (97% homology), we examined its vaccine and diagnostic potential. No Bsp22-specific antibodies were, however, detected in serum samples from 36 patients with clinically and serologically confirmed whooping cough disease (pertussis syndrome). Moreover, although the induction of Bsp22 secretion by the laboratory-adapted 18323 strain in the course of mice lung infection was observed, the B. pertussis 18323-infected mice did not mount any detectable serum antibody response against Bsp22. Furthermore, immunization with recombinant Bsp22 protein yielded induction of high Bsp22-specific serum antibody titers but did not protect mice against an intranasal challenge with B. pertussis 18323. Unlike for B. bronchiseptica, hence, the Bsp22 protein is nonimmunogenic, and/or the serum antibody response to it is suppressed, during B. pertussis infections of humans and mice. PMID:23690400

Rho-ROCK signaling differentially regulates chondrocyte spreading on fibronectin and bone sialoprotein.

PubMed

Gill, Kamal S; Beier, Frank; Goldberg, Harvey A

2008-07-01

The mammalian growth plate is a dynamic structure rich in extracellular matrix (ECM). Interactions of growth plate chondrocytes with ECM proteins regulate cell behavior. In this study, we compared chondrocyte adhesion and spreading dynamics on fibronectin (FN) and bone sialoprotein (BSP). Chondrocyte adhesion and spreading were also compared with fibroblasts to analyze potential cell-type-specific effects. Chondrocyte adhesion to BSP is independent of posttranslational modifications but is dependent on the RGD sequence in BSP. Whereas chondrocytes and fibroblasts adhered at similar levels on FN and BSP, cells displayed more actin-dependent spread on FN despite a 16x molar excess of BSP adsorbed to plastic. To identify intracellular mediators responsible for this difference in spreading, we investigated focal adhesion kinase (FAK)-Src and Rho-Rho kinase (ROCK) signaling. Although activated FAK localized to the vertices of adhered chondrocytes, levels of FAK activation did not correlate with the extent of spreading. Furthermore, Src inhibition reduced chondrocyte spreading on both FN and BSP, suggesting that FAK-Src signaling is not responsible for less cell spreading on BSP. In contrast, inhibition of Rho and ROCK in chondrocytes increased cell spreading on BSP and membrane protrusiveness on FN but did not affect cell adhesion. In fibroblasts, Rho inhibition increased fibroblast spreading on BSP while ROCK inhibition changed membrane protrusiveness of FN and BSP. In summary, we identify a novel role for Rho-ROCK signaling in regulating chondrocyte spreading and demonstrate both cell- and matrix molecule-specific mechanisms controlling cell spreading.

Rho-ROCK signaling differentially regulates chondrocyte spreading on fibronectin and bone sialoprotein

PubMed Central

Gill, Kamal S.; Beier, Frank; Goldberg, Harvey A.

2008-01-01

The mammalian growth plate is a dynamic structure rich in extracellular matrix (ECM). Interactions of growth plate chondrocytes with ECM proteins regulate cell behavior. In this study, we compared chondrocyte adhesion and spreading dynamics on fibronectin (FN) and bone sialoprotein (BSP). Chondrocyte adhesion and spreading were also compared with fibroblasts to analyze potential cell-type-specific effects. Chondrocyte adhesion to BSP is independent of posttranslational modifications but is dependent on the RGD sequence in BSP. Whereas chondrocytes and fibroblasts adhered at similar levels on FN and BSP, cells displayed more actin-dependent spread on FN despite a 16× molar excess of BSP adsorbed to plastic. To identify intracellular mediators responsible for this difference in spreading, we investigated focal adhesion kinase (FAK)-Src and Rho-Rho kinase (ROCK) signaling. Although activated FAK localized to the vertices of adhered chondrocytes, levels of FAK activation did not correlate with the extent of spreading. Furthermore, Src inhibition reduced chondrocyte spreading on both FN and BSP, suggesting that FAK-Src signaling is not responsible for less cell spreading on BSP. In contrast, inhibition of Rho and ROCK in chondrocytes increased cell spreading on BSP and membrane protrusiveness on FN but did not affect cell adhesion. In fibroblasts, Rho inhibition increased fibroblast spreading on BSP while ROCK inhibition changed membrane protrusiveness of FN and BSP. In summary, we identify a novel role for Rho-ROCK signaling in regulating chondrocyte spreading and demonstrate both cell- and matrix molecule-specific mechanisms controlling cell spreading. PMID:18463228

CREB-1 and AP-1 transcription factors JunD and Fra-2 regulate bone sialoprotein gene expression in human breast cancer cells.

PubMed

Detry, C; Lamour, V; Castronovo, V; Bellahcène, A

2008-02-01

Bone sialoprotein (BSP) expression is detected in a variety of human osteotropic cancers. High expression of BSP in breast and prostate primary carcinomas is associated with progression and bone metastases development. In this study, we examined the transcriptional regulation of BSP gene expression in MDA-MB-231 and MCF-7 human breast cancer cells compared with Saos-2 human osteoblast-like cells. BSP human promoter deletion analyses delineated a -56/-84 region, which comprises a cAMP response element (CRE) that was sufficient for maximal promoter activity in breast cancer cell lines. We found that the basic fibroblast growth factor response element (FRE) also located in the proximal promoter was a crucial regulator of human BSP promoter activity in Saos-2 but not in breast cancer cells. Promoter activity experiments in combination with DNA mobility shift assays demonstrated that BSP promoter activity is under the control of the CRE element, through CREB-1, JunD and Fra-2 binding, in MDA-MB-231, MCF-7 and in Saos-2 cells. Forskolin, a protein kinase A pathway activator, failed to enhance BSP transcriptional activity suggesting that CRE site behaves as a constitutive rather than an inducible element in these cell lines. Over-expression of JunD and Fra-2 increased BSP promoter activity and upregulated endogenous BSP protein expression in MCF-7 and Saos-2 cells while siRNA-mediated inhibition of both factors expression significantly reduced BSP protein level in MDA-MB-231. Collectively, these data provide with new transcriptional mechanisms, implicating CREB and AP-1 factors, that control BSP gene expression in breast cancer cells.

MaMR: High-performance MapReduce programming model for material cloud applications

NASA Astrophysics Data System (ADS)

Jing, Weipeng; Tong, Danyu; Wang, Yangang; Wang, Jingyuan; Liu, Yaqiu; Zhao, Peng

2017-02-01

With the increasing data size in materials science, existing programming models no longer satisfy the application requirements. MapReduce is a programming model that enables the easy development of scalable parallel applications to process big data on cloud computing systems. However, this model does not directly support the processing of multiple related data, and the processing performance does not reflect the advantages of cloud computing. To enhance the capability of workflow applications in material data processing, we defined a programming model for material cloud applications that supports multiple different Map and Reduce functions running concurrently based on hybrid share-memory BSP called MaMR. An optimized data sharing strategy to supply the shared data to the different Map and Reduce stages was also designed. We added a new merge phase to MapReduce that can efficiently merge data from the map and reduce modules. Experiments showed that the model and framework present effective performance improvements compared to previous work.

The ASM-NSF Biology Scholars Program: An Evidence-Based Model for Faculty Development.

PubMed

Chang, Amy L; Pribbenow, Christine M

2016-05-01

The American Society for Microbiology (ASM) established its ASM-NSF (National Science Foundation) Biology Scholars Program (BSP) to promote undergraduate education reform by 1) supporting biologists to implement evidence-based teaching practices, 2) engaging life science professional societies to facilitate biologists' leadership in scholarly teaching within the discipline, and 3) participating in a teaching community that fosters disciplinary-level science, technology, engineering, and mathematics (STEM) reform. Since 2005, the program has utilized year-long residency training to provide a continuum of learning and practice centered on principles from the scholarship of teaching and learning (SoTL) to more than 270 participants ("scholars") from biology and multiple other disciplines. Additionally, the program has recruited 11 life science professional societies to support faculty development in SoTL and discipline-based education research (DBER). To identify the BSP's long-term outcomes and impacts, ASM engaged an external evaluator to conduct a study of the program's 2010-2014 scholars (n = 127) and society partners. The study methods included online surveys, focus groups, participant observation, and analysis of various documents. Study participants indicate that the program achieved its proposed goals relative to scholarship, professional society impact, leadership, community, and faculty professional development. Although participants also identified barriers that hindered elements of their BSP participation, findings suggest that the program was essential to their development as faculty and provides evidence of the BSP as a model for other societies seeking to advance undergraduate science education reform. The BSP is the longest-standing faculty development program sponsored by a collective group of life science societies. This collaboration promotes success across a fragmented system of more than 80 societies representing the life sciences and helps catalyze biology education reform efforts.

runt Homology Domain Transcription Factors (Runx, Cbfa, and AML) Mediate Repression of the Bone Sialoprotein Promoter: Evidence for Promoter Context-Dependent Activity of Cbfa Proteins

PubMed Central

Javed, Amjad; Barnes, George L.; Jasanya, B. O.; Stein, Janet L.; Gerstenfeld, Louis; Lian, Jane B.; Stein, Gary S.

2001-01-01

Expression of the bone sialoprotein (BSP) gene, a marker of bone formation, is largely restricted to cells in mineralized tissues. Recent studies have shown that the Cbfa1 (also known as Runx2, AML-3, and PEBP2αA) transcription factor supports commitment and differentiation of progenitor cells to hypertrophic chondrocytes and osteoblasts. This study addresses the functional involvement of Cbfa sites in expression of the Gallus BSP gene. Gel mobility shift analyses with nuclear extracts from ROS 17/2.8 osteoblastic cells revealed that multiple Cbfa consensus sequences are functional Cbfa DNA binding sites. Responsiveness of the 1.2-kb Gallus BSP promoter to Cbfa factors Cbfa1, Cbfa2, and Cbfa3 was assayed in osseous and nonosseous cells. Each of the Cbfa factors mediated repression of the wild-type BSP promoter, in contrast to their well known activation of various hematopoietic and skeletal phenotypic genes. Suppression of BSP by Cbfa factors was not observed in BSP promoters in which Cbfa sites were deleted or mutated. Expression of the endogenous BSP gene in Gallus osteoblasts was similarly downregulated by forced expression of Cbfa factors. Our data indicate that Cbfa repression of the BSP promoter does not involve the transducin-like enhancer (TLE) proteins. Neither coexpression of TLE1 or TLE2 nor the absence of the TLE interaction motif of Cbfa1 (amino acids 501 to 513) influenced repressor activity. However, removal of the C terminus of Cbfa1 (amino acids 362 to 513) relieved suppression of the BSP promoter. Our results, together with the evolutionary conservation of the seven Cbfa sites in the Gallus and human BSP promoters, suggest that suppressor activity by Cbfa is of significant physiologic consequence and may contribute to spatiotemporal expression of BSP during bone development. PMID:11283267

Skeletal development of mice lacking bone sialoprotein (BSP)--impairment of long bone growth and progressive establishment of high trabecular bone mass.

PubMed

Bouleftour, Wafa; Boudiffa, Maya; Wade-Gueye, Ndeye Marième; Bouët, Guénaëlle; Cardelli, Marco; Laroche, Norbert; Vanden-Bossche, Arnaud; Thomas, Mireille; Bonnelye, Edith; Aubin, Jane E; Vico, Laurence; Lafage-Proust, Marie Hélène; Malaval, Luc

2014-01-01

Adult Ibsp-knockout mice (BSP-/-) display shorter stature, lower bone turnover and higher trabecular bone mass than wild type, the latter resulting from impaired bone resorption. Unexpectedly, BSP knockout also affects reproductive behavior, as female mice do not construct a proper "nest" for their offsprings. Multiple crossing experiments nonetheless indicated that the shorter stature and lower weight of BSP-/- mice, since birth and throughout life, as well as their shorter femur and tibia bones are independent of the genotype of the mothers, and thus reflect genetic inheritance. In BSP-/- newborns, µCT analysis revealed a delay in membranous primary ossification, with wider cranial sutures, as well as thinner femoral cortical bone and lower tissue mineral density, reflected in lower expression of bone formation markers. However, trabecular bone volume and osteoclast parameters of long bones do not differ between genotypes. Three weeks after birth, osteoclast number and surface drop in the mutants, concomitant with trabecular bone accumulation. The growth plates present a thinner hypertrophic zone in newborns with lower whole bone expression of IGF-1 and higher IHH in 6 days old BSP-/- mice. At 3 weeks the proliferating zone is thinner and the hypertrophic zone thicker in BSP-/- than in BSP+/+ mice of either sex, maybe reflecting a combination of lower chondrocyte proliferation and impaired cartilage resorption. Six days old BSP-/- mice display lower osteoblast marker expression but higher MEPE and higher osteopontin(Opn)/Runx2 ratio. Serum Opn is higher in mutants at day 6 and in adults. Thus, lack of BSP alters long bone growth and membranous/cortical primary bone formation and mineralization. Endochondral development is however normal in mutant mice and the accumulation of trabecular bone observed in adults develops progressively in the weeks following birth. Compensatory high Opn may allow normal endochondral development in BSP-/- mice, while impairing primary mineralization.

ATF4, A Novel Mediator of the Anabolic Actions of PTH on Bone

DTIC Science & Technology

2010-07-01

increased the expression of genes known to be associated with osteoblast differentiation including osteocalcin (Ocn), bone sialoprotein (Bsp...differentiation including osteocalcin (Ocn) (2.2-fold), bone sialoprotein (Bsp) (4.2-fold), alkaline phosphatase (Alp) (3.2-fold), a1(I) collagen (Col1... sialoprotein (BSP) gene transcription is mediated through a pituitary-specific transcription factor-1 (Pit-1) motif in the rat BSP gene promoter. Matrix Biol

GATA4 negatively regulates bone sialoprotein expression in osteoblasts.

PubMed

Song, Insun; Jeong, Byung-Chul; Choi, Yong Jun; Chung, Yoon-Sok; Kim, Nacksung

2016-06-01

GATA4 has been reported to act as a negative regulator in osteoblast differentiation by inhibiting the Dlx5 transactivation of Runx2 via the attenuation of the binding ability of Dlx5 to the Runx2 promoter region. Here, we determine the role of GATA4 in the regulation of bone sialoprotein (Bsp) in osteoblasts. We observed that the overexpression of Runx2 or Sox9 induced the Bsp expression in osteoblastic cells. Silencing GATA4 further enhanced the Runx2- and Sox9-mediated Bsp promoter activity, whereas GATA4 overexpression down-regulated Bsp promoter activity mediated by Runx2 and Sox9. GATA4 also interacted with Runx2 and Sox9, by attenuating the binding ability of Runx2 and Sox9 to the Bsp promoter region. Our data suggest that GATA4 acts as a negative regulator of Bsp expression in osteoblasts. [BMB Reports 2016; 49(6): 343-348].

Runx2- and histone deacetylase 3-mediated repression is relieved in differentiating human osteoblast cells to allow high bone sialoprotein expression.

PubMed

Lamour, Virginie; Detry, Cédric; Sanchez, Christelle; Henrotin, Yves; Castronovo, Vincent; Bellahcène, Akeila

2007-12-14

Bone sialoprotein (BSP) is a bone matrix glycoprotein whose expression coincides with terminal osteoblastic differentiation and the onset of mineralization. In this study we show that BSP expression is considerably increased in confluent Saos-2 human osteosarcoma cells and in differentiating normal human osteoblasts, concomitantly with the decrease of Runx2, a key transcription factor controlling bone formation. Therefore, we investigated the role of Runx2 in the regulation of BSP expression in Saos-2 cells. Using a mobility shift assay, we demonstrated that Runx2 binds to the BSP promoter only in preconfluent cells. Histone deacetylase 3 (HDAC3) has been recently shown to act as a Runx2 co-repressor. Chromatin immunoprecipitation assays demonstrated that both Runx2 and HDAC3 are detectable at the BSP promoter in preconfluent Saos-2 cells but not when they are confluent and overexpress BSP. Consistently, nuclear Runx2 protein level is down-regulated, whereas Saos-2 cells became increasingly confluent. Finally, the suppression of HDAC3, Runx2, or both by RNA interference induced the expression of BSP at both mRNA and protein levels in Saos-2 cells. Our data demonstrate that Runx2 and HDAC3 repress BSP gene expression and that this repression is suspended upon osteoblastic cell differentiation. Both the nuclear disappearance of Runx2 and the non-recruitment of HDAC3 represent new means to relieve Runx2-mediated suppression of BSP expression, thus allowing the acquisition of a fully differentiated and mineralization-competent phenotype by osteoblast cells.

Effects of quercetin and quercetin 3-glucuronide on the expression of bone sialoprotein gene.

PubMed

Kim, Dong-Soon; Takai, Hideki; Arai, Masato; Araki, Shouta; Mezawa, Masaru; Kawai, Yoshichika; Murota, Kaeko; Terao, Junji; Ogata, Yorimasa

2007-06-01

Quercetin is a typical flavonol-type flavonoid and is present in a variety of vegetables, and their antioxidant effect implies their possible role in the prevention of oxidative stress related chronic diseases. Bone sialoprotein (BSP) is a noncollagenous protein of the extracellular matrix in the mineralized connective tissues that has been implicated in the nucleation of hydroxyapatite crystals. Previously, we reported that isoflavone (genistein) activated BSP gene transcription is mediated through an inverted CCAAT box in the proximal BSP gene promoter. The present study investigates the regulation of BSP transcription in a rat osteoblast-like cell line, ROS 17/2.8 cells, by quercetin and its conjugated metabolite quercetin 3-glucuronide. Quercetin and quercetin 3-glucuronide (5 microM) increased the BSP mRNA levels at 12 h and quercetin upregulated the Cbfa1/Runx2 mRNA expression at 12 h. From transient transfection assays using various sized BSP promoter-luciferase constructs, quercetin increased the luciferase activity of the construct (pLUC3), including the promoter sequence nucleotides -116 to -43. Transcriptional stimulations by quercetin were almost completely abrogated in the constructs that included 2 bp mutations in the inverted CCAAT and FRE elements whereas the CCAAT-protein complex did not change after stimulation by quercetin according to gel shift assays. Quercetin increased the nuclear protein binding to the FRE and 3'-FRE. These data suggest that quercetin and quercetin 3-glucuronide increased the BSP mRNA expression, and that the inverted CCAAT and FRE elements in the promoter of the BSP gene are required for quercetin induced BSP transcription.

Correlation between calcification and bone sialoprotein and osteopontin in papillary thyroid carcinoma.

PubMed

Wu, Gang; Guo, Jing-Jing; Ma, Zhen-Yu; Wang, Jie; Zhou, Zhong-Wen; Wang, Yi

2015-01-01

The correlation between calcification and papillary thyroid carcinoma has received increasing attention. We investigated the ability of bone sialoprotein (BSP) and osteopontin (OPN) protein levels to diagnose papillary thyroid carcinoma (PTC), and explored the correlation between BSP and OPN protein levels and calcification in PTC. Archival PTC specimens from patients with PTC with calcification and lateral cervical lymph node metastasis (LNM) were included in this retrospective immunohistochemical study. The protein levels of BSP and OPN were analysed immunohistochemically using routinely prepared tissue sections. PTC specimens from 66 patients with PTC were reviewed retrospectively (25 patients with histological calcification seen in paraffin sections, 41 patients without calcification; 35 patients with lateral cervical LNM, 31 patients without LNM). The percentage of samples that had cells that demonstrated positive protein staining differed significantly between PTC specimens, benign thyroid nodules, and adjacent normal follicular epithelium (BSP: 87.88%, 55.00%, and 42.50%, respectively; OPN: 83.33%, 70.00% and 50.00%, respectively). There was a significant difference in the immunohistochemical score (IHS) for BSP and OPN protein staining between PTC specimens with and without calcification (P < 0.05). The level of BSP protein staining was found to be significantly correlated with the level of OPN protein staining in PTC specimens. We conclude that the strong correlation between BSP and OPN and PTC suggests a role for BSP and OPN in calcification and tumor progression of PTC. BSP and OPN might be useful tumour markers for the diagnosis of PTC with limited value, because both of them had low specificity.

Activation of the mitogen-activated protein kinase pathway by bone sialoprotein regulates osteoblast differentiation.

PubMed

Gordon, Jonathan A R; Hunter, Graeme K; Goldberg, Harvey A

2009-01-01

Bone sialoprotein (BSP) is an abundant protein in the extracellular matrix of bone that has been suggested to have several different physiological functions, including the nucleation of hydroxyapatite (HA), promotion of cell attachment and binding of collagen. Studies in our lab have demonstrated that increased expression of BSP in osteoblast cells can increase expression of the osteoblast-related genes Runx2 and Osx as well as alkaline phosphatase and osteocalcin and increase matrix mineralization. To determine the molecular mechanisms responsible for the BSP-mediated increase in osteoblastic differentiation, several functional domain mutants of BSP were expressed in primary rat bone osteoblastic cells, including the contiguous glutamic acid sequences (polyGlu) and the arginine-glycine-aspartic acid (RGD) motif. Markers of osteoblast differentiation, including matrix mineralization and alkaline phosphatase staining, were increased in cells expressing BSP mutants of the polyGlu sequences but not in cells expressing RGD-mutated BSP. We also determined the dependence on integrin-associated pathways in promoting BSP-mediated differentiation responses in osteoblasts by demonstrating the activation of focal adhesion kinase, MAP kinase-associated proteins ERK1/2, ribosomal s6 kinase 2 and the AP-1 protein cFos. Thus, the mechanism regulating osteoblast differentiation by BSP was determined to be dependent on integrin-mediated intracellular signaling pathways. Copyright 2008 S. Karger AG, Basel.

Mathematical model of the oxidation of ferrous iron by a biofilm of Thiobacillus ferrooxidans.

PubMed

Mesa, M M; Macías, M; Cantero, D

2002-01-01

Microbial oxidation of ferrous iron may be a viable alternative method of producing ferric sulfate, which is a reagent used for removal of H(2)S from biogas. The paper introduces a kinetic study of the biological oxidation of ferrous iron by Thiobacillus ferrooxidans immobilized on biomass support particles (BSP) composed of polyurethane foam. On the basis of the data obtained, a mathematical model for the bioreactor was subsequently developed. In the model described here, the microorganisms adhere by reversible physical adsorption to the ferric precipitates that are formed on the BSP. The model can also be considered as an expression for the erosion of microorganisms immobilized due to the agitation of the medium by aeration.

Phosphorylation of Ser136 is critical for potent bone sialoprotein-mediated nucleation of hydroxyapatite crystals.

PubMed

Baht, Gurpreet S; O'Young, Jason; Borovina, Antonia; Chen, Hong; Tye, Coralee E; Karttunen, Mikko; Lajoie, Gilles A; Hunter, Graeme K; Goldberg, Harvey A

2010-05-27

Acidic phosphoproteins of mineralized tissues such as bone and dentin are believed to play important roles in HA (hydroxyapatite) nucleation and growth. BSP (bone sialoprotein) is the most potent known nucleator of HA, an activity that is thought to be dependent on phosphorylation of the protein. The present study identifies the role phosphate groups play in mineral formation. Recombinant BSP and peptides corresponding to residues 1-100 and 133-205 of the rat sequence were phosphorylated with CK2 (protein kinase CK2). Phosphorylation increased the nucleating activity of BSP and BSP-(133-205), but not BSP-(1-100). MS analysis revealed that the major site phosphorylated within BSP-(133-205) was Ser136, a site adjacent to the series of contiguous glutamate residues previously implicated in HA nucleation. The critical role of phosphorylated Ser136 in HA nucleation was confirmed by site-directed mutagenesis and functional analyses. Furthermore, peptides corresponding to the 133-148 sequence of rat BSP were synthesized with or without a phosphate group on Ser136. As expected, the phosphopeptide was a more potent nucleator. The mechanism of nucleation was investigated using molecular-dynamics simulations analysing BSP-(133-148) interacting with the {100} crystal face of HA. Both phosphorylated and non-phosphorylated sequences adsorbed to HA in extended conformations with alternating residues in contact with and facing away from the crystal face. However, this alternating-residue pattern was more pronounced when Ser136 was phosphorylated. These studies demonstrate a critical role for Ser136 phosphorylation in BSP-mediated HA nucleation and identify a unique mode of interaction between the nucleating site of the protein and the {100} face of HA.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Midura, R.J.; McQuillan, D.J.; Benham, K.J.

The rat osteosarcoma cell line (UMR 106-01) synthesizes and secretes relatively large amounts of a sulfated glycoprotein into its culture medium (approximately 240 ng/10(6) cells/day). This glycoprotein was purified, and amino-terminal sequence analysis identified it as bone sialoprotein (BSP). (35S)Sulfate, (3H)glucosamine, and (3H)tyrosine were used as metabolic precursors to label the BSP. Sulfate esters were found on N- and O-linked oligosaccharides and on tyrosine residues, with about half of the total tyrosines in the BSP being sulfated. The proportion of 35S activity in tyrosine-O-sulfate (approximately 70%) was greater than that in N-linked (approximately 20%) and O-linked (approximately 10%) oligosaccharides. Frommore » the deduced amino acid sequence for rat BSP, the results indicate that on average approximately 12 tyrosine residues, approximately 3 N-linked, and approximately 2 O-linked oligosaccharides are sulfated/molecule. The carboxyl-terminal quarter of the BSP probably contains most, if not all, of the sulfated tyrosine residues because this region of the polypeptide contains the necessary requirements for tyrosine sulfation. Oligosaccharide analyses indicated that for every N-linked oligosaccharide on the BSP, there are also approximately 2 hexa-, approximately 5 tetra-, and approximately 2 trisaccharides O-linked to serine and threonine residues. On average, the BSP synthesized by UMR 106-01 cells would contain a total of approximately 3 N-linked and approximately 25 of the above O-linked oligosaccharides. This large number of oligosaccharides is in agreement with the known carbohydrate content (approximately 50%) of the BSP.A« less

Glycosylation status of bone sialoprotein and its role in mineralization.

PubMed

Xu, Lan; Zhang, Zhenqing; Sun, Xue; Wang, Jingjing; Xu, Wei; Shi, Lv; Lu, Jiaojiao; Tang, Juan; Liu, Jingjing; Su, Xiong

2017-11-15

The highly glycosylated bone sialoprotein (BSP) is an abundant non-collagenous phosphoprotein in bone which enhances osteoblast differentiation and new bone deposition in vitro and in vivo. However, the structural details of its different glycosylation linkages have not been well studied and their functions in bone homeostasis are not clear. Previous studies suggested that the O-glycans, but not the N-glycans on BSP, are highly sialylated. Herein, we employed tandem mass spectrometry (MS/MS) to demonstrate that the N-glycanson the recombinant human integrin binding sialoprotein (rhiBSP) are also enriched in sialic acids (SAs) at their termini. We also identified multiple novel sites of N-glycan modification. Treatment of rhiBSP enhances osteoblast differentiation and mineralization of MC3T3-E1 cells and this effect could be partially reversed by efficient enzymatic removal of its N-glycans. Removal of all terminal SAs has a greater effect in reversing the effect of rhiBSP on osteogenesis, especially on mineralization, suggesting that sialylation at the termini of both N-glycans and O-glycans plays an important role in this regulation. Moreover, BSP-conjugated SAs may affect mineralization via ERK activation of VDR expression. Collectively, our results identified novel N-glycans enriched in SAs on the rhiBSP and demonstrated that SAs at both N- and O-glycans are important for BSP regulation of osteoblast differentiation and mineralization in vitro. Copyright © 2017 Elsevier Inc. All rights reserved.

Interaction of milk proteins and Binder of Sperm (BSP) proteins from boar, stallion and ram semen.

PubMed

Plante, Geneviève; Lusignan, Marie-France; Lafleur, Michel; Manjunath, Puttaswamy

2015-08-15

Mammalian semen contains a family of closely related proteins known as Binder of SPerm (BSP proteins) that are added to sperm at ejaculation. BSP proteins extract lipids from the sperm membrane thereby extensively modifying its composition. These changes can ultimately be detrimental to sperm storage. We have demonstrated that bovine BSP proteins interact with major milk proteins and proposed that this interaction could be the basis of sperm protection by milk extenders. In the present study, we investigated if homologous BSP proteins present in boar, stallion and ram seminal plasma display a similar affinity for the milk proteins in order to assess whether the mechanism of sperm protection by milk for these species could be general. Skim milk was incubated with seminal plasma proteins (boar, stallion and ram), chromatographed on a Sepharose CL-4B column and protein fractions were analyzed by immunoblotting. Boar, stallion and ram BSP proteins displayed affinity for a milk protein fraction (F1) mainly composed of α-lactalbumin, β-lactoglobulin, and κ-casein. They also had affinity for another milk protein fraction (F2) composed mostly of casein micelles. However, stallion BSP showed higher affinity for the fraction (F1). These results further extend our view that the association of BSP proteins with milk proteins could be a general feature of the mechanism of mammalian sperm protection by milk to prevent detrimental effect of prolonged exposure of sperm to seminal plasma.

Effect of bone sialoprotein coating of ceramic and synthetic polymer materials on in vitro osteogenic cell differentiation and in vivo bone formation.

PubMed

Schaeren, Stefan; Jaquiéry, Claude; Wolf, Francine; Papadimitropoulos, Adam; Barbero, Andrea; Schultz-Thater, Elke; Heberer, Michael; Martin, Ivan

2010-03-15

In this study, we addressed whether Bone Sialoprotein (BSP) coating of various substrates could enhance the in vitro osteogenic differentiation and in vivo bone formation capacity of human Bone Marrow Stromal Cells (BMSC). Moreover, we tested whether synthetic polymer-based porous scaffolds, despite the absence of a mineral component, could support ectopic bone formation by human BMSC if coated with BSP. Adsorption of recombinant human BSP on tissue culture-treated polystyrene (TCTP), beta-tricalcium phosphate (Osteologic) or synthetic polymer (Polyactive) substrates was dose dependent, but did not consistently accelerate or enhance in vitro BMSC osteogenic differentiation, as assessed by the mRNA expression of osteoblast-related genes. Similarly, BSP coating of porous beta-tricalcium phosphate scaffolds (Skelite) did not improve the efficiency of bone tissue formation following loading with BMSC and ectopic implantation in nude mice. Finally, Polyactive foams seeded with BMSC did not form bone tissue in the same ectopic assay, even if coated with BSP. We conclude that BSP coating of a variety of substrates is not directly associated with an enhancement of osteoprogenitor cell differentiation in vitro or in vivo, and that presentation of BSP on polymeric materials is not sufficient to prime BMSC functional osteoblastic differentiation in vivo. (c) 2009 Wiley Periodicals, Inc.

Binder of Sperm Proteins protect ram spermatozoa from freeze-thaw damage.

PubMed

Pini, Taylor; Farmer, Kiri; Druart, Xavier; Teixeira-Gomes, Ana Paula; Tsikis, Guillaume; Labas, Valerie; Leahy, Tamara; de Graaf, Simon P

2018-06-01

Cryopreservation causes sub-lethal damage which limits the fertility of frozen thawed spermatozoa. Seminal plasma has been investigated as a cryoprotectant, but has yielded inconsistent results due to considerable variation in its constituents. Individual seminal plasma proteins offer an ideal alternative to whole seminal plasma, and several have been correlated with freezing success. Binder of Sperm Proteins (BSPs) are abundant ram seminal plasma proteins which have been suggested to have significant protective effects on ram spermatozoa during cold shock. This is in direct opposition to bull spermatozoa, where BSPs cause sperm deterioration during in vitro handling. We investigated the potential of BSP1 and BSP5 to prevent freezing associated damage to important functional parameters of ram spermatozoa. BSPs purified by size exclusion chromatography improved post thaw motility and penetration through artificial mucus. Highly purified BSP1 and BSP5, isolated by gelatin affinity and RP-HPLC, improved motility and membrane integrity, and reduced post thaw protein tyrosine phosphorylation. Exposure to BSP5 before freezing increased the amount of phosphatidylethanolamine on the sperm surface after thawing. Neither BSP1 nor BSP5 prevented freezing associated changes in membrane lipid disorder. These results suggest that BSPs may significantly improve freezing outcomes of ram spermatozoa. Copyright © 2018 Elsevier Inc. All rights reserved.

Blocking the expression of both bone sialoprotein (BSP) and osteopontin (OPN) impairs the anabolic action of PTH in mouse calvaria bone.

PubMed

Bouleftour, Wafa; Bouet, Guenaelle; Granito, Renata Neves; Thomas, Mireille; Linossier, Marie-Thérèse; Vanden-Bossche, Arnaud; Aubin, Jane E; Lafage-Proust, Marie-Hélène; Vico, Laurence; Malaval, Luc

2015-03-01

Osteopontin (OPN) and bone sialoprotein (BSP) are coexpressed in osteoblasts and osteoclasts, and display overlapping properties. We used daily injection of parathyroid hormone 1-84 (iPTH) over the calvaria of BSP knockout (-/-) mice to investigate further their functional specificity and redundancy. iPTH stimulated bone formation in both +/+ and -/- mice, increasing to the same degree periosteum, osteoid and total bone thickness. Expression of OPN, osterix, osteocalcin (OCN) and DMP1 was also increased by iPTH in both genotypes. In contrast to +/+, calvaria cell cultures from -/- mice revealed few osteoblast colonies, no mineralization and little expression of OCN, MEPE or DMP1. In contrast, OPN levels were 5× higher in -/- versus +/+ cultures. iPTH increased alkaline phosphatase (ALP) activity in cell cultures of both genotypes, with higher OCN and the induction of mineralization in -/- cultures. siRNA blocking of OPN expression did not alter the anabolic action of the hormone in BSP +/+ calvaria, while it blunted iPTH effects in -/- mice, reduced to a modest increase in periosteum thickness. In -/- (not +/+) cell cultures, siOPN blocked the stimulation by iPTH of ALP activity and OCN expression, as well as the induction of mineralization. Thus, full expression of either OPN or BSP is necessary for the anabolic effect of PTH at least in the ectopic calvaria injection model. This suggests that OPN may compensate for the lack of BSP in the response to this hormonal challenge, and provides evidence of functional overlap between these cognate proteins. © 2014 Wiley Periodicals, Inc., A Wiley Company.

Oxidized low-density lipoprotein and upregulated expression of osteonectin and bone sialoprotein in vascular smooth muscle cells.

PubMed

Farrokhi, Effat; Samani, Keihan Ghatreh; Chaleshtori, Morteza Hashemzadeh

2014-01-01

Oxidative stress has been associated with the progression of atherosclerosis and activation of genes that lead to increased deposition of proteins in the extracellular matrix. Bone sialoprotein (BSP) and osteonectin are proteins involved in the initiation and progression of vascular calcification. To investigate the effect of oxidized low-density lipoprotein on osteonectin and BSP expression in human aorta vascular smooth muscle cells (HA/VSMCs). We treated HA/VSMCs with oxidized low-density lipoprotein (oxLDL) and measured the relative expression of osteonectin and BSP genes using the real-time polymerase chain reaction (PCR) method. We investigated the protein levels produced by each gene using the western blotting technique. oxLDL increased osteonectin and BSP levels (mean [SD], 9.1 [2.1]-fold and 4.2 [0.75]-fold, respectively) after 48 hours. The western blotting results also confirmed the increased levels of osteonectin and BSP. oxLDL may enhance vascular calcification by promoting the expression of osteonectin and BSP. Copyright© by the American Society for Clinical Pathology (ASCP).

A comparative study of broccoli sprouts powder and standard triple therapy on cardiovascular risk factors following H.pylori eradication: a randomized clinical trial in patients with type 2 diabetes

PubMed Central

2014-01-01

Background In this clinical trial we compared the effects of broccoli sprouts powder, as an alternative and complementary treatment, to those of standard triple therapy, as a common medical treatment, on cardiovascular risk factors following the H.pylori eradication in patients with type 2 diabetes. Methods Eighty-six type 2 diabetic patients with positive H.pylori stool antigen test (HpSAg) were randomized to receive one of the three following regimens: STT) Standard triple therapy (omeprazole 20 mg, clarithromycin 500 mg, amoxicillin 1000 mg, twice a day for 14 days), BSP) 6 g/d broccoli sprouts powder for 28 days, and combination of these as STT + BSP. After 4 weeks of treatment, H.pylori eradication rates were assessed by HpSAg. Anthropometric measures, blood pressure, serum lipids and lipoproteins as well as serum high sensitive- C reactive protein were also assessed at baseline and at the second examination. Results Seventy-seven participants completed the study [STT (n = 28), BSP (n = 25), STT + BSP (n = 24)]. The H.pylori eradication rates were 89.3%, 56.0% and 91.7% in STT, BSP and STT + BSP groups, respectively. After the treatment, both systolic and diastolic blood pressure significantly decreased in STT + BSP group (P < 0.05). Serum triglycerides and TG/HDL-C ratio increased in STT patients group (<0.05). Serum hs-CRP levels significantly decreased in the patients who were treated with BSP per se (3.0 ± 2.5 at baseline vs. 2.3 ± 2.1 after the treatment, P < 0.05). Conclusion Compared to standard triple therapy, BSP regimen in addition to considerable effects on H.pylori eradication had also favorable properties on cardiovascular risk factors following the H.pylori eradication. PMID:24940565

How does bone sialoprotein promote the nucleation of hydroxyapatite? A molecular dynamics study using model peptides of different conformations.

PubMed

Yang, Yang; Cui, Qiang; Sahai, Nita

2010-06-15

Bone sialoprotein (BSP) is a highly phosphorylated, acidic, noncollagenous protein in bone matrix. Although BSP has been proposed to be a nucleator of hydroxyapatite (Ca(5)(PO(4))(3)OH), the major mineral component of bone, no detailed mechanism for the nucleation process has been elucidated at the atomic level to date. In the present work, using a peptide model, we apply molecular dynamics (MD) simulations to study the conformational effect of a proposed nucleating motif of BSP (a phosphorylated, acidic, 10 amino-acid residue sequence) on controlling the distributions of Ca(2+) and inorganic phosphate (Pi) ions in solution, and specifically, we explore whether a nucleating template for orientated hydroxyapatite could be formed in different peptide conformations. Both the alpha-helical conformation and the random coil structure have been studied, and inorganic solutions without the peptide are simulated as reference. Ca(2+) distributions around the peptide surface and interactions between Ca(2+) and Pi in the presence of the peptide are examined in detail. From the MD simulations, although in some cases for the alpha-helical conformation, we observe that a Ca(2+) equilateral triangle forms around the surface of peptide, which matches the distribution of Ca(2+) ions on the (001) face of the hydroxyapatite crystal, we do not consistently find a stable nucleating template formation in general for either the helical conformation or the random coil structure. Therefore, independent of conformations, the BSP nucleating motif is more likely to help nucleate an amorphous calcium phosphate cluster, which ultimately converts to crystalline hydroxyapatite.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hand, Jenny L.; Day, Derek E.; McMeeking, Gavin M.

During the 2006 FLAME study (Fire Laboratory at Missoula Experiment), laboratory burns of biomass fuels were performed to investigate the physico-chemical, optical, and hygroscopic properties of fresh biomass smoke. As part of the experiment, two nephelometers simultaneously measured dry and humidified light scattering coefficients (bsp(dry) and bsp(RH), respectively) in order to explore the role of relative humidity (RH) on the optical properties of biomass smoke aerosols. Results from burns of several biomass fuels showed large variability in the humidification factor (f(RH) = bsp(RH)/bsp(dry)). Values of f(RH) at RH=85-90% ranged from 1.02 to 2.15 depending on fuel type. We incorporated measuredmore » chemical composition and size distribution data to model the smoke hygroscopic growth to investigate the role of inorganic and organic compounds on water uptake for these aerosols. By assuming only inorganic constituents were hygroscopic, we were able to model the water uptake within experimental uncertainty, suggesting that inorganic species were responsible for most of the hygroscopic growth. In addition, humidification factors at 85-90% RH increased for smoke with increasing inorganic salt to carbon ratios. Particle morphology as observed from scanning electron microscopy revealed that samples of hygroscopic particles contained soot chains either internally or externally mixed with inorganic potassium salts, while samples of weak to non-hygroscopic particles were dominated by soot and organic constituents. This study provides further understanding of the compounds responsible for water uptake by young biomass smoke, and is important for accurately assessing the role of smoke in climate change studies and visibility regulatory efforts.« less

MC3T3-E1 cell adhesion to hydroxyapatite with adsorbed bone sialoprotein, bone osteopontin, and bovine serum albumin.

PubMed

Bernards, Matthew T; Qin, Chunlin; Jiang, Shaoyi

2008-07-15

Native bone tissue is composed of a complex matrix of collagen, non-collagenous proteins, and hydroxyapatite (HAP). Bone sialoprotein (BSP) and bone osteopontin (OPN) are members of the non-collagenous protein family termed the SIBLING (small integrin-binding ligand, N-linked glycoproteins) proteins, which are primarily found in mineralized tissues. Previously, OPN was shown to exhibit a preferential orientation for MC3T3-E1 cell adhesion when it was specifically bound to collagen, while the MC3T3-E1 cell adhesion was shown to be dependant on the conformational flexibility of BSP specifically bound to collagen. Additionally, OPN was shown to play a greater role than BSP for cell binding to collagen. In this work, the orientations and conformations of BSP and OPN specifically bound to HAP are probed under similar conditions. Radiolabeled adsorption isotherms were obtained for BSP and OPN on HAP formed from a simulated body fluid, and the results show that HAP has the capacity to bind significantly more BSP than OPN. An in vitro MC3T3-E1 cell adhesion assay was then performed to compare the cell binding ability of adsorbed BSP and OPN specifically bound to HAP. It was found that there is a preference for cell binding to HAP with adsorbed BSP as compared to OPN, but not to a statistically significant level. However, the maximum cell binding was observed on HAP substrates with adsorbed heat denatured bovine serum albumin (BSA). The influence of BSA on cell binding was shown to be concentration dependant and it is believed that the adsorbed BSA modulates the proliferation state of the bound cells.

MC3T3-E1 Cell Adhesion to Hydroxyapatite with Adsorbed Bone Sialoprotein, Bone Osteopontin, and Bovine Serum Albumin

PubMed Central

Bernards, Matthew T.; Qin, Chunlin; Jiang, Shaoyi

2008-01-01

Native bone tissue is composed of a complex matrix of collagen, non-collagenous proteins, and hydroxyapatite (HAP). Bone sialoprotein (BSP) and bone osteopontin (OPN) are members of the non-collagenous protein family termed the SIBLING (small integrin-binding ligand, N-linked glycoproteins) proteins, which are primarily found in mineralized tissues. Previously, OPN was shown to exhibit a preferential orientation for MC3T3-E1 cell adhesion when it was specifically bound to collagen, while the MC3T3-E1 cell adhesion was shown to be dependant on the conformational flexibility of BSP specifically bound to collagen. Additionally, OPN was shown to play a greater role than BSP for cell binding to collagen. In this work, the orientations and conformations of BSP and OPN specifically bound to HAP are probed under similar conditions. Radiolabeled adsorption isotherms were obtained for BSP and OPN on HAP formed from a simulated body fluid, and the results show that HAP has the capacity to bind significantly more BSP than OPN. An in vitro MC3T3-E1 cell adhesion assay was then performed to compare the cell binding ability of adsorbed BSP and OPN specifically bound to HAP. It was found that there is a preference for cell binding to HAP with adsorbed BSP as compared to OPN, but not to a statistically significant level. However, the maximum cell binding was observed on HAP substrates with adsorbed heat denatured bovine serum albumin (BSA). The influence of BSA on cell binding was shown to be concentration dependant and it is believed that the adsorbed BSA modulates the proliferation state of the bound cells. PMID:18420388

The role of bone sialoprotein in the tendon-bone insertion.

PubMed

Marinovich, Ryan; Soenjaya, Yohannes; Wallace, Gregory Q; Zuskov, Andre; Dunkman, Andrew; Foster, Brian L; Ao, Min; Bartman, Kevin; Lam, Vida; Rizkalla, Amin; Beier, Frank; Somerman, Martha J; Holdsworth, David W; Soslowsky, Louis J; Lagugné-Labarthet, François; Goldberg, Harvey A

2016-01-01

Tendons/ligaments insert into bone via a transitional structure, the enthesis, which is susceptible to injury and difficult to repair. Fibrocartilaginous entheses contain fibrocartilage in their transitional zone, part of which is mineralized. Mineral-associated proteins within this zone have not been adequately characterized. Members of the Small Integrin Binding Ligand N-linked Glycoprotein (SIBLING) family are acidic phosphoproteins expressed in mineralized tissues. Here we show that two SIBLING proteins, bone sialoprotein (BSP) and osteopontin (OPN), are present in the mouse enthesis. Histological analyses indicate that the calcified zone of the quadriceps tendon enthesis is longer in Bsp(-/-) mice, however no difference is apparent in the supraspinatus tendon enthesis. In an analysis of mineral content within the calcified zone, micro-CT and Raman spectroscopy reveal that the mineral content in the calcified fibrocartilage of the quadriceps tendon enthesis are similar between wild type and Bsp(-/-) mice. Mechanical testing of the patellar tendon shows that while the tendons fail under similar loads, the Bsp(-/-) patellar tendon is 7.5% larger in cross sectional area than wild type tendons, resulting in a 16.5% reduction in failure stress. However, Picrosirius Red staining shows no difference in collagen organization. Data collected here indicate that BSP is present in the calcified fibrocartilage of murine entheses and suggest that BSP plays a regulatory role in this structure, influencing the growth of the calcified fibrocartilage in addition to the weakening of the tendon mechanical properties. Based on the phenotype of the Bsp(-/-) mouse enthesis, and the known in vitro functional properties of the protein, BSP may be a useful therapeutic molecule in the reattachment of tendons and ligaments to bone. Copyright © 2016 International Society of Matrix Biology. All rights reserved.

AP1 binding site is another target of FGF2 regulation of bone sialoprotein gene transcription.

PubMed

Takai, Hideki; Araki, Shouta; Mezawa, Masaru; Kim, Dong-Soon; Li, Xinyue; Yang, Li; Li, Zhengyang; Wang, Zhitao; Nakayama, Youhei; Ogata, Yorimasa

2008-02-29

Bone sialoprotein (BSP) is an early marker of osteoblast differentiation. We previously reported that fibroblast growth factor 2 (FGF2) regulates BSP gene transcription via FGF2 response element (FRE) in the proximal promoter of rat BSP gene. We here report that activator protein 1 (AP1) binding site overlapping with glucocorticoid response element (GRE) AP1/GRE in the rat BSP gene promoter is another target of FGF2. Using the osteoblastic cell line ROS17/2.8, we determined that BSP mRNA levels increased by 10 ng/ml FGF2 at 6 and 12 h. Runx2 protein levels increased by FGF2 (10 ng/ml) at 3 h. Treatment of ROS17/2.8 cells with FGF2 (10 ng/ml, 12 h) increased luciferase activities of constructs including -116 to +60 and -938 to +60 of the rat BSP gene promoter. Effects of FGF2 abrogated in constructs included 2 bp mutations in the FRE and AP1/GRE elements. Luciferase activities induced by FGF2 were blocked by tyrosine kinase inhibitor herbimycin A, src-tyrosine kinase inhibitor PP1 and MAP kinase kinase inhibitor U0126. Gel shift analyses showed that FGF2 increased binding of FRE and AP1/GRE elements. Notably, the AP1/GRE-protein complexes were supershifted by Smad1 and c-Fos antibodies, c-Jun and Dlx5 antibodies disrupted the complexes formation, on the other hand AP1/GRE-protein complexes did not change by Runx2 antibody. These studies demonstrate that FGF2 stimulates BSP gene transcription by targeting the FRE and AP1/GRE elements in the rat BSP gene promoter.

A rat osteogenic cell line (UMR 106-01) synthesizes a highly sulfated form of bone sialoprotein.

PubMed

Midura, R J; McQuillan, D J; Benham, K J; Fisher, L W; Hascall, V C

1990-03-25

The rat osteosarcoma cell line (UMR 106-01) synthesizes and secretes relatively large amounts of a sulfated glycoprotein into its culture medium (approximately 240 ng/10(6) cells/day). This glycoprotein was purified, and amino-terminal sequence analysis identified it as bone sialoprotein (BSP). [35S]Sulfate, [3H]glucosamine, and [3H]tyrosine were used as metabolic precursors to label the BSP. Sulfate esters were found on N- and O-linked oligosaccharides and on tyrosine residues, with about half of the total tyrosines in the BSP being sulfated. The proportion of 35S activity in tyrosine-O-sulfate (approximately 70%) was greater than that in N-linked (approximately 20%) and O-linked (approximately 10%) oligosaccharides. From the deduced amino acid sequence for rat BSP (Oldberg, A., Franzén, A., and Heinegård, D. (1988) J. Biol. Chem. 263, 19430-19432), the results indicate that on average approximately 12 tyrosine residues, approximately 3 N-linked, and approximately 2 O-linked oligosaccharides are sulfated/molecule. The carboxyl-terminal quarter of the BSP probably contains most, if not all, of the sulfated tyrosine residues because this region of the polypeptide contains the necessary requirements for tyrosine sulfation. Oligosaccharide analyses indicated that for every N-linked oligosaccharide on the BSP, there are also approximately 2 hexa-, approximately 5 tetra-, and approximately 2 trisaccharides O-linked to serine and threonine residues. On average, the BSP synthesized by UMR 106-01 cells would contain a total of approximately 3 N-linked and approximately 25 of the above O-linked oligosaccharides. This large number of oligosaccharides is in agreement with the known carbohydrate content (approximately 50%) of the BSP.

Perioperative transfusion management in gastric cancer surgery: Analysis of the Spanish subset of the EURECCA oesophago-gastric cancer registry.

PubMed

Osorio, Javier; Jericó, Carlos; Miranda, Coro; Garsot, Elisenda; Luna, Alexis; Miró, Mónica; Santamaría, Maite; Artigau, Eva; Rodríguez-Santiago, Joaquín; Castro, Sandra; Feliu, Josep; Aldeano, Aurora; Olona, Carles; Momblan, Dulce; Ruiz, David; Galofré, Gonzalo; Pros, Inmaculada; García-Albéniz, Xabier; Lozano, Miguel; Pera, Manuel

2018-05-14

This study evaluated allogenic packed red blood cell (aPRBC) transfusion rates in patients undergoing resection for gastric cancer and the implementation of blood-saving protocols (BSP). Retrospective study of all gastric cancer patients operated on with curative intent in Catalonia and Navarra (2011-2013) and included in the Spanish subset of the EURECCA Oesophago-Gastric Cancer Registry. Hospitals with BSP were defined as those with a preoperative haemoglobin (Hb) optimisation circuit associated with restrictive transfusion strategies. Predictors of aPRBC transfusion were identified by multinomial logistic regression analysis. A total of 652 patients were included, 274 (42.0%) of which received aPRBC transfusion. Six of the 19 participating hospitals had BSP and treated 145 (22.2%) patients. Low Hb level at diagnosis (10 vs 12.4g/dL), ASA score III/IV, pT3-4, open surgery, associated visceral resection, and having being operated on in a hospital without BSP were predictors of aPRBC transfusion, while low Hb level, associated visceral resection, and non-BSP hospital remained predictors in the multivariate analysis. In case of comparable risk factors for aPRBC transfusion, there was a higher use of preoperative intravenous iron treatment (26.2% vs 13.2%) and a lower percentage of transfusions (31.7% vs 45%) in hospitals with BSP. The perioperative transfusion rate in gastric cancer was 42%. Hospitals with BSP showed a significant reduction of blood transfusions but treated only 22% of patients. Main predictors of aPRBC were low Hb level, associated visceral resection, and undergoing surgery at a hospital without BSP. Copyright © 2018 AEC. Publicado por Elsevier España, S.L.U. All rights reserved.

Bovine spastic paresis: A review of the genetic background and perspectives for the future.

PubMed

Goeckmann, Victoria; Rothammer, Sophie; Medugorac, Ivica

2016-10-01

Bovine spastic paresis (BSP) is a sporadic, progressive neuromuscular disease that is thought to affect all breeds of cattle. The disease manifests as a unilateral or bilateral hyperextension of the hind limb due to increased muscle tone or permanent spasm of mainly the gastrocnemius and/or the quadriceps muscle. Clinical signs only appear in rising, standing and moving animals, which is an important diagnostic feature. Although several medical treatments have been described, surgical procedures such as neurectomy or tenectomy are generally indicated. Even though complete recovery can be achieved, BSP-affected animals should not be used for breeding, since BSP is commonly considered a hereditary disease. The condition therefore negatively affects animal welfare, economics and breeding. When first described in 1922, BSP was already assumed to be heritable, and this assumption has been perpetuated by subsequent authors who have only discussed its possible modes of inheritance, which included monogenetic and polygenetic modes and gene-environment interactions. Besides some clinical aspects and the consideration of the tarsal joint angle as a BSP-correlated trait, this review mainly focuses on the assumed genetic aspects of BSP. Evaluation of the published literature demonstrates that to date, irrevocable proof for the assumed heritability of BSP is still missing. The assumption of heredity is further contradicted by known allele frequencies and incidences of proven hereditary diseases in cattle, such as arachnomelia or bovine spinal muscular atrophy. Consequently, future research is needed to determine the cause of spastic paresis. Procedures that will help test the null-hypothesis ('BSP is not hereditary') and possible modes of inheritance are discussed in this review. Copyright © 2016 Elsevier Ltd. All rights reserved.

A comparative signaling cost analysis of Macro Mobility scheme in NEMO (MM-NEMO) with mobility management protocol

NASA Astrophysics Data System (ADS)

Islam, Shayla; Abdalla, Aisha H.; Habaebi, Mohamed H.; Latif, Suhaimi A.; Hassan, Wan H.; Hasan, Mohammad K.; Ramli, H. A. M.; Khalifa, Othman O.

2013-12-01

NEMO BSP is an upgraded addition to Mobile IPv6 (MIPv6). As MIPv6 and its enhancements (i.e. HMIPv6) possess some limitations like higher handoff latency, packet loss, NEMO BSP also faces all these shortcomings by inheritance. Network Mobility (NEMO) is involved to handle the movement of Mobile Router (MR) and it's Mobile Network Nodes (MNNs) during handoff. Hence it is essential to upgrade the performance of mobility management protocol to obtain continuous session connectivity with lower delay and packet loss in NEMO environment. The completion of handoff process in NEMO BSP usually takes longer period since MR needs to register its single primary care of address (CoA) with home network that may cause performance degradation of the applications running on Mobile Network Nodes. Moreover, when a change in point of attachment of the mobile network is accompanied by a sudden burst of signaling messages, "Signaling Storm" occurs which eventually results in temporary congestion, packet delays or even packet loss. This effect is particularly significant for wireless environment where a wireless link is not as steady as a wired link since bandwidth is relatively limited in wireless link. Hence, providing continuous Internet connection without any interruption through applying multihoming technique and route optimization mechanism in NEMO are becoming the center of attention to the current researchers. In this paper, we propose a handoff cost model to compare the signaling cost of MM-NEMO with NEMO Basic Support Protocol (NEMO BSP) and HMIPv6.The numerical results shows that the signaling cost for the MM-NEMO scheme is about 69.6 % less than the NEMO-BSP and HMIPv6.

Fibroblast growth factor 2 and cyclic AMP synergistically regulate bone sialoprotein gene expression.

PubMed

Shimizu, Emi; Nakayama, Youhei; Nakajima, Yu; Kato, Naoko; Takai, Hideki; Kim, Dong-Soon; Arai, Masato; Saito, Ryoichiro; Sodek, Jaro; Ogata, Yorimasa

2006-07-01

Bone sialoprotein (BSP) is a noncollagenous protein of the mineralized bone extracellular matrix. We here report that FGF2 and cAMP act synergistically to stimulate BSP gene expression. Treatment of ROS 17/2.8 cells with either 10 ng/ml FGF2 or 1 microM FSK for 6 h resulted in 5.4- and 8.2-fold increases, respectively, in the levels of BSP mRNA. However, in the presence of both FGF2 and forskolin (FGF/FSK), BSP mRNA levels were increased synergistically by 20.4-fold. Using a luciferase reporter construct, encompassing BSP promoter nucleotides -116 to +60, transcription was also increased synergistically by 15.0-fold with FGF/FSK, compared to stimulations of 2.6- and 5.3-fold, respectively, for FGF2 and FSK alone. Transcriptional stimulation by FGF/FSK abrogated in constructs included 2 bp mutations in the inverted CCAAT, CRE, FRE and Pit-1 elements. Whereas the FRE-protein complex was increased by FGF2 and FGF/FSK, the Pit-1-protein complex was decreased by FSK and FGF/FSK. Notably, transcriptional activity induced by FGF/FSK was blocked by protein kinase A, tyrosine kinase and MEK inhibitors. These studies indicate that the combinatorial effects of FGF and FSK act through PKA, tyrosine kinase and MAP-kinase-dependent pathways, which target the inverted CCAAT, CRE, FRE and Pit-1 elements in the BSP gene to synergistically increase BSP expression.

Fibroblast growth factor 2 regulates bone sialoprotein gene transcription in human breast cancer cells.

PubMed

Li, Zhengyang; Wang, Zhitao; Yang, Li; Li, Xinyue; Sasaki, Yoko; Wang, Shuang; Araki, Shouta; Mezawa, Masaru; Takai, Hideki; Nakayama, Youhei; Ogata, Yorimasa

2010-03-01

Bone sialoprotein (BSP) is a major non-collagenous, extracellular matrix glycoprotein associated with mineralized tissues. Fibroblast growth factor 2 (FGF2) is recognized as a potent mitogen for a variety of mesenchymal cells. FGF2 produced by osteoblasts accumulates in the bone matrix and acts as an autocrine/paracrine regulator of osteoblasts. We previously reported that FGF2 regulates BSP gene transcription through the FGF2 response element (FRE) and activator protein 1 (AP1) binding site overlapping with the glucocorticoid response element in the rat BSP gene promoter. In the present study, FGF2 (10 ng/ml) increased BSP and Runx2 mRNA levels at 6 h in MCF7 human breast cancer cells. Transient transfection analyses were performed using chimeric constructs of the human BSP gene promoter linked to a luciferase reporter gene. Treatment of MCF7 cells with FGF2 (10 ng/ml) increased the luciferase activity of the constructs between -84LUC and -927LUC. Gel mobility shift analyses showed that FGF2 increased the binding of AP1 and CRE2. The CRE2- and AP1-protein complexes were disrupted by antibodies against CREB1, c-Fos, c-Jun, Fra2, p300 and Runx2. These studies demonstrate that FGF2 stimulates BSP transcription in MCF7 human breast cancer cells by targeting the AP1 and CRE2 elements in the human BSP gene promoter.

Nicotine suppresses bone sialoprotein gene expression.

PubMed

Nakayama, Y; Mezawa, M; Araki, S; Sasaki, Y; Wang, S; Han, J; Li, X; Takai, H; Ogata, Y

2009-10-01

Tobacco smoking is a risk factor for periodontitis and osteoporosis. Nicotine is a major component of tobacco, and has been reported to inhibit proliferation and differentiation of osteoblasts. Bone sialoprotein (BSP) is a mineralized tissue-specific protein expressed by differentiated osteoblasts that appears to function in the initial mineralization of bone. The purpose of this study was to determine the effects of nicotine on bone metabolism. We used rat osteobast-like UMR106 and ROS 17/2.8 cells and rat stromal bone marrow RBMC-D8 cells. To determine the molecular basis of the transcriptional regulation of the BSP gene by nicotine, we conducted Northern hybridization, transient transfection analyses with chimeric constructs of the BSP gene promoter linked to a luciferase reporter gene and gel mobility shift assays. Nicotine (250 microg/mL) decreased the BSP mRNA levels at 12 and 24 h in UMR106 and ROS 17/2.8 cells. From transient transfection assays using various sized BSP promoter-luciferase constructs, nicotine decreased the luciferase activities of the construct, including the promoter sequence nucleotides -116 to +60, in UMR106 and RBMC-D8 cells. Nicotine decreased the nuclear protein binding to the cAMP response element (CRE), fibroblast growth factor 2 response element (FRE) and homeodomain protein-binding site (HOX) at 12 and 24 h. This study indicates that nicotine suppresses BSP transcription mediated through CRE, FRE and HOX elements in the proximal promoter of the rat BSP gene.

Prostate Cancer Progression and Serum SIBLING (Small Integrin Binding N-linked Glycoprotein) Levels

DTIC Science & Technology

2006-10-01

members include bone sialoprotein (BSP), osteopontin (OPN), dentin matrix protein-1 (DMP1), dentin sialophosphoprotein (DSPP) and matrix extracellular...quantitatively determining the levels of bone sialoprotein (BSP), osteopontin (OPN), and dentin sialophosphoprotein (DSPP). In addition we have a...panels e and f). 6 Figure 1. Serum levels of SIBLINGs in prostate cancer sera. Serum levels of (a) bone sialoprotein (BSP), (c) dentin

Peri-implant bone formation and implant integration strength of peptide-modified p(AAM-co-EG/AAC) interpenetrating polymer network-coated titanium implants.

PubMed

Barber, Thomas A; Ho, James E; De Ranieri, Aladino; Virdi, Amarjit S; Sumner, Dale R; Healy, Kevin E

2007-02-01

Interpenetrating polymer networks (IPNs) of poly (acrylamide-co-ethylene glycol/acrylic acid) functionalized with an -Arg-Gly-Asp- (RGD) containing 15 amino acid peptides, derived from rat bone sialoprotein (bsp-RGD(15), were grafted to titanium implants in an effort to modulate bone formation in the peri-implant region in the rat femoral ablation model. Bone-implant contact (BIC) and bone formation within the medullary canal were determined using microcomputed tomography at 2 and 4 weeks postimplantation. BIC for bsp-RGD(15)-IPN implants was enhanced relative to hydroxyapatite tricalcium phosphate (HA-TCP) coated implants, but was similar to all other groups. Aggregate bone formation neither indicated a dose-dependent effect of bsp-RGD(15) nor a meaningful trend. Mechanical testing of implant fixation revealed that only the HA-TCP coated implants supported significant (>1 MPa) interfacial shear strength, despite exhibiting lower overall BIC, an indication that bone ingrowth into the rougher coating was the primary mode of implant fixation. While no evidence was found to support the hypothesis that bsp-RGD(15)-modified IPN coated implants significantly impacted bone-implant bonding, these results point to the lack of correlation between in vitro studies employing primary osteoblasts and in vivo wound healing in the peri-implant region. Copyright 2006 Wiley Periodicals, Inc.

The ASM-NSF Biology Scholars Program: An Evidence-Based Model for Faculty Development

PubMed Central

Chang, Amy L.; Pribbenow, Christine M.

2016-01-01

The American Society for Microbiology (ASM) established its ASM-NSF (National Science Foundation) Biology Scholars Program (BSP) to promote undergraduate education reform by 1) supporting biologists to implement evidence-based teaching practices, 2) engaging life science professional societies to facilitate biologists’ leadership in scholarly teaching within the discipline, and 3) participating in a teaching community that fosters disciplinary-level science, technology, engineering, and mathematics (STEM) reform. Since 2005, the program has utilized year-long residency training to provide a continuum of learning and practice centered on principles from the scholarship of teaching and learning (SoTL) to more than 270 participants (“scholars”) from biology and multiple other disciplines. Additionally, the program has recruited 11 life science professional societies to support faculty development in SoTL and discipline-based education research (DBER). To identify the BSP’s long-term outcomes and impacts, ASM engaged an external evaluator to conduct a study of the program’s 2010–2014 scholars (n = 127) and society partners. The study methods included online surveys, focus groups, participant observation, and analysis of various documents. Study participants indicate that the program achieved its proposed goals relative to scholarship, professional society impact, leadership, community, and faculty professional development. Although participants also identified barriers that hindered elements of their BSP participation, findings suggest that the program was essential to their development as faculty and provides evidence of the BSP as a model for other societies seeking to advance undergraduate science education reform. The BSP is the longest-standing faculty development program sponsored by a collective group of life science societies. This collaboration promotes success across a fragmented system of more than 80 societies representing the life sciences and helps catalyze biology education reform efforts. PMID:27158300

Influence of seminal plasma on the kinematics of boar spermatozoa during freezing.

PubMed

Rodríguez-Martínez, H; Saravia, F; Wallgren, M; Roca, J; Peña, F J

2008-11-01

Sperm motility is, for its relation to cell viability and fertility, a central component of the spermiogram, where consideration of motion patterns allows discrimination of sub-populations among boar spermatozoa. Extension and cryo-preservation imposes changes in these patterns in connection to handling, additives, temperature changes and the removal of boar seminal plasma (BSP) which apparently makes spermatozoa susceptible to oxidative stress, thus affecting survival and motility post-thaw. Detailed kinematic analyses during sperm cooling are sparse, particularly when considering the instrumentation and settings used for analyses, the effect of extenders, and of the BSP the processed spermatozoa are exposed to. Spermatozoa present in the first collectable 10mL of the sperm-rich fraction of the ejaculate (portion 1, P1-BSP), have shown an increased ability to sustain motility during and after cryo-preservation than spermatozoa immersed in the rest of the ejaculate (portion 2, P2). When P2-spermatozoa were cleansed from their BSP and exposed for 60min to pooled P1-BSP, their motility post-thaw increased to similar levels as P1-spermatozoa. This BSP-influence is sire-dependent, presumably related to the protein concentration in the different ejaculate portions, and apparently unrelated to changes in membrane integrity or membrane stability through conventional, controlled cooling.

Adhesion of MC3T3-E1 cells to bone sialoprotein and bone osteopontin specifically bound to collagen I.

PubMed

Bernards, Matthew T; Qin, Chunlin; Ratner, Buddy D; Jiang, Shaoyi

2008-09-01

Bone sialoprotein (BSP) and bone osteopontin (OPN) are members of the SIBLING (small integrin-binding ligand, N-linked glycoproteins) family of proteins commonly found in mineralized tissues. Previously, OPN was shown to exhibit a preferential orientation for MC3T3-E1 cell adhesion when it was specifically bound to collagen. In this work, the orientation of BSP under similar circumstances is examined and compared with OPN. Radiolabeled adsorption isotherms were obtained for BSP bound to both tissue culture polystyrene (TCPS) and collagen-coated TCPS. The results show that collagen has the capacity to bind almost twice as much OPN under identical conditions. An in vitro MC3T3-E1 cell adhesion assay was then performed to compare the cell binding ability of BSP on either TCPS or collagen-coated TCPS with identical amounts of adsorbed protein. It was found that there is no significant difference in the cell binding ability of BSP on either of the substrates. For cell binding studies on collagen-coated TCPS, it was shown that there are a greater number of cells bound to substrates with adsorbed OPN as compared with BSP. The preferable orientation of OPN for cell binding coupled with the higher binding capability of collagen for OPN indicates that OPN is more important than BSP for osteoblast adhesion to the collagen matrix. In addition, a cell inhibition assay was performed to show that all of the cell binding that occurred throughout these studies was dependent upon integrin interactions with the RGD cell binding moiety.

Adhesion of MC3T3-E1 cells to bone sialoprotein and bone osteopontin specifically bound to collagen I

PubMed Central

Bernards, Matthew T.; Qin, Chunlin; Ratner, Buddy D.; Jiang, Shaoyi

2009-01-01

Bone sialoprotein (BSP) and bone osteopontin (OPN) are members of the SIBLING (small integrin-binding ligand, N-linked glycoproteins) family of proteins commonly found in mineralized tissues. Previously, OPN was shown to exhibit a preferential orientation for MC3T3-E1 cell adhesion when it was specifically bound to collagen. In this work, the orientation of BSP under similar circumstances is examined and compared with OPN. Radiolabeled adsorption isotherms were obtained for BSP bound to both tissue culture polystyrene (TCPS) and collagen-coated TCPS. The results show that collagen has the capacity to bind almost twice as much OPN under identical conditions. An in vitro MC3T3-E1 cell adhesion assay was then performed to compare the cell binding ability of BSP on either TCPS or collagen-coated TCPS with identical amounts of adsorbed protein. It was found that there is no significant difference in the cell binding ability of BSP on either of the substrates. For cell binding studies on collagen-coated TCPS, it was shown that there are a greater number of cells bound to substrates with adsorbed OPN as compared with BSP. The preferable orientation of OPN for cell binding coupled with the higher binding capability of collagen for OPN indicates that OPN is more important than BSP for osteoblast adhesion to the collagen matrix. In addition, a cell inhibition assay was performed to show that all of the cell binding that occurred throughout these studies was dependent upon integrin interactions with the RGD cell binding moiety. PMID:18041732

Insulin-like growth factor-I increases bone sialoprotein (BSP) expression through fibroblast growth factor-2 response element and homeodomain protein-binding site in the proximal promoter of the BSP gene.

PubMed

Nakayama, Youhei; Nakajima, Yu; Kato, Naoko; Takai, Hideki; Kim, Dong-Soon; Arai, Masato; Mezawa, Masaru; Araki, Shouta; Sodek, Jaro; Ogata, Yorimasa

2006-08-01

Insulin-like growth factor-I (IGF-I) promotes bone formation by stimulating proliferation and differentiation of osteoblasts. Bone sialoprotein (BSP), is thought to function in the initial mineralization of bone, is selectively expressed by differentiated osteoblast. To determine the molecular mechanism of IGF-I regulation of osteogenesis, we analyzed the effects of IGF-I on the expression of BSP in osteoblast-like Saos2 and in rat stromal bone marrow (RBMC-D8) cells. IGF-I (50 ng/ml) increased BSP mRNA levels at 12 h in Saos2 cells. In RBMC-D8 cells, IGF-I increased BSP mRNA levels at 3 h. From transient transfection assays, a twofold increase in transcription by IGF-I was observed at 12 h in pLUC3 construct that included the promoter sequence from -116 to +60. Effect of IGF-I was abrogated by 2-bp mutations in either the FGF2 response element (FRE) or homeodomain protein-binding site (HOX). Gel shift analyses showed that IGF-I increased binding of nuclear proteins to the FRE and HOX elements. Notably, the HOX-protein complex was supershifted by Smad1 antibody, while the FRE-protein complex was shifted by Smad1 and Cbfa1 antibodies. Dlx2 and Dlx5 antibodies disrupted the formation of the FRE- and HOX-protein complexes. The IGF-I effects on the formation of FRE-protein complexes were abolished by tyrosine kinase inhibitor herbimycin A (HA), PI3-kinase/Akt inhibitor LY249002, and MAP kinase kinase inhibitor U0126, while IGF-I effects on HOX-protein complexes were abolished by HA and LY249002. These studies demonstrate that IGF-I stimulates BSP transcription by targeting the FRE and HOX elements in the proximal promoter of BSP gene.

Unliganded estrogen receptor α stimulates bone sialoprotein gene expression.

PubMed

Takai, Hideki; Matsumura, Hiroyoshi; Matsui, Sari; Kim, Kyung Mi; Mezawa, Masaru; Nakayama, Yohei; Ogata, Yorimasa

2014-04-10

Estrogen is one of the steroid hormones essential for skeletal development. The estrogen receptor (ER) is a transcription factor and a member of the steroid receptor superfamily. There are two different forms of the ER, usually referred to as α and β, each encoded by a separate gene. Hormone-activated ERs form dimers, since the two forms are coexpressed in many cell types. Bone sialoprotein (BSP) is a tissue-specific acidic glycoprotein that is expressed by differentiated osteoblasts, odontoblasts and cementoblasts during the initial formation of mineralized tissue. To determine the molecular basis of the tissue-specific expression of BSP and its regulation by estrogen and the ER, we have analyzed the effects of β-estradiol and ERα on BSP gene transcription. ERα protein levels were increased after ERα overexpression in ROS17/2.8 cells. While BSP mRNA levels were increased by ERα overexpression, the endogenous and overexpressed BSP mRNA levels were not changed by β-estradiol (10(-8)M, 24 h). Luciferase activities of different sized BSP promoter constructs (pLUC3~6) were increased by ERα overexpression, whereas basal and induced luciferase activities by ERα overexpression were not influenced by β-estradiol. Effects of ERα overexpression were abrogated by 2 bp mutations in either the cAMP response element (CRE) or activator protein 1 (AP1)/glucocorticoid response element (GRE). Gel shift analyses showed that ERα overexpression increased binding to the CRE and AP1/GRE elements. Notably, the CRE-protein complexes were disrupted by ERα, CREB and phospho-CREB antibodies. The AP1/GRE-protein complexes were supershifted by the c-Fos antibody. These studies demonstrate that ERα stimulates BSP gene transcription in a ligand-independent manner by targeting the CRE and AP1/GRE elements in the rat BSP gene promoter. Copyright © 2014 Elsevier B.V. All rights reserved.

Applications of transgenics in studies of bone sialoprotein.

PubMed

Zhang, Jin; Tu, Qisheng; Chen, Jake

2009-07-01

Bone sialoprotein (BSP) is a major non-collagenous protein in mineralizing connective tissues such as dentin, cementum and calcified cartilage tissues. As a member of the Small Integrin-Binding Ligand, N-linked Glycoprotein (SIBLING) gene family of glycoproteins, BSP is involved in regulating hydroxyapatite crystal formation in bones and teeth, and has long been used as a marker gene for osteogenic differentiation. In the most recent decade, new discoveries in BSP gene expression and regulation, bone remodeling, bone metastasis, and bone tissue engineering have been achieved with the help of transgenic mice. In this review, we discuss these new discoveries obtained from the literatures and from our own laboratory, which were derived from the use of transgenic mouse mutants related to BSP gene or its promoter activity.

Regulation of bone sialoprotein mRNA by steroid hormones

PubMed Central

1989-01-01

In this report we demonstrate an increase in the steady-state level of bone sialoprotein (BSP) mRNA in rat calvaria and a rat osteosarcoma cell line (ROS 17/2.8) after treatment with the synthetic glucocorticoid, dexamethasone. In contrast, 1.25-dihydroxyvitamin D3 reduced the amount of BSP mRNA in calvaria and inhibited the dexamethasone induction in ROS 17/2.8 cells. The increase in BSP mRNA is most likely due to an increase in the transcriptional rate. The stability of mRNA was unchanged after dexamethasone treatment with a half-life of approximately 5 h. Nuclear transcription experiments with nuclei isolated from ROS 17/2.8 cells showed an increased BSP mRNA synthesis in cells treated with dexamethasone. PMID:2592421

Nucleation of hydroxyapatite by bone sialoprotein.

PubMed Central

Hunter, G K; Goldberg, H A

1993-01-01

Bone sialoprotein (BSP) and osteopontin, the major phosphorylated proteins of mammalian bone, have been proposed to function in the initiation of mineralization. To test this hypothesis, the effects of BSP and osteopontin on hydroxyapatite crystal formation were determined by using a steady-state agarose gel system. At low calcium phosphate concentrations, no accumulation of calcium and phosphate occurred in control gels or gels containing osteopontin. Gels containing BSP at 1-5 micrograms/ml, however, exhibited a visible precipitation band and significantly elevated Ca + PO4 contents. By powder x-ray diffraction, the precipitate formed in the presence of BSP was shown to be hydroxyapatite. These findings suggest that bone sialoprotein may be involved in the nucleation of hydroxyapatite at the mineralization front of bone. Images Fig. 4 PMID:8397409

Androgen receptor stimulates bone sialoprotein (BSP) gene transcription via cAMP response element and activator protein 1/glucocorticoid response elements.

PubMed

Takai, Hideki; Nakayama, Youhei; Kim, Dong-Soon; Arai, Masato; Araki, Shouta; Mezawa, Masaru; Nakajima, Yu; Kato, Naoko; Masunaga, Hiroshi; Ogata, Yorimasa

2007-09-01

Bone sialoprotein (BSP) is an early marker of osteoblast differentiation. Androgens are steroid hormones that are essential for skeletal development. The androgen receptor (AR) is a transcription factor and a member of the steroid receptor superfamily that plays an important role in male sexual differentiation and prostate cell proliferation. To determine the molecular mechanism involved in the stimulation of bone formation, we have analyzed the effects of androgens and AR effects on BSP gene transcription. AR protein levels were increased after AR overexpression in ROS17/2.8 cells. BSP mRNA levels were increased by AR overexpression. However, the endogenous and overexpressed BSP mRNA levels were not changed by DHT (10(-8) M, 24 h). Whereas luciferase (LUC) activities in all constructs, including a short construct (nts -116 to +60), were increased by AR overexpression, the basal and LUC activities enhanced by AR overexpression were not induced by DHT (10(-8)M, 24 h). The effect of AR overexpression was abrogated by 2 bp mutations in either the cAMP response element (CRE) or activator protein 1 (AP1)/glucocorticoid response element (GRE). Gel shift analyses showed that AR overexpression increased binding to the CRE and AP1/GRE elements. Notably, the CRE-protein complexes were supershifted by phospho-CREB antibody, and CREB, c-Fos, c-Jun, and AR antibodies disrupted the complexes formation. The AP1/GRE-protein complexes were supershifted by c-Fos antibody and c-Jun, and AR antibodies disrupted the complexes formation. These studies demonstrate that AR stimulates BSP gene transcription by targeting the CRE and AP1/GRE elements in the promoter of the rat BSP gene.

Bone sialoprotein, but not osteopontin, deficiency impairs the mineralization of regenerating bone during cortical defect healing.

PubMed

Monfoulet, Laurent; Malaval, Luc; Aubin, Jane E; Rittling, Susan R; Gadeau, Alain P; Fricain, Jean-Christophe; Chassande, Olivier

2010-02-01

Bone healing is a complex multi-step process, which depends on the position and size of the lesion, and on the mechanical stability of the wounded area. To address more specifically the mechanisms involved in cortical bone healing, we created drill-hole defects in the cortex of mouse femur, a lesion that triggers intramembranous repair, and compared the roles of bone sialoprotein (BSP) and osteopontin (OPN), two proteins of the extracellular matrix, in the repair process. Bone regeneration was analyzed by ex vivo microcomputerized X-ray tomography and histomorphometry of bones of BSP-deficient, OPN-deficient and wild-type mice. In all mouse strains, the cortical gap was bridged with woven bone within 2 weeks and no mineralized tissue was observed in the marrow. Within 3 weeks, lamellar cortical bone filled the gap. The amount and degree of mineralization of the woven bone was not affected by OPN deficiency, but cortical bone healing was delayed in BSP-deficient mice due to delayed mineralization. Gene expression studies showed a higher amount of BSP transcripts in the repair bone of OPN-deficient mice, suggesting a possible compensation of OPN function by BSP in OPN-null mice. Our data suggest that BSP, but not OPN, plays a role in primary bone formation and mineralization of newly formed bone during the process of cortical bone healing. (c) 2009 Elsevier Inc. All rights reserved.

Butyric acid stimulates bone sialoprotein gene transcription.

PubMed

Yang, Li; Li, Zhengyang; Li, Xinyue; Wang, Zhitao; Wang, Shuang; Sasaki, Yoko; Takai, Hideki; Ogata, Yorimasa

2010-06-01

Butyric acid (sodium butyrate; BA) is an extracellular metabolite secreted from periodontopathic bacteria present in subgingival plaque. BA induces apoptosis of T and B cells, and acts as a potent inhibitor of histone deacetylases. Bone sialoprotein (BSP) is thought to function in the initial mineralization of bone, and may be crucial for osteoblast differentiation, bone matrix mineralization and tumor metastasis. In the present study we investigated the regulation of BSP transcription by BA in rat osteoblast-like ROS17/2.8 cells. At 12 h, BA (10(-4) M) increased the level of BSP mRNA, and enhanced the luciferase activity of the construct pLUC3, which includes the promoter sequence between nucleotides -116 and +60. Transcriptional stimulation by BA was abrogated in the pLUC3 construct which containing a 2-bp mutation in the fibroblast growth factor 2 response element (FRE). Gel shift analyses showed that BA increased the binding of nuclear protein to FRE. These data suggest that BA increases the transcription of the BSP gene mediated through FRE in the rat BSP gene promoter, and induces osteoblast activity in the early stage of bone formation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu Lingling; Zaidi, Samir; Peng Yuanzhen

Strontium ranelate, a new agent for the treatment of osteoporosis, has been shown stimulate bone formation in various experimental models. This study examines the effect of strontium ranelate on gene expression in osteoblasts, as well as the formation of mineralized (von Kossa-positive) colony-forming unit-osteoblasts (CFU-obs). Bone marrow-derived stromal cells cultured for 21 days under differentiating conditions, when exposed to strontium ranelate, displayed a significant time- and concentration-dependent increase in the expression of the master gene, Runx2, as well as bone sialoprotein (BSP), but interestingly without effects on osteocalcin. This was associated with a significant increase in the formation of CFU-obsmore » at day 21 of culture. In U-33 pre-osteoblastic cells, strontium ranelate significantly enhanced the expression of Runx2 and osteocalcin, but not BSP. Late, more mature osteoblastic OB-6 cells showed significant elevations in BSP and osteocalcin, but with only minimal effects on Runx2. In conclusion, strontium ranelate stimulates osteoblast differentiation, but the induction of the program of gene expression appears to be cell type-specific. The increased osteoblastic differentiation is the likely basis underlying the therapeutic bone-forming actions of strontium ranelate.« less

Applications of Transgenics in Studies of Bone Sialoprotein

PubMed Central

Zhang, Jin; Tu, Qisheng; Chen, Jake

2010-01-01

Bone sialoprotein (BSP) is a major non-collagenous protein in mineralizing connective tissues such as dentin, cementum and calcified cartilage tissues. As a member of the SIBLING (Small Integrin-Binding Ligand, N-linked Glycoprotein) gene family of glycoproteins, BSP is involved in regulating hydroxyapatite crystal formation in bones and teeth, and has long been used as a marker gene for osteogenic differentiation. In the most recent decade, new discoveries in BSP gene expression and regulation, bone remodeling, bone metastasis, and bone tissue engineering have been achieved with the help of transgenic mice. In this review, we discuss these new discoveries obtained from the literatures and from our own laboratory, which were derived from the use of transgenic mouse mutants related to BSP gene or its promoter activity. PMID:19326395

Bletilla striata polysaccharide stimulates inducible nitric oxide synthase and proinflammatory cytokine expression in macrophages.

PubMed

Diao, Huajia; Li, Xin; Chen, Jiangning; Luo, Yi; Chen, Xi; Dong, Lei; Wang, Chunming; Zhang, Chenyu; Zhang, Junfeng

2008-02-01

Bletilla striata, a traditional Chinese medicine, has been used for the treatment of alimentary canal mucosal damage, ulcers, bleeding, bruises and burns. B. striata polysaccharide (BSP) isolated from B. striata was found to enhance vascular endothelial cell (EC) proliferation and vascular endothelial growth factor (VEGF) expression. However, the wound healing mechanism of BSP is not well understood. In this study, the results show that treatment with BSP induces coordinate changes in inducible nitric oxide synthase (iNOS), tumor necrosis factor alpha (TNF-alpha) and interleukin 1 beta (IL-1beta) mRNA levels and enhances the expression of these cytokines, but has no effect on interferon gamma (IFN-gamma) level. In this study, we partially elucidate the wound healing mechanism of BSP.

Regulation of human bone sialoprotein gene transcription by platelet-derived growth factor-BB.

PubMed

Mezawa, Masaru; Araki, Shouta; Takai, Hideki; Sasaki, Yoko; Wang, Shuang; Li, Xinyue; Kim, Dong-Soon; Nakayama, Youhei; Ogata, Yorimasa

2009-04-15

Platelet-derived growth factor (PDGF) is produced by mesenchymal cells and released by platelets following aggregation and is synthesized by osteoblasts. In bone, PDGF stimulates proliferation and differentiation of osteoblasts. PDGF also increases bone resorption, most likely by increasing the number of osteoclasts. Bone sialoprotein (BSP) is thought to function in the initial mineralization of bone, selectively expressed by differentiated osteoblast. To determine the molecular mechanisms PDGF regulation of human BSP gene transcription, we have analyzed the effects of PDGF-BB on osteoblast-like Saos2 and ROS17/2.8 cells. PDGF-BB (5 ng/ml) increased BSP mRNA and protein levels at 12 h in Saos2 cells, and induced BSP mRNA expression at 3 h, reached maximal at 12 h in ROS17/2.8 cells. Transient transfection analyses were performed using chimeric constructs of the human BSP gene promoter linked to a luciferase reporter gene. Treatment of Saos2 cells with PDGF-BB (5 ng/ml, 12 h) increased luciferase activities of all constructs between -184LUC to -2672LUC including the human BSP gene promoter. Effects of PDGF-BB abrogated in constructs included 2 bp mutations in the two cAMP response elements (CRE1 and CRE2), activator protein 1(3) (AP1(3)) and shear stress response element 1 (SSRE1). Luciferase activities induced by PDGF-BB were blocked by protein kinase A inhibitor H89 and tyrosine kinase inhibitor herbimycin A. Gel mobility shift analyses showed that PDGF-BB increased binding of CRE1, CRE2, AP1(3) and SSRE1 elements. CRE1- and CRE2-protein complexes were supershifted by CREB1 and phospho-CREB1 antibodies. Notably, AP1(3)-protein complexes were supershifted by c-Fos and JunD, and disrupted by CREB1, phospho-CREB1, c-Jun and Fra2 antibodies. These studies, therefore, demonstrate that PDGF-BB stimulates human BSP transcription by targeting the CRE1, CRE2, AP1(3) and SSRE1 elements in the human BSP gene promoter.

Endothelin-1 regulates rat bone sialoprotein gene transcription.

PubMed

Li, Xinyue; Wang, Zhitao; Yang, Li; Li, Zhengyang; Ogata, Yorimasa

2010-06-01

Endothelin-1 (ET-1) was originally discovered as a vasoconstrictor protein excreted by vascular endothelial cells. Recently, tumor-produced ET-1 has been considered to stimulate osteoblasts to form new bone, and to be an important mediator of osteoblastic bone metastasis. ET-1 has high affinity for two different membrane receptors, ET(A)R and ET(B)R, which are expressed by many types of cells including osteoblasts. Bone sialoprotein (BSP) is a phosphorylated and sulfated glycoprotein associated with mineralized connective tissues. To investigate the effects of ET-1 on BSP transcription, we used rat osteoblast-like ROS17/2.8 cells. Levels of BSP and osteopontin mRNA were increased at 12 h after treatment with ET-1 (10 ng/ml), and ET-1 at the same concentration induced luciferase activity of a -116 to +60 BSP promoter construct at 6 h. Transcriptional activity of -84BSPLUC, which contains the cAMP response element (CRE), was increased by ET-1. Furthermore, at 6 h, ET-1 (10 ng/ml) increased the binding of nuclear protein to CRE, the FGF2 response element (FRE) and the homeodomain protein-binding site (HOX). Antibodies against CREB1, JunD and Fra2 disrupted the formation of CRE-protein complexes, while antibodies against Runx2 and Dlx5 reduced the formation of FRE- and HOX-protein complexes. These findings indicate that ET-1 increases BSP transcription via the CRE, FRE and HOX sites in the rat BSP gene promoter.

Bone sialoprotein is predictive of bone metastases in resectable non-small-cell lung cancer: a retrospective case-control study.

PubMed

Papotti, Mauro; Kalebic, Thea; Volante, Marco; Chiusa, Luigi; Bacillo, Elisa; Cappia, Susanna; Lausi, Paolo; Novello, Silvia; Borasio, Piero; Scagliotti, Giorgio V

2006-10-20

Bone metastases (BM) in non-small-cell lung cancer (NSCLC) may be detected at diagnosis or during the course of the disease, and are associated with a worse prognosis. Currently, there are no predictive or diagnostic markers to identify high-risk patients for metastatic bone dissemination. Thirty patients with resected NSCLC who subsequently developed BM were matched for clinicopathologic parameters to 30 control patients with resected NSCLC without any metastases and 26 patients with resected NSCLC and non-BM lesions. Primary tumors were investigated by immunohistochemistry for 10 markers involved in bone resorption or development of metastases. Differences among groups were estimated by chi2 test, whereas the prognostic impact of clinicopathologic parameters and marker expression was evaluated by univariate (Wilcoxon and Mantel-Cox tests) and multivariate (Cox proportional hazards regression model) analyses. The presence of bone sialoprotein (BSP) was strongly associated with bone dissemination (P < .001) and, independently, with worse outcome (P = .02, Mantel-Cox test), as defined by overall survival. To evaluate BSP protein expression in nonselected NSCLC, a series of 120 consecutive resected lung carcinomas was added to the study, and BSP prevalence reached 40%. No other markers showed a statistically significant difference among the three groups or demonstrated a prognostic impact, in terms of both overall survival and time interval to metastases. BSP protein expression in the primary resected NSCLC is strongly associated with BM progression and could be useful in identifying high-risk patients who could benefit from novel modalities of surveillance and preventive treatment.

Transcriptional regulation of bone sialoprotein gene by Porphyromonas gingivalis lipopolysaccharide.

PubMed

Li, Xinyue; Kato, Naoko; Mezawa, Masaru; Li, Zhengyang; Wang, Zhitao; Yang, Li; Sasaki, Yoko; Kaneko, Takashi; Takai, Hideki; Yoshimura, Atsutoshi; Ogata, Yorimasa

2010-07-01

Lipopolysaccharide (LPS) is a major mediator of inflammatory response. Periodontopathic bacterium Porphyromonas gingivalis LPS has quite different character from Escherichia coli LPS. E. coli LPS is agonist for Toll-like receptor 4 (TLR4), whereas P. gingivalis LPS worked as antagonist for TLR4. Bone sialoprotein (BSP) is an early marker of osteoblast differentiation. To investigate the effects of P. gingivalis LPS on BSP transcription, we used rat osteoblast-like ROS17/2.8 cells. BSP mRNA levels were decreased by 0.1 microg/ml and increased by 0.01 microg/ml P. gingivalis LPS at 12 h. Results of luciferase assays showed that 0.1 microg/ml decreased and 0.01 microg/ml P. gingivalis LPS increased BSP transcription in -116 to +60 BSP construct. The effects of P. gingivalis LPS were abrogated by double mutations in cAMP response element (CRE) and FGF2 response element (FRE). Tyrosine kinase inhibitor herbimycin A, ERK1/2 inhibitor and antioxidant N-acetylcystein inhibited effects of P. gingivalis LPS. Protein kinase A inhibitor and PI3-kinase/Akt inhibitor only abolished the effect of 0.01 microg/ml P. gingivalis LPS. Furthermore, 0.1 microg/ml LPS decreased the CRE- and FRE-protein complexes formation, whereas 0.01 microg/ml P. gingivalis LPS increased the nuclear protein binding to CRE and FRE. ChIP assays revealed increased binding of CREB1, JunD, Fra2, Runx2, Dlx5, and Smad1 to a chromatin fragment containing the CRE and FRE by 0.01 microg/ml P. gingivalis LPS. These studies therefore indicated that 0.1 microg/ml suppressed, and 0.01 microg/ml P. gingivalis LPS increased BSP gene transcription mediated through CRE and FRE elements in the rat BSP gene promoter. J. Cell. Biochem. 110: 823-833, 2010. (c) 2010 Wiley-Liss, Inc.

In situ hybridization and immunohistochemistry of bone sialoprotein and secreted phosphoprotein 1 (osteopontin) in the developing mouse mandibular condylar cartilage compared with limb bud cartilage

PubMed Central

Shibata, Shunichi; Fukada, Kenji; Suzuki, Shoichi; Ogawa, Takuya; Yamashita, Yasuo

2002-01-01

Mandibular condylar cartilage is often classified as a secondary cartilage, differing from the primary cartilaginous skeleton in its rapid progress from progenitor cells to hypertrophic chondrocytes. In this study we used in situ hybridization and immunohistochemistry to investigate whether the formation of primary (tibial) and secondary (condylar) cartilage also differs with respect to the expression of two major non-collagenous glycoproteins of bone matrix, bone sialoprotein (BSP) and secreted phosphoprotein 1 (Spp1, osteopontin). The mRNAs for both molecules were never expressed until hypertrophic chondrocytes appeared. In the tibial cartilage, hypertrophic chondrocytes first appeared at E14 and the expression of BSP and Spp1 mRNAs was detected in the lower hypertrophic cell zone, but the expression of BSP mRNA was very weak. In the condylar cartilage, hypertrophic chondrocytes appeared at E15 as soon as cartilage tissue appeared. The mRNAs for both molecules were expressed in the newly formed condylar cartilage, although the proteins were not detected by immunostaining; BSP mRNA in the condylar cartilage was more extensively expressed than that in the tibial cartilage at the corresponding stage (first appearance of hypertrophic cell zone). Endochondral bone formation started at E15 in the tibial cartilage and at E16 in the condylar cartilage. At this stage (first appearance of endochondral bone formation), BSP mRNA was also more extensively expressed in the condylar cartilage than in the tibial cartilage. The hypertrophic cell zone in the condylar cartilage rapidly extended during E15–16. These results indicate that the formation process of the mandibular condylar cartilage differs from that of limb bud cartilage with respect to the extensive expression of BSP mRNA and the rapid extension of the hypertrophic cell zone at early stages of cartilage formation. Furthermore, these results support the hypothesis that, in vivo, BSP promotes the initiation of mineralization. PMID:12033735

Differential abundances of four forms of Binder of SPerm 1 in the seminal plasma of Bos taurus indicus bulls with different patterns of semen freezability.

PubMed

Magalhães, Marcos Jorge; Martins, Leonardo Franco; Senra, Renato Lima; Santos, Thaís Ferreira Dos; Okano, Denise Silva; Pereira, Paulo Roberto Gomes; Faria-Campos, Alessandra; Campos, Sérgio Vale Aguiar; Guimarães, José Domingos; Baracat-Pereira, Maria Cristina

2016-08-01

The Binder of SPerm 1 (BSP1) protein is involved in the fertilization and semen cryopreservation processes and is described to be both beneficial and detrimental to sperm. Previously, the relationship of BSP1 with freezability events has not been completely understood. The objective of this work was to determine the differential abundance of the forms of the BSP1 protein in cryopreserved seminal plasma of Bos taurus indicus bulls with different patterns of semen freezability using proteomics. A wide cohort of adult bulls with high genetic value from an artificial insemination center was used as donors of high quality, fresh semen. Nine bulls presenting different patterns of semen freezability were selected. Two-dimensional gel electrophoresis showed differential abundance in a group of seven protein spots in the frozen/thawed seminal plasma from the bulls, ranging from 15 to 17 kDa, with pI values from 4.6 to 5.8. Four of these spots were confirmed to be BSP1 using mass spectrometry, proteomics, biochemical, and computational analysis (Tukey's test at P < 0.05). The protein spot weighing 15.52 ± 0.53 kDa with a pI value of 5.78 ± 0.12 is highlighted by its high abundance in bulls with low semen freezability and its absence in bulls presenting high semen freezability. This is the first report showing that more than two forms of BSP1 are found in the seminal plasma of Nelore adult bulls and not all animals have a similar abundance of each BSP1 form. Different BSP1 forms may be involved in different events of fertilization and the cryopreservation process. Copyright © 2016 Elsevier Inc. All rights reserved.

Reliability and utility of the Behaviour Support Plan Quality Evaluation tool (BSP-QEII) for auditing and quality development in services for adults with intellectual disability and challenging behaviour.

PubMed

McVilly, K; Webber, L; Paris, M; Sharp, G

2013-08-01

Having an objective means of evaluating the quality of behaviour support plans (BSPs) could assist service providers and statutory authorities to monitor and improve the quality of support provided to people with intellectual disability (ID) who exhibit challenging behaviour. The Behaviour Support Plan Quality Evaluation Guide II (BSP-QEII) was developed to monitor and assess BSPs prepared by teachers to support children with disability in the school system. This study investigated the application of the BSP-QEII to the assessment of BSPs for adults with ID in community support services. The inter-rater reliability of the BSP-QEII was assessed. The utility of the BPS-QEII was then investigated with reference to a time series study of matched pairs of BSPs, developed for the same clients over a period of approximately 3 years. Differences in plan quality measured across a number of service and systemic variables were also investigated. The BSP-QEII was found to have good inter-rater reliability and good utility for audit purposes. It was able to discriminate changes in plan quality over time. Differences in plan quality were also evident across different service types, where specialist staff had or had not been involved, and in some instances where a statutory format for the plan had or had not been used. There were no differences between plans developed by government and community sector agencies, nor were there any regional differences across the jurisdiction. The BSP-QEII could usefully be adopted as an audit tool for measuring the quality of BSPs for adults with ID. In addition to being used for research and administrative auditing, the principles underpinning the BSP-QEII could also be useful to guide policy and educational activities for staff in community based services for adults with ID. © 2012 The Authors. Journal of Intellectual Disability Research © 2012 John Wiley & Sons Ltd, MENCAP & IASSID.

Bundle Security Protocol for ION

NASA Technical Reports Server (NTRS)

Burleigh, Scott C.; Birrane, Edward J.; Krupiarz, Christopher

2011-01-01

This software implements bundle authentication, conforming to the Delay-Tolerant Networking (DTN) Internet Draft on Bundle Security Protocol (BSP), for the Interplanetary Overlay Network (ION) implementation of DTN. This is the only implementation of BSP that is integrated with ION.

Structural Requirements For Bone Sialoprotein Binding And Modulation Of Matrix Metalloproteinase-2

PubMed Central

Jain, Alka; Karadag, Abdullah; Fisher, Larry W.; Fedarko, Neal S.

2008-01-01

Bone sialoprotein (BSP) has been shown to induce limited gelatinase activity in latent matrix metalloproteinase-2 (MMP-2) without removal of the propeptide and to restore enzymatic activity to MMP-2 previously inhibited by tissue inhibitor of matrix metalloproteinase-2 (TIMP2). The current study identifies structural domains in human BSP and MMP-2 that contribute to these interactions. The 26 amino acid domain encoded by exon 4 of BSP is shown by a series of binding and activity assays to be involved in the displacement of MMP-2′s propeptide from the active site and thereby inducing the protease activity. Binding assays in conjunction with enzyme activity assays demonstrate that both amino- and carboxy-terminal domains of BSP contribute to restoration of activity to TIMP2-inhibited MMP-2, while the MMP-2 hemopexin domain is not required for reactivation. PMID:18729384

Structural requirements for bone sialoprotein binding and modulation of matrix metalloproteinase-2.

PubMed

Jain, Alka; Karadag, Abdullah; Fisher, Larry W; Fedarko, Neal S

2008-09-23

Bone sialoprotein (BSP) has been shown to induce limited gelatinase activity in latent matrix metalloproteinase-2 (MMP-2) without removal of the propeptide and to restore enzymatic activity to MMP-2 previously inhibited by tissue inhibitor of matrix metalloproteinase-2 (TIMP2). The current study identifies structural domains in human BSP and MMP-2 that contribute to these interactions. The 26 amino acid domain encoded by exon 4 of BSP is shown by a series of binding and activity assays to be involved in the displacement of MMP-2's propeptide from the active site and thereby inducing the protease activity. Binding assays in conjunction with enzyme activity assays demonstrate that both amino- and carboxy-terminal domains of BSP contribute to restoration of activity to TIMP2-inhibited MMP-2, while the MMP-2 hemopexin domain is not required for reactivation.

Structural and Functional Analysis of Cell Wall-anchored Polypeptide Adhesin BspA in Streptococcus agalactiae*

PubMed Central

Rego, Sara; Heal, Timothy J.; Pidwill, Grace R.; Till, Marisa; Robson, Alice; Lamont, Richard J.; Sessions, Richard B.; Jenkinson, Howard F.; Race, Paul R.; Nobbs, Angela H.

2016-01-01

Streptococcus agalactiae (group B Streptococcus, GBS) is the predominant cause of early-onset infectious disease in neonates and is responsible for life-threatening infections in elderly and immunocompromised individuals. Clinical manifestations of GBS infection include sepsis, pneumonia, and meningitis. Here, we describe BspA, a deviant antigen I/II family polypeptide that confers adhesive properties linked to pathogenesis in GBS. Heterologous expression of BspA on the surface of the non-adherent bacterium Lactococcus lactis confers adherence to scavenger receptor gp340, human vaginal epithelium, and to the fungus Candida albicans. Complementary crystallographic and biophysical characterization of BspA reveal a novel β-sandwich adhesion domain and unique asparagine-dependent super-helical stalk. Collectively, these findings establish a new bacterial adhesin structure that has in effect been hijacked by a pathogenic Streptococcus species to provide competitive advantage in human mucosal infections. PMID:27311712

Mechanical tensile stress effects on the expression of bone sialoprotein in bovine cementoblasts.

PubMed

Yu, Hongyou; Ren, Yijin; Sandham, Andrew; Ren, Aishu; Huang, Lan; Bai, Ding

2009-03-01

To develop a new cementoblast culture method and to detect bone sialoprotein (BSP) expression in response to high and low mechanical tensile stress in cementoblast in vitro. Cementoblasts were collected from the roots of newborn bovine teeth and were identified with cementum-derived attachment protein (CAP) antibody 3G9. Cell proliferation was evaluated by MTT [3-(4,5-dimethylthazol-2-yl)-2,5-diphenyl tetrazolium bromide] assay, and mineralization was confirmed by von Kossa staining. Mechanical tensile stress was applied in vitro to the cementoblast with the use of a uniaxial four-point bending system with 2000 or 4000 microstrains, at a frequency of 0.5 Hz for 3, 6, 12, 24, or 36 hours. BSP mRNA level was quantified by real-time quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR). A large amount of cementoblast was observed to be expressing CAP. Cementoblasts had a proliferation tendency similar to that of osteoblasts but different from that of periodontal ligament (PDL) cells. Cementoblasts had the ability to become mineralized between osteoblasts and PDL cells. The mechanical tensile stress significantly up-regulated BSP mRNA expression, which reached a peak at 24 hours in both 2000 and 4000 microstrain groups (P < .01) and was tenfold and sixfold higher than that of controls, respectively. BSP expression dropped toward baseline levels at 36 hours in both groups. Mechanical tensile stress up-regulated the expression of BSP. Low mechanical tensile stress induced earlier and more intensive up-regulation of BSP mRNA; this might represent the optimal stimuli for cementoblast activity.

Parathyroid hormone regulation of the human bone sialoprotein gene transcription is mediated through two cAMP response elements.

PubMed

Araki, Shouta; Mezawa, Masaru; Sasaki, Yoko; Yang, Li; Li, Zhengyang; Takai, Hideki; Nakayama, Youhei; Ogata, Yorimasa

2009-03-01

Parathyroid hormone (PTH) regulates serum calcium and inorganic phosphate levels through its actions on kidney and bone. Bone sialoprotein (BSP) is an early marker of osteoblast differentiation and bone metabolism. We here report that two cAMP response elements (CRE) in the human BSP gene promoter are target of PTH. In human osteoblast-like Saos2 cells, PTH (human 1-34 PTH, 10 nM) increased BSP mRNA and protein levels at 3 h. From transient transfection assays, 2- to 2.5-fold increase in transcription by PTH was observed at 3 and 6 h in -184, -211, -428, -868, and -927 luciferase constructs that included the human BSP gene promoter. Effect of PTH was abrogated by 2 bp mutations in either the CRE1 (-79 to -72) or CRE2 (-674 to -667). Luciferase activities induced by PTH were blocked by protein kinase A inhibitor H89 and tyrosine kinase inhibitor herbimycin A. Gel shift analyses showed that PTH increased binding of nuclear proteins to the CRE1 and CRE2 elements. The CRE1-protein and CRE2-protein complexes were disrupted by CRE binding protein 1 (CREB1) antibodies and supershifted by phospho-CREB1 antibody. ChIP assays detected binding of CREB1 and phospho-CREB1 to a chromatin fragment containing CRE1 and CRE2, and increased binding of phospho-CREB1 to the both sites. These studies demonstrate that PTH stimulates human BSP gene transcription by targeting the two CREs in the promoter of the human BSP gene.

REMOVING BIASES IN RESOLVED STELLAR MASS MAPS OF GALAXY DISKS THROUGH SUCCESSIVE BAYESIAN MARGINALIZATION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martínez-García, Eric E.; González-Lópezlira, Rosa A.; Bruzual A, Gustavo

2017-01-20

Stellar masses of galaxies are frequently obtained by fitting stellar population synthesis models to galaxy photometry or spectra. The state of the art method resolves spatial structures within a galaxy to assess the total stellar mass content. In comparison to unresolved studies, resolved methods yield, on average, higher fractions of stellar mass for galaxies. In this work we improve the current method in order to mitigate a bias related to the resolved spatial distribution derived for the mass. The bias consists in an apparent filamentary mass distribution and a spatial coincidence between mass structures and dust lanes near spiral arms.more » The improved method is based on iterative Bayesian marginalization, through a new algorithm we have named Bayesian Successive Priors (BSP). We have applied BSP to M51 and to a pilot sample of 90 spiral galaxies from the Ohio State University Bright Spiral Galaxy Survey. By quantitatively comparing both methods, we find that the average fraction of stellar mass missed by unresolved studies is only half what previously thought. In contrast with the previous method, the output BSP mass maps bear a better resemblance to near-infrared images.« less

Effectiveness of Bus Signal Priority : Final Report

DOT National Transportation Integrated Search

2002-01-01

Effectiveness of Bus Signal Priority (BSP) study evaluates BSP?s impact on traffic operations. The goal was to examine how different situations, such as the level of congestion, placement of bus stops, presence of express bus service, and number of t...

Cancer Secretome May Influence BSP and DSP Expression in Human Salivary Gland Cells

PubMed Central

Hamilton, Samantha Lynn; Ferando, Blake; Eapen, Asha Sarah; Yu, Jennifer Chian; Joy, Anita Rose

2016-01-01

One of the biggest challenges in managing head and neck cancers, especially salivary gland cancers, is the identification of secreted biomarkers of the disease that can be evaluated noninvasively. A relevant source of enriched tumor markers could potentially be found in the tumor secretome. Although numerous studies have evaluated secretomes from various cancers, the influence of the cancer secretome derived from salivary gland cancers on the behavior of normal cells has not yet been elucidated. Our data indicate that secretome derived from salivary gland cancer cells can influence the expression of two potential biomarkers of oral cancer—namely, bone sialoprotein (BSP) and dentin sialoprotein (DSP)—in normal salivary gland cells. Using routine immunohistochemistry, immunofluorescence, and immunoblotting techniques, we demonstrate an enrichment of BSP and DSP in human salivary gland (HSG) cancer tissue, unique localizations of BSP and DSP in HSG cancer cells, and enriched expression of BSP and DSP in normal salivary gland cells exposed to a cancer secretome. The secretome domain of the cancer microenvironment could alter signaling cascades responsible for normal cell proliferation, migration, and invasion, thus enhancing cancer cell survival and the potential for cancer progression. The cancer secretome may be critical in maintaining and stimulating “cancer-ness,” thus potentially promoting specific hallmarks of metastasis. PMID:27881474

Cancer Secretome May Influence BSP and DSP Expression in Human Salivary Gland Cells.

PubMed

Hamilton, Samantha Lynn; Ferando, Blake; Eapen, Asha Sarah; Yu, Jennifer Chian; Joy, Anita Rose

2017-03-01

One of the biggest challenges in managing head and neck cancers, especially salivary gland cancers, is the identification of secreted biomarkers of the disease that can be evaluated noninvasively. A relevant source of enriched tumor markers could potentially be found in the tumor secretome. Although numerous studies have evaluated secretomes from various cancers, the influence of the cancer secretome derived from salivary gland cancers on the behavior of normal cells has not yet been elucidated. Our data indicate that secretome derived from salivary gland cancer cells can influence the expression of two potential biomarkers of oral cancer-namely, bone sialoprotein (BSP) and dentin sialoprotein (DSP)-in normal salivary gland cells. Using routine immunohistochemistry, immunofluorescence, and immunoblotting techniques, we demonstrate an enrichment of BSP and DSP in human salivary gland (HSG) cancer tissue, unique localizations of BSP and DSP in HSG cancer cells, and enriched expression of BSP and DSP in normal salivary gland cells exposed to a cancer secretome. The secretome domain of the cancer microenvironment could alter signaling cascades responsible for normal cell proliferation, migration, and invasion, thus enhancing cancer cell survival and the potential for cancer progression. The cancer secretome may be critical in maintaining and stimulating "cancer-ness," thus potentially promoting specific hallmarks of metastasis.

Isothiocyanate metabolism, distribution, and interconversion in mice following consumption of thermally processed broccoli sprouts or purified sulforaphane

PubMed Central

Bricker, Gregory V.; Riedl, Kenneth M.; Ralston, Robin A.; Tober, Kathleen L.; Oberyszyn, Tatiana M.; Schwartz, Steven J.

2014-01-01

Scope Broccoli sprouts are a rich source of glucosinolates, a group of phytochemicals that when hydrolyzed, are associated with cancer prevention. Our objectives were to investigate the metabolism, distribution, and interconversion of isothiocyanates (ITCs) in mice fed thermally processed broccoli sprout powders (BSPs) or the purified ITC sulforaphane. Methods and results For 1 wk, mice were fed a control diet (n = 20) or one of four treatment diets (n = 10 each) containing nonheated BSP, 60°C mildly heated BSP, 5-min steamed BSP, or 3 mmol purified sulforaphane. Sulforaphane and erucin metabolite concentrations in skin, liver, kidney, bladder, lung, and plasma were quantified using HPLC-MS/MS. Thermal intensity of BSP processing had disparate effects on ITC metabolite concentrations upon consumption. Mild heating generally resulted in the greatest ITC metabolite concentrations in vivo, followed by the nonheated and steamed BSP diets. We observed interconversion between sulforaphane and erucin species or metabolites, and report that erucin is the favored form in liver, kidney, and bladder, even when only sulforaphane is consumed. Conclusion ITC metabolites were distributed to all tissues analyzed, suggesting the potential for systemic benefits. We report for the first time tissue-dependent ratio of sulforaphane and erucin, though further investigation is warranted to assess biological activity of individual forms. PMID:24975513

Binary space partitioning trees and their uses

NASA Technical Reports Server (NTRS)

Bell, Bradley N.

1989-01-01

Binary Space Partitioning (BSP) trees have some qualities that make them useful in solving many graphics related problems. The purpose is to describe what a BSP tree is, and how it can be used to solve the problem of hidden surface removal, and constructive solid geometry. The BSP tree is based on the idea that a plane acting as a divider subdivides space into two parts with one being on the positive side and the other on the negative. A polygonal solid is then represented as the volume defined by the collective interior half spaces of the solid's bounding surfaces. The nature of how the tree is organized lends itself well for sorting polygons relative to an arbitrary point in 3 space. The speed at which the tree can be traversed for depth sorting is fast enough to provide hidden surface removal at interactive speeds. The fact that a BSP tree actually represents a polygonal solid as a bounded volume also makes it quite useful in performing the boolean operations used in constructive solid geometry. Due to the nature of the BSP tree, polygons can be classified as they are subdivided. The ability to classify polygons as they are subdivided can enhance the simplicity of implementing constructive solid geometry.

Bovine seminal PDC-109 protein: an overview of biochemical and functional properties.

PubMed

Srivastava, N; Jerome, A; Srivastava, S K; Ghosh, S K; Kumar, Amit

2013-04-01

Although long-term storage of bovine semen is desirable for wider use, successful cryopreservation depends on several factors, including various proteins present in seminal plasma. One such group of proteins, viz. bovine seminal plasma (BSP) proteins represents the major protein fraction in bovine seminal plasma. They constitute three major heparin-binding (HB-) acidic proteins secreted by seminal vesicles, viz. BSP-A1/-A2 (PDC-109), BSP-A3 and BSP-30-kDa. By purification studies it was deduced that PDC-109 is a polypeptide of 109 amino acids and contains two tandem repeating fibronectin type-II (Fn-II) domains, preceded by a 23 residue N-terminal domain. Though BSP-A1 and BSP-A2 are biochemically similar they differ only in glycosylation and their mixture is called PDC-109 or gonadostatins. PDC-109 exists as a polydisperse, multimeric self-associated molecule and possesses multifunctional properties, viz. binding to the surface of plasma membrane of spermatozoa causing conformational change in the sperm surface proteins and enhances motility. Besides binding, PDC-109 protein provokes cholesterol efflux from sperm membrane and promotes sperm reservoir by interacting with oviductal membrane. Interaction of sperm with PDC-109 protein induces sperm capacitation and acrosome reaction. However, prolonged exposure of spermatozoa with free floating PDC-109 protein as during processing for preservation, increases cholesterol efflux from spermatozoa. The efflux of sperm membrane cholesterol and disturbance in cholesterol:phospholipids ratio causes destabilization of plasma membrane thereby inducing cryoinjury to the sperm. In this review, the biochemical, functional properties of PDC-109 protein and its role during semen cryopreservation is summarized. Copyright © 2013 Elsevier B.V. All rights reserved.

Overexpression of bone sialoprotein leads to an uncoupling of bone formation and bone resorption in mice.

PubMed

Valverde, Paloma; Zhang, Jin; Fix, Amanda; Zhu, Ji; Ma, Wenli; Tu, Qisheng; Chen, Jake

2008-11-01

The purpose of this study was to determine the effects of bone sialoprotein (BSP) overexpression in bone metabolism in vivo by using a homozygous transgenic mouse line that constitutively overexpresses mouse BSP cDNA driven by the cytomegalovirus (CMV) promoter. CMV-BSP transgenic (TG) mice and wildtype mice were weighed, and their length, BMD, and trabecular bone volume were measured. Serum levels of RANKL, osteocalcin, osteoprotegerin (OPG), TRACP5b, and PTH were determined. Bone histomorphometry, von Kossa staining, RT-PCR analysis, Western blot, MTS assay, in vitro mineralization assay, and TRACP staining were also performed to delineate phenotypes of this transgenic mouse line. Compared with wildtype mice, adult TG mice exhibit mild dwarfism, lower values of BMD, and lower trabecular bone volume. TG mice serum contained increased calcium levels and decreased PTH levels, whereas the levels of phosphorus and magnesium were within normal limits. TG mice serum also exhibited lower levels of osteoblast differentiation markers and higher levels of markers, indicating osteoclastic activity and bone resorption. H&E staining, TRACP staining, and bone histomorphometry showed that adult TG bones were thinner and the number of giant osteoclasts in TG mice was higher, whereas there were no significant alterations in osteoblast numbers between TG mice and WT mice. Furthermore, the vertical length of the hypertrophic zone in TG mice was slightly enlarged. Moreover, ex vivo experiments indicated that overexpression of BSP decreased osteoblast population and increased osteoclastic activity. Partly because of its effects in enhancing osteoclastic activity and decreasing osteoblast population, BSP overexpression leads to an uncoupling of bone formation and resorption, which in turn results in osteopenia and mild dwarfism in mice. These findings are expected to help the development of therapies to metabolic bone diseases characterized by high serum level of BSP.

Insulin-like growth factor-II regulates bone sialoprotein gene transcription.

PubMed

Choe, Jin; Sasaki, Yoko; Zhou, Liming; Takai, Hideki; Nakayama, Yohei; Ogata, Yorimasa

2016-09-01

Insulin-like growth factor-I and -II (IGF-I and IGF-II) have been found in bone extracts of several different species, and IGF-II is the most abundant growth factor stored in bone. Bone sialoprotein (BSP) is a noncollagenous extracellular matrix glycoprotein associated with mineralized connective tissues. In this study, we have investigated the regulation of BSP transcription by IGF-II in rat osteoblast-like ROS17/2.8 cells. IGF-II (50 ng/ml) increased BSP mRNA and protein levels after 6-h stimulation, and enhanced luciferase activities of the constructs pLUC3 (-116 to +60), pLUC4 (-425 to +60), pLUC5 (-801 to +60) and pLUC6 (-938 to +60). Effects of IGF-II were inhibited by tyrosine kinase, extracellular signal-regulated kinase1/2 and phosphatidylinositol 3-kinase inhibitors, and abrogated by 2-bp mutations in cAMP response element (CRE), FGF2 response element (FRE) and homeodomain protein-binding site (HOX). The results of gel shift assays showed that nuclear proteins binding to CRE, FRE and HOX sites were increased by IGF-II (50 ng/ml) at 3 and 6 h. CREB1, phospho-CREB1, c-Fos and c-Jun antibodies disrupted the formation of the CRE-protein complexes. Dlx5 and Runx2 antibodies disrupted the FRE- and HOX-protein complex formations. These studies therefore demonstrated that IGF-II increased BSP transcription by targeting CRE, FRE and HOX elements in the proximal promoter of the rat BSP gene. Moreover, phospho-CREB1, c-Fos, c-Jun, Dlx5 and Runx2 transcription factors appear to be key regulators of IGF-II effects on BSP transcription.

Bone sialoprotein and osteopontin in bone metastasis of osteotropic cancers.

PubMed

Kruger, Thomas E; Miller, Andrew H; Godwin, Andrew K; Wang, Jinxi

2014-02-01

The mechanisms underlying malignant cell metastasis to secondary sites such as bone are complex and no doubt multifactorial. Members of the small integrin-binding ligand N-linked glycoproteins (SIBLINGs) family, particularly bone sialoprotein (BSP) and osteopontin (OPN), exhibit multiple activities known to promote malignant cell proliferation, detachment, invasion, and metastasis of several osteotropic cancers. The expression level of BSP and OPN is elevated in a variety of human cancers, particularly those that metastasize preferentially to the skeleton. Recent studies suggest that the "osteomimicry" of malignant cells is not only conferred by transmembrane receptors bound by BSP and OPN, but includes the "switch" in gene expression repertoire typically expressed in cells of skeletal lineage. Understanding the role of BSP and OPN in tumor progression, altered pathophysiology of bone microenvironment, and tumor metastasis to bone will likely result in development of better diagnostic approaches and therapeutic regimens for osteotropic malignant diseases. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Whole-exome sequencing for variant discovery in blepharospasm.

PubMed

Tian, Jun; Vemula, Satya R; Xiao, Jianfeng; Valente, Enza Maria; Defazio, Giovanni; Petrucci, Simona; Gigante, Angelo Fabio; Rudzińska-Bar, Monika; Wszolek, Zbigniew K; Kennelly, Kathleen D; Uitti, Ryan J; van Gerpen, Jay A; Hedera, Peter; Trimble, Elizabeth J; LeDoux, Mark S

2018-05-16

Blepharospasm (BSP) is a type of focal dystonia characterized by involuntary orbicularis oculi spasms that are usually bilateral, synchronous, and symmetrical. Despite strong evidence for genetic contributions to BSP, progress in the field has been constrained by small cohorts, incomplete penetrance, and late age of onset. Although several genetic etiologies for dystonia have been identified through whole-exome sequencing (WES), none of these are characteristically associated with BSP as a singular or predominant manifestation. We performed WES on 31 subjects from 21 independent pedigrees with BSP. The strongest candidate sequence variants derived from in silico analyses were confirmed with bidirectional Sanger sequencing and subjected to cosegregation analysis. Cosegregating deleterious variants (GRCH37/hg19) in CACNA1A (NM_001127222.1: c.7261_7262delinsGT, p.Pro2421Val), REEP4 (NM_025232.3: c.109C>T, p.Arg37Trp), TOR2A (NM_130459.3: c.568C>T, p.Arg190Cys), and ATP2A3 (NM_005173.3: c.1966C>T, p.Arg656Cys) were identified in four independent multigenerational pedigrees. Deleterious variants in HS1BP3 (NM_022460.3: c.94C>A, p.Gly32Cys) and GNA14 (NM_004297.3: c.989_990del, p.Thr330ArgfsTer67) were identified in a father and son with segmental cranio-cervical dystonia first manifest as BSP. Deleterious variants in DNAH17, TRPV4, CAPN11, VPS13C, UNC13B, SPTBN4, MYOD1, and MRPL15 were found in two or more independent pedigrees. To our knowledge, none of these genes have previously been associated with isolated BSP, although other CACNA1A mutations have been associated with both positive and negative motor disorders including ataxia, episodic ataxia, hemiplegic migraine, and dystonia. Our WES datasets provide a platform for future studies of BSP genetics which will demand careful consideration of incomplete penetrance, pleiotropy, population stratification, and oligogenic inheritance patterns. © 2018 The Authors. Molecular Genetics & Genomic Medicine published by Wiley Periodicals, Inc.

Validation Test Report for the BioCast Optical Forecast Model Version 1.0

DTIC Science & Technology

2015-04-09

can generate such as: total absorption (a), backscattering (bb), chlorophyll (chl), sea surface temperature (SST), diver visibility, etc. The...optical backscattering coefficient BSP - Battle Space Profiler CHARTS - Compact Hydrographic Airborne Rapid Total Survey Chl - Chlorophyll EO

Complete Nucleotide Sequence Analysis of a Novel Bacillus subtilis-Infecting Bacteriophage BSP10 and Its Effect on Poly-Gamma-Glutamic Acid Degradation

PubMed Central

Ghosh, Kuntal; Senevirathne, Amal; Kang, Hai Seong; Hyun, Woo Bin; Kim, Ji Eun; Kim, Kwang-Pyo

2018-01-01

While the harmful effects of lactic acid bacterial bacteriophages in the dairy industry are well-established, the importance of Bacillus subtilis-infecting bacteriophages on soybean fermentation is poorly-studied. In this study, we isolated a B. subtilis-infecting bacteriophage BSP10 from Meju (a brick of dried fermented soybean) and further characterized it. This Myoviridae family bacteriophage exhibited a narrow host range against B. subtilis strains (17/52, 32.7%). The genome of bacteriophage BSP10 is 153,767 bp long with 236 open reading frames and 5 tRNAs. Comparative genomics (using dot plot, progressiveMauve alignment, heat-plot, and BLASTN) and phylogenetic analysis strongly suggest its incorporation as a new species in the Nit1virus genus. Furthermore, bacteriophage BSP10 was efficient in the growth inhibition of B. subtilis ATCC 15245 in liquid culture and in Cheonggukjang (a soybean fermented food) fermentation. Artificial contamination of as low as 102 PFU/g of bacteriophage BSP10 during Cheonggukjang fermentation significantly reduced bacterial numbers by up to 112 fold in comparison to the control (no bacteriophage). Moreover, for the first time, we experimentally proved that B. subtilis-infecting bacteriophage greatly enhanced poly-γ-glutamic acid degradation during soybean fermentation, which is likely to negatively affect the functionalities of Cheonggukjang. PMID:29734701

Kaempferol stimulates bone sialoprotein gene transcription and new bone formation.

PubMed

Yang, Li; Takai, Hideki; Utsunomiya, Tadahiko; Li, Xinyue; Li, Zhengyang; Wang, Zhitao; Wang, Shuang; Sasaki, Yoko; Yamamoto, Hirotsugu; Ogata, Yorimasa

2010-08-15

Kaempferol is a typical flavonol-type flavonoid that is present in a variety of vegetables and fruits, and has a protective effect on postmenopausal bone loss. Bone sialoprotein (BSP) is thought to function in the initial mineralization of bone and could be crucial for osteoblast differentiation, bone matrix mineralization and tumor metastasis. In the present study we investigated the regulation of BSP transcription by kaempferol in rat osteoblast-like UMR106 cells, and the effect of kaempferol on new bone formation. Kaempferol (5 microM) increased BSP and Osterix mRNA levels at 12 h and up-regulated Runx2 mRNA expression at 6 h. Kaempferol increased luciferase activity of the construct pLUC3, which including the promoter sequence between nucleotides -116 to +60. Transcriptional stimulation by kaempferol abrogated in constructs included 2 bp mutations in the inverted CCAAT, CRE, and FRE elements. Gel shift analyses showed that kaempferol increased nuclear protein binding to CRE and FRE elements, whereas the CCAAT-protein complex did not change after kaempferol stimulation. Twelve daily injections of 5 microM kaempferol directly into the periosteum of parietal bones of newborn rats increased new bone formation. These data suggest that kaempferol increased BSP gene transcription mediated through inverted CCAAT, CRE, and FRE elements in the rat BSP gene promoter, and could induce osteoblast activities in the early stage of bone formation. (c) 2010 Wiley-Liss, Inc.

Isothiocyanate metabolism, distribution, and interconversion in mice following consumption of thermally processed broccoli sprouts or purified sulforaphane.

PubMed

Bricker, Gregory V; Riedl, Kenneth M; Ralston, Robin A; Tober, Kathleen L; Oberyszyn, Tatiana M; Schwartz, Steven J

2014-10-01

Broccoli sprouts are a rich source of glucosinolates, a group of phytochemicals that when hydrolyzed, are associated with cancer prevention. Our objectives were to investigate the metabolism, distribution, and interconversion of isothiocyanates (ITCs) in mice fed thermally processed broccoli sprout powders (BSPs) or the purified ITC sulforaphane. For 1 wk, mice were fed a control diet (n = 20) or one of four treatment diets (n = 10 each) containing nonheated BSP, 60°C mildly heated BSP, 5-min steamed BSP, or 3 mmol purified sulforaphane. Sulforaphane and erucin metabolite concentrations in skin, liver, kidney, bladder, lung, and plasma were quantified using HPLC-MS/MS. Thermal intensity of BSP processing had disparate effects on ITC metabolite concentrations upon consumption. Mild heating generally resulted in the greatest ITC metabolite concentrations in vivo, followed by the nonheated and steamed BSP diets. We observed interconversion between sulforaphane and erucin species or metabolites, and report that erucin is the favored form in liver, kidney, and bladder, even when only sulforaphane is consumed. ITC metabolites were distributed to all tissues analyzed, suggesting the potential for systemic benefits. We report for the first time tissue-dependent ratio of sulforaphane and erucin, though further investigation is warranted to assess biological activity of individual forms. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Binder of Sperm Proteins 1 and 5 have contrasting effects on the capacitation of ram spermatozoa.

PubMed

Pini, Taylor; de Graaf, Simon P; Druart, Xavier; Tsikis, Guillaume; Labas, Valerie; Teixeira-Gomes, Ana Paula; Gadella, Barend M; Leahy, Tamara

2018-06-01

Binder of Sperm Proteins (BSPs) are the most abundant seminal plasma protein family in the ram and bull. They have been extensively studied in the bull but less is known about their function in ovine seminal plasma and current knowledge suggests that BSPs may have different effects in these two species. In the bull, they facilitate capacitation and destabilize the sperm membrane during in vitro handling, whereas in the ram, they appear to stabilize the sperm membrane and prevent cryopreservation-induced capacitation-like changes. Further investigation into the effects of BSPs on ram spermatozoa under capacitating conditions is required to further clarify their physiological roles in the ram. We investigated the effects of Binder of Sperm Proteins 1 and 5 on epididymal ram spermatozoa in conditions of low, moderate, and high cAMP. BSPs had minimal effects on sperm function in low-cAMP conditions, but caused significant changes under cAMP upregulation. BSP1 stabilized the membrane and qualitatively reduced protein tyrosine phosphorylation, but significantly increased cholesterol efflux and induced spontaneous acrosome reactions. BSP5 slightly increased spontaneous acrosome reactions and caused sperm necrosis. However, BSP5 had minimal effects on membrane lipid order and cholesterol efflux and did not inhibit protein tyrosine phosphorylation. These findings demonstrate that under maximal cAMP upregulation, BSP1 affected ram spermatozoa in a manner comparable to bull spermatozoa, while BSP5 did not.

Secretary | Center for Cancer Research

Cancer.gov

The Basic Science Program (BSP) pursues independent, multidisciplinary research programs in basic or applied molecular biology, immunology, retrovirology, cancer biology, or human genetics. Research efforts and support are an integral part of the Center for Cancer Research (CCR) at the Frederick national Laboratory for Cancer Research (FNLCR). The BSP Office provides

In vitro characterization of peptide-modified p(AAm-co-EG/AAc) IPN-coated titanium implants.

PubMed

Barber, Thomas A; Gamble, Lara J; Castner, David G; Healy, Kevin E

2006-07-01

Interpenetrating polymer networks (IPNs) of poly(acrylamide-co-ethylene glycol/acrylic acid) [p(AAm-co-EG/AAc)] functionalized with an -Arg-Gly-Asp- containing peptide derived from rat bone sialoprotein [bsp-RGD(15)] were grafted to titanium implants in an effort to modulate osteoblast behavior in vitro. Surface characterization data were consistent with the presence of an IPN, and ligand density measurements established that the range of peptide density on the modified implants spanned three orders of magnitude (0.01-20 pmol/cm2). In vitro biological characterization of the modified implants employing the primary rat calvarial osteoblast (RCO) model resulted in the identification of a critical ligand density (0.01

Delivery of the bioactive gas hydrogen sulfide during cold preservation of rat liver: effects on hepatic function in an ex vivo model.

PubMed

Balaban, Cecilia L; Rodriguez, Joaquín V; Guibert, Edgardo E

2011-05-01

The insults sustained by transplanted livers (hepatectomy, hypothermic preservation, and normothermic reperfusion) could compromise hepatic function. Hydrogen sulfide (H₂S) is a physiologic gaseous signaling molecule, like nitric oxide (NO) and carbon monoxide (CO). We examined the effect of diallyl disulfide as a H₂S donor during hypothermic preservation and reperfusion on intrahepatic resistance (IVR), lactate dehydrogenase (LDH) release, bile production, oxygen consumption, bromosulfophthalein (BSP) depuration and histology in an isolated perfused rat liver model (IPRL), after 48 h of hypothermic storage (4 °C) in University of Wisconsin solution (UW, Viaspan). Livers were retrieved from male Wistar rats. Three experimental groups were analyzed: Control group (CON): IPRL was performed after surgery; UW: IPRL was performed in livers preserved (48 h-4 °C) in UW; and UWS: IPRL was performed in livers preserved (48 h-4 °C) in UW in the presence of 3.4 mM diallyl disulfide. Hypothermic preservation injuries were manifested at reperfusion by a slight increment in IHR and LDH release compared with the control group. Also, bile production for the control group (1.32 µL/min/g of liver) seemed to be diminished after preservation by 73% in UW and 69% in UW H₂S group at the end of normothermic reperfusion. Liver samples analyzed by hematoxylin/eosin clearly showed the deleterious effect of cold storage process, partially reversed (dilated sinusoids and vacuolization attenuation) by the addition of a H₂S delivery compound to the preservation solution. Hepatic clearance (HC) of BSP was affected by cold storage of livers, but there were no noticeable differences between livers preserved with or without diallyl disulfide. Meanwhile, livers preserved in the presence of H₂S donor showed an enhanced capacity for BSP uptake (k(A) CON = 0.29 min⁻¹; k(A) UW = 0.29 min⁻¹ ; k(A) UWS = 0.36 min ⁻¹). In summary, our animal model suggests that hepatic hypothermic preservation for transplantation affects liver function and hepatic depuration of BSP, and implies that the inclusion of an H₂S donor during hypothermic preservation could improve standard methods of preparing livers for transplant. © 2011, Copyright the Authors. Artificial Organs © 2011, International Center for Artificial Organs and Transplantation and Wiley Periodicals, Inc.

Secretary | Center for Cancer Research

Cancer.gov

We are looking for a pleasant, organized, dependable person to serve as a full-time secretary in the Basic Science Program (BSP) at the Frederick National Laboratory for Cancer Research (FNCLR).  The BSP provides procurement and logistical support to the laboratories of the Center for Cancer Research.  Tasks include high volume procurement (blanket orders, purchase requests,

Collagen Scaffolds in Bone Sialoprotein-Mediated Bone Regeneration

PubMed Central

Kruger, Thomas E.; Miller, Andrew H.; Wang, Jinxi

2013-01-01

Decades of research in bioengineering have resulted in the development of many types of 3-dimentional (3D) scaffolds for use as drug delivery systems (DDS) and for tissue regeneration. Scaffolds may be comprised of different natural fibers and synthetic polymers as well as ceramics in order to exert the most beneficial attributes including biocompatibility, biodegradability, structural integrity, cell infiltration and attachment, and neovascularization. Type I collagen scaffolds meet most of these criteria. In addition, type I collagen binds integrins through RGD and non-RGD sites which facilitates cell migration, attachment, and proliferation. Type I collagen scaffolds can be used for bone tissue repair when they are coated with osteogenic proteins such as bone morphogenic protein (BMP) and bone sialoprotein (BSP). BSP, a small integrin-binding ligand N-linked glycoprotein (SIBLING), has osteogenic properties and plays an essential role in bone formation. BSP also mediates mineral deposition, binds type I collagen with high affinity, and binds αvβ 3 and αvβ 5 integrins which mediate cell signaling. This paper reviews the emerging evidence demonstrating the efficacy of BSP-collagen scaffolds in bone regeneration. PMID:23653530

Collagen scaffolds in bone sialoprotein-mediated bone regeneration.

PubMed

Kruger, Thomas E; Miller, Andrew H; Wang, Jinxi

2013-01-01

Decades of research in bioengineering have resulted in the development of many types of 3-dimentional (3D) scaffolds for use as drug delivery systems (DDS) and for tissue regeneration. Scaffolds may be comprised of different natural fibers and synthetic polymers as well as ceramics in order to exert the most beneficial attributes including biocompatibility, biodegradability, structural integrity, cell infiltration and attachment, and neovascularization. Type I collagen scaffolds meet most of these criteria. In addition, type I collagen binds integrins through RGD and non-RGD sites which facilitates cell migration, attachment, and proliferation. Type I collagen scaffolds can be used for bone tissue repair when they are coated with osteogenic proteins such as bone morphogenic protein (BMP) and bone sialoprotein (BSP). BSP, a small integrin-binding ligand N-linked glycoprotein (SIBLING), has osteogenic properties and plays an essential role in bone formation. BSP also mediates mineral deposition, binds type I collagen with high affinity, and binds α v β 3 and α v β 5 integrins which mediate cell signaling. This paper reviews the emerging evidence demonstrating the efficacy of BSP-collagen scaffolds in bone regeneration.

AFM study of morphology and mechanical properties of a chimeric spider silk and bone sialoprotein protein for bone regeneration

PubMed Central

Gomes, Sílvia; Numata, Keiji; Leonor, Isabel B.; Mano, João F.; Reis, Rui L.; Kaplan, David L.

2011-01-01

Atomic force microscopy (AFM) was used to assess a new chimeric protein consisting of a fusion protein of the consensus repeat for Nephila clavipes spider dragline protein and bone sialoprotein (6mer+BSP). The elastic modulus of this protein in film form was assessed through force curves, and film surface roughness was also determined. The results showed a significant difference between the elastic modulus of the chimeric silk protein, 6mer+BSP, and control films consisting of only the silk component (6mer). The behaviour of the 6mer+BSP and 6mer proteins in aqueous solution in the presence of calcium (Ca) ions was also assessed to determine interactions between the inorganic and organic components related to bone interactions, anchoring and biomaterial network formation. The results demonstrated the formation of protein networks in the presence of Ca2+ ions, characteristics that may be important in the context of controlling materials assembly and properties related to bone-formation with this new chimeric silk-BSP protein. PMID:21370930

AFM study of morphology and mechanical properties of a chimeric spider silk and bone sialoprotein protein for bone regeneration.

PubMed

Gomes, Sílvia; Numata, Keiji; Leonor, Isabel B; Mano, João F; Reis, Rui L; Kaplan, David L

2011-05-09

Atomic force microscopy (AFM) was used to assess a new chimeric protein consisting of a fusion protein of the consensus repeat for Nephila clavipes spider dragline protein and bone sialoprotein (6mer+BSP). The elastic modulus of this protein in film form was assessed through force curves, and film surface roughness was also determined. The results showed a significant difference among the elastic modulus of the chimeric silk protein, 6mer+BSP, and control films consisting of only the silk component (6mer). The behavior of the 6mer+BSP and 6mer proteins in aqueous solution in the presence of calcium (Ca) ions was also assessed to determine interactions between the inorganic and organic components related to bone interactions, anchoring, and biomaterial network formation. The results demonstrated the formation of protein networks in the presence of Ca(2+) ions, characteristics that may be important in the context of controlling materials assembly and properties related to bone formation with this new chimeric silk-BSP protein.

Overexpression of Bone Sialoprotein Leads to an Uncoupling of Bone Formation and Bone Resorption in Mice

PubMed Central

Valverde, Paloma; Zhang, Jin; Fix, Amanda; Zhu, Ji; Ma, Wenli; Tu, Qisheng; Chen, Jake

2008-01-01

The purpose of this study was to determine the effects of bone sialoprotein (BSP) overexpression in bone metabolism in vivo by using a homozygous transgenic mouse line that constitutively overexpresses mouse BSP cDNA driven by the cytomegalovirus (CMV) promoter. CMV-BSP transgenic (TG) mice and wildtype mice were weighed, and their length, BMD, and trabecular bone volume were measured. Serum levels of RANKL, osteocalcin, osteoprotegerin (OPG), TRACP5b, and PTH were determined. Bone histomorphometry, von Kossa staining, RT-PCR analysis, Western blot, MTS assay, in vitro mineralization assay, and TRACP staining were also performed to delineate phenotypes of this transgenic mouse line. Compared with wildtype mice, adult TG mice exhibit mild dwarfism, lower values of BMD, and lower trabecular bone volume. TG mice serum contained increased calcium levels and decreased PTH levels, whereas the levels of phosphorus and magnesium were within normal limits. TG mice serum also exhibited lower levels of osteoblast differentiation markers and higher levels of markers, indicating osteoclastic activity and bone resorption. H&E staining, TRACP staining, and bone histomorphometry showed that adult TG bones were thinner and the number of giant osteoclasts in TG mice was higher, whereas there were no significant alterations in osteoblast numbers between TG mice and WT mice. Furthermore, the vertical length of the hypertrophic zone in TG mice was slightly enlarged. Moreover, ex vivo experiments indicated that overexpression of BSP decreased osteoblast population and increased osteoclastic activity. Partly because of its effects in enhancing osteoclastic activity and decreasing osteoblast population, BSP overexpression leads to an uncoupling of bone formation and resorption, which in turn results in osteopenia and mild dwarfism in mice. These findings are expected to help the development of therapies to metabolic bone diseases characterized by high serum level of BSP. PMID:18597627

Determination of osteogenic or adipogenic lineages in muscle-derived stem cells (MDSCs) by a collagen-binding peptide (CBP) derived from bone sialoprotein (BSP)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Choi, Yoon Jung; Lee, Jue Yeon; Lee, Seung Jin

Highlights: Black-Right-Pointing-Pointer CBP sequence is identified from BSP and has collagen binding activity. Black-Right-Pointing-Pointer CBP directly activates the MAPK signaling, especially ERK1/2. Black-Right-Pointing-Pointer CBP increase osteoblastic differentiation by the activation of Runx2. Black-Right-Pointing-Pointer CBP decrease adipogenic differentiation by the inhibition of PPAR{gamma}. -- Abstract: Bone sialoprotein (BSP) is a mineralized, tissue-specific, non-collagenous protein that is normally expressed only in mineralized tissues such as bone, dentin, cementum, and calcified cartilage, and at sites of new mineral formation. The binding of BSP to collagen is thought to be important for initiating bone mineralization and bone cell adhesion to the mineralized matrix. Severalmore » recent studies have isolated stem cells from muscle tissue, but their functional properties are still unclear. In this study, we examined the effects of a synthetic collagen-binding peptide (CBP) on the differentiation efficiency of muscle-derived stem cells (MDSCs). The CBP sequence (NGVFKYRPRYYLYKHAYFYPHLKRFPVQ) corresponds to residues 35-62 of bone sialoprotein (BSP), which are located within the collagen-binding domain in BSP. Interestingly, this synthetic CBP inhibited adipogenic differentiation but increased osteogenic differentiation in MDSCs. The CBP also induced expression of osteoblastic marker proteins, including alkaline phosphatase (ALP), type I collagen, Runt-related transcription factor 2 (Runx2), and osteocalcin; prevented adipogenic differentiation in MDSCs; and down-regulated adipose-specific mRNAs, such as adipocyte protein 2 (aP2) and peroxisome proliferator-activated receptor {gamma}. The CBP increased Extracellular signal-regulated kinases (ERK) 1/2 protein phosphorylation, which is important in lineage determination. These observations suggest that this CBP determines the osteogenic or adipogenic lineage in MDSCs by activating ERK1/2. Taken together, a novel CBP could be a useful candidate for regenerating bone and treating osteoporosis, which result from an imbalance in osteogenesis and adipogenesis differentiation.« less

Mineralization defects in cementum and craniofacial bone from loss of bone sialoprotein

PubMed Central

Foster, B.L.; Ao, M.; Willoughby, C.; Soenjaya, Y.; Holm, E.; Lukashova, L.; Tran, A. B.; Wimer, H.F.; Zerfas, P.M.; Nociti, F.H.; Kantovitz, K.R.; Quan, B.D.; Sone, E.D.; Goldberg, H.A.; Somerman, M.J.

2015-01-01

Bone sialoprotein (BSP) is a multifunctional extracellular matrix protein found in mineralized tissues, including bone, cartilage, tooth root cementum (both acellular and cellular types), and dentin. In order to define the role BSP plays in the process of biomineralization of these tissues, we analyzed cementogenesis, dentinogenesis, and osteogenesis (intramembranous and endochondral) in craniofacial bone in Bsp null mice and wild-type (WT) controls over a developmental period (1-60 days post natal; dpn) by histology, immunohistochemistry, undecalcified histochemistry, microcomputed tomography (microCT), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and quantitative PCR (qPCR). Regions of intramembranous ossification in the alveolus, mandible, and calvaria presented delayed mineralization and osteoid accumulation, assessed by von Kossa and Goldner's trichrome stains at 1 and 14 dpn. Moreover, Bsp−/− mice featured increased cranial suture size at the early time point, 1 dpn. Immunostaining and PCR demonstrated that osteoblast markers, osterix, alkaline phosphatase, and osteopontin were unchanged in Bsp null mandibles compared to WT. Bsp−/− mouse molars featured a lack of functional acellular cementum formation by histology, SEM, and TEM, and subsequent loss of Sharpey's collagen fiber insertion into the tooth root structure. Bsp−/− mouse alveolar and mandibular bone featured equivalent or fewer osteoclasts at early ages (1 and 14 dpn), however, increased RANKL immunostaining and mRNA, and significantly increased number of osteoclast-like cells (2-5 fold) were found at later ages (26 and 60 dpn), corresponding to periodontal breakdown and severe alveolar bone resorption observed following molar teeth entering occlusion. Dentin formation was unperturbed in Bsp−/− mouse molars, with no delay in mineralization, no alteration in dentin dimensions, and no differences in odontoblast markers analyzed. No defects were identified in endochondral ossification in the cranial base, and craniofacial morphology was unaffected in Bsp−/− mice. These analyses confirm a critical role for BSP in processes of cementogenesis and intramembranous ossification of craniofacial bone, whereas endochondral ossification in the cranial base was minimally affected and dentinogenesis was normal in Bsp−/− molar teeth. Dissimilar effects of loss of BSP on mineralization of dental and craniofacial tissues suggest local differences in the role of BSP and/or yet to be defined interactions with site-specific factors. PMID:25963390

Component biomass equations for black spruce in Maine

Treesearch

M. M. Czapowskyj; D. J. Robison; R. D. Briggs; E. H. White; E. H. White

1985-01-01

Component biomass prediction equations are presented for young black spruce (Picea mariana B.S.P. (Mill,:)) in northern Maine. A weighted least squares model was used to construct the eq~iationsfo r small trees from 1 to 15 cm d.b.h., and an ordinary least squares model for trees less than 2 m in height. A linearized allometric model was also tested but was not used....

Determination of osteogenic or adipogenic lineages in muscle-derived stem cells (MDSCs) by a collagen-binding peptide (CBP) derived from bone sialoprotein (BSP).

PubMed

Choi, Yoon Jung; Lee, Jue Yeon; Lee, Seung Jin; Chung, Chong-Pyoung; Park, Yoon Jeong

2012-03-09

Bone sialoprotein (BSP) is a mineralized, tissue-specific, non-collagenous protein that is normally expressed only in mineralized tissues such as bone, dentin, cementum, and calcified cartilage, and at sites of new mineral formation. The binding of BSP to collagen is thought to be important for initiating bone mineralization and bone cell adhesion to the mineralized matrix. Several recent studies have isolated stem cells from muscle tissue, but their functional properties are still unclear. In this study, we examined the effects of a synthetic collagen-binding peptide (CBP) on the differentiation efficiency of muscle-derived stem cells (MDSCs). The CBP sequence (NGVFKYRPRYYLYKHAYFYPHLKRFPVQ) corresponds to residues 35-62 of bone sialoprotein (BSP), which are located within the collagen-binding domain in BSP. Interestingly, this synthetic CBP inhibited adipogenic differentiation but increased osteogenic differentiation in MDSCs. The CBP also induced expression of osteoblastic marker proteins, including alkaline phosphatase (ALP), type I collagen, Runt-related transcription factor 2 (Runx2), and osteocalcin; prevented adipogenic differentiation in MDSCs; and down-regulated adipose-specific mRNAs, such as adipocyte protein 2 (aP2) and peroxisome proliferator-activated receptor γ. The CBP increased Extracellular signal-regulated kinases (ERK) 1/2 protein phosphorylation, which is important in lineage determination. These observations suggest that this CBP determines the osteogenic or adipogenic lineage in MDSCs by activating ERK1/2. Taken together, a novel CBP could be a useful candidate for regenerating bone and treating osteoporosis, which result from an imbalance in osteogenesis and adipogenesis differentiation. Copyright © 2012 Elsevier Inc. All rights reserved.

Prostate Cancer Progression and Serum SIBLING (Small Integrin Binding N-Linked Glycoprotein)Levels

DTIC Science & Technology

2007-10-01

termed SIBLINGs (for small integrin binding ligand N-linked glycoproteins) whose members include bone sialoprotein (BSP), osteopontin (OPN), dentin...enzyme-linked immunosorbent assays (ELISAs) for quantitatively determining the levels of bone sialoprotein (BSP), osteopontin (OPN), dentin...synthesized as a chimeric protein, composed of three parts: dentin sialoprotein (DSP), dentin glycoprotein (DGP) and dentin phosphoprotein (DPP, also

Immunocytochemical characterization of ectopic enamel deposits and cementicles in human teeth.

PubMed

Bosshardt, Dieter D; Nanci, Antonio

2003-02-01

Despite the relative frequency and clinical relevance of radicular enamel deposits and cementicles, their etiology and nature are unknown. The purpose of the present study was therefore to evaluate the presence and distribution of mineralization-associated non-collagenous matrix proteins (NCPs) in various types of root-associated ectopic mineralizations. Human teeth were processed for embedding in epoxy or acrylic resins. Tissue sections were incubated with antibodies to amelogenins (AMEL), bone sialoprotein (BSP), and osteopontin (OPN). Radicular enamel deposits contained residual organic matrix that labeled for AMEL. In contrast, BSP and OPN were not detected in the residual enamel matrix, they were found in the cementum deposited on its surface as well as in collagen-free cementicle-like structures in the adjacent periodontal ligament. True cementicles consisted of a collagenous matrix intermixed with a non-collagenous ground substance. Labeling for BSP and OPN was mainly associated with the interfibrillar ground substance. No immunoreactivity for AMEL was detected in cementicles. These data indicate that ectopic enamel deposits on the root retain a high amount of AMEL, whereas cementicles contain BSP and OPN, two NCPs typically found in bone and cementum. These NCPs may, like in their normal tissue counterparts, play a role in the mineralization process.

Detection of burst suppression patterns in EEG using recurrence rate.

PubMed

Liang, Zhenhu; Wang, Yinghua; Ren, Yongshao; Li, Duan; Voss, Logan; Sleigh, Jamie; Li, Xiaoli

2014-01-01

Burst suppression is a unique electroencephalogram (EEG) pattern commonly seen in cases of severely reduced brain activity such as overdose of general anesthesia. It is important to detect burst suppression reliably during the administration of anesthetic or sedative agents, especially for cerebral-protective treatments in various neurosurgical diseases. This study investigates recurrent plot (RP) analysis for the detection of the burst suppression pattern (BSP) in EEG. The RP analysis is applied to EEG data containing BSPs collected from 14 patients. Firstly we obtain the best selection of parameters for RP analysis. Then, the recurrence rate (RR), determinism (DET), and entropy (ENTR) are calculated. Then RR was selected as the best BSP index one-way analysis of variance (ANOVA) and multiple comparison tests. Finally, the performance of RR analysis is compared with spectral analysis, bispectral analysis, approximate entropy, and the nonlinear energy operator (NLEO). ANOVA and multiple comparison tests showed that the RR could detect BSP and that it was superior to other measures with the highest sensitivity of suppression detection (96.49%, P = 0.03). Tracking BSP patterns is essential for clinical monitoring in critically ill and anesthetized patients. The purposed RR may provide an effective burst suppression detector for developing new patient monitoring systems.

Pilot Study of Topical Acetyl Hexapeptide-8 in Treatment of Blepharospasm in Patients Receiving Botulinum Neurotoxin Therapy

PubMed Central

Lungu, Codrin; Considine, Elaine; Zahir, Sana; Ponsati, Berta; Arrastia, Silvia; Hallett, Mark

2016-01-01

Background Injectable botulinum neurotoxin (BoNT) is the principal effective treatment for blepharospasm (BSP). This trial explores the safety and efficacy of topical Acetyl Hexapeptide-8 (AH8), a competitive SNAP25 inhibitor, as a potential new therapy in BSP. Methods Double-blind, placebo-controlled, randomized trial of daily topical application of AH8 in 24 patients with BSP. The primary outcome was time to return to baseline Jankovic Rating Scale (JBRS) after a BoNT injection simultaneously with initiation of AH8. Patients displaying a strictly regular pattern of response to 3-monthly injections of BoNT were included. Results There were no significant adverse events. There was a trend for longer time until return to baseline JBRS after injection in the active group compared to placebo (3.7 vs 3.0 months), and for better scores in the active group. One third (4/12) of the patients in the active group had a significant extension of symptom control after BoNT (range: 3.3-7.1 months). Conclusions Topical AH8 is safe and promising for extending the duration of action of BoNT therapy for BSP. PMID:23146065

Serine proteases in rodent hippocampus.

PubMed

Davies, B J; Pickard, B S; Steel, M; Morris, R G; Lathe, R

1998-09-04

Brain serine proteases are implicated in developmental processes, synaptic plasticity, and in disorders including Alzheimer's disease. The spectrum of the major enzymes expressed in brain has not been established previously. We now present a systematic study of the serine proteases expressed in adult rat and mouse hippocampus. Using a combination of techniques including polymerase chain reaction amplification and Northern blotting we show that tissue-type plasminogen activator (t-PA) is the major species represented. Unexpectedly, the next most abundant species were RNK-Met-1, a lymphocyte protease not reported previously in brain, and two new family members, BSP1 (brain serine protease 1) and BSP2. We report full-length sequences of the two new proteases; homologies indicate that these are of tryptic specificity. Although BSP2 is expressed in several brain regions, BSP1 expression is strikingly restricted to hippocampus. Other enzymes represented, but at lower levels, included elastase IV, proteinase 3, complement C2, chymotrypsin B, chymotrypsin-like protein, and Hageman factor. Although thrombin and urokinase-type plasminogen activator were not detected in the primary screen, low level expression was confirmed using specific polymerase chain reaction primers. In contrast, and despite robust expression of t-PA, the usual t-PA substrate plasminogen was not expressed at detectable levels.

Accelerated Tumor Cell Death by Angiogenic Modifiers

DTIC Science & Technology

2004-08-01

factors; extracellular matrix; 3-D cell culture; cancer metastasis Running title: Tumor-Stroma Interaction Abbreviations: BSP, bone sialoprotein ; ECM...such as osteocalcin (OC), bone sialoprotein (BSP), osteopontin (OPN), osteonectin (ON or SPARC), 18 osteoprotegerin (OPG), PTHrP, M-CSF, RANK and...Waltregny, D., Bellahcene, A., Van Riet, I., Fisher, L. W., Young, M., Fernandez, P. and et al. Prognostic value of bone sialoprotein expression in

Predicting wildfire behavior in black spruce forests in Alaska.

Treesearch

Rodney A. Norum

1982-01-01

The current fire behavior system, when properly adjusted, accurately predicts forward rate of spread and flame length of wildfires in black spruce (Picea mariana (Mill.) B.S.P.) forests in Alaska. After fire behavior was observed and quantified, adjustment factors were calculated and assigned to the selected fuel models to correct the outputs to...

Effects of Tiered Training on General Educators' Use of Specific Praise

ERIC Educational Resources Information Center

Thompson, Michele Terry; Marchant, Michelle; Anderson, Darlene; Prater, Mary Anne; Gibb, Gordon

2012-01-01

Research suggests a compelling correlation between teacher behavior and effective learning environments. Focusing on the evidence-based teaching skill of offering behavior-specific praise (BSP), the researchers worked with three elementary-level general educators in a tiered model of training generally known as response to intervention (RtI).…

A New Algorithm to Diagnose Atrial Ectopic Origin from Multi Lead ECG Systems - Insights from 3D Virtual Human Atria and Torso

PubMed Central

Alday, Erick A. Perez; Colman, Michael A.; Langley, Philip; Butters, Timothy D.; Higham, Jonathan; Workman, Antony J.; Hancox, Jules C.; Zhang, Henggui

2015-01-01

Rapid atrial arrhythmias such as atrial fibrillation (AF) predispose to ventricular arrhythmias, sudden cardiac death and stroke. Identifying the origin of atrial ectopic activity from the electrocardiogram (ECG) can help to diagnose the early onset of AF in a cost-effective manner. The complex and rapid atrial electrical activity during AF makes it difficult to obtain detailed information on atrial activation using the standard 12-lead ECG alone. Compared to conventional 12-lead ECG, more detailed ECG lead configurations may provide further information about spatio-temporal dynamics of the body surface potential (BSP) during atrial excitation. We apply a recently developed 3D human atrial model to simulate electrical activity during normal sinus rhythm and ectopic pacing. The atrial model is placed into a newly developed torso model which considers the presence of the lungs, liver and spinal cord. A boundary element method is used to compute the BSP resulting from atrial excitation. Elements of the torso mesh corresponding to the locations of the placement of the electrodes in the standard 12-lead and a more detailed 64-lead ECG configuration were selected. The ectopic focal activity was simulated at various origins across all the different regions of the atria. Simulated BSP maps during normal atrial excitation (i.e. sinoatrial node excitation) were compared to those observed experimentally (obtained from the 64-lead ECG system), showing a strong agreement between the evolution in time of the simulated and experimental data in the P-wave morphology of the ECG and dipole evolution. An algorithm to obtain the location of the stimulus from a 64-lead ECG system was developed. The algorithm presented had a success rate of 93%, meaning that it correctly identified the origin of atrial focus in 75/80 simulations, and involved a general approach relevant to any multi-lead ECG system. This represents a significant improvement over previously developed algorithms. PMID:25611350

Secretary | Center for Cancer Research

Cancer.gov

We are looking for a pleasant, organized, dependable person to serve as a full-time secretary in the Basic Science Program (BSP) at the Frederick National Laboratory for Cancer Research (FNCLR).  The BSP provides procurement and logistical support to the laboratories of the Center for Cancer Research.  Tasks include high volume procurement (blanket orders, purchase requests, credit card), sorting and distributing mail, travel coordination, and spending/budget monitoring. 

Effect of bone sialoprotein and collagen coating on cell attachment to TICER and pure titanium implant surfaces.

PubMed

Graf, H-L; Stoeva, S; Armbruster, F P; Neuhaus, J; Hilbig, H

2008-07-01

To improve integration between implants and biological tissues, this study compared bone sialoprotein (BSP) as a surface-coating material against the major organic and inorganic components of bone, collagen type I and hydroxyapatite (TICER). The expression of osteocalcin, osteonectin and transforming growth factor ss was evaluated using immunohistochemical staining procedures. The distribution patterns of osteoblasts on the surface of pure titanium with a smooth machined surface and a rough surface (TICER) were determined by image processing using confocal laser scanning microscopy. The results compared to uncoated control materials showed that, at all times investigated, the number of cells on the surface of the TICER and pure titanium samples differed significantly (P<0.1), demonstrating the superiority of TICER over pure titanium in this respect. For pure titanium implants, collagen-precoated surfaces were not beneficial for the attachment of bone-derived cells with the exception of day 3 in vitro (P<0.01). BSP-precoated implant surfaces displayed non-significantly higher numbers of settled cells. BSP-precoated implant surfaces were beneficial for osteoinduction as revealed by osteocalcin and osteonectin expression. BSP precoating of the rough TICER implant surface enhanced the osteoinductive effect much more than did collagen precoating. These results contribute to the consideration of at least two distinct pathways of osseointegration.

Loss of hippocampal serine protease BSP1/neuropsin predisposes to global seizure activity.

PubMed

Davies, B; Kearns, I R; Ure, J; Davies, C H; Lathe, R

2001-09-15

Serine proteases in the adult CNS contribute both to activity-dependent structural changes accompanying learning and to the regulation of excitotoxic cell death. Brain serine protease 1 (BSP1)/neuropsin is a trypsin-like serine protease exclusively expressed, within the CNS, in the hippocampus and associated limbic structures. To explore the role of this enzyme, we have used gene targeting to disrupt this gene in mice. Mutant mice were viable and overtly normal; they displayed normal hippocampal long-term synaptic potentiation (LTP) and exhibited no deficits in spatial navigation (water maze). Nevertheless, electrophysiological studies revealed that the hippocampus of mice lacking this specifically expressed protease possessed an increased susceptibility for hyperexcitability (polyspiking) in response to repetitive afferent stimulation. Furthermore, seizure activity on kainic acid administration was markedly increased in mutant mice and was accompanied by heightened immediate early gene (c-fos) expression throughout the brain. In view of the regional selectivity of BSP1/neuropsin brain expression, the observed phenotype may selectively reflect limbic function, further implicating the hippocampus and amygdala in controlling cortical activation. Within the hippocampus, our data suggest that BSP1/neuropsin, unlike other serine proteases, has little effect on physiological synaptic remodeling and instead plays a role in limiting neuronal hyperexcitability induced by epileptogenic insult.

A brain-machine interface for control of medically-induced coma.

PubMed

Shanechi, Maryam M; Chemali, Jessica J; Liberman, Max; Solt, Ken; Brown, Emery N

2013-10-01

Medically-induced coma is a drug-induced state of profound brain inactivation and unconsciousness used to treat refractory intracranial hypertension and to manage treatment-resistant epilepsy. The state of coma is achieved by continually monitoring the patient's brain activity with an electroencephalogram (EEG) and manually titrating the anesthetic infusion rate to maintain a specified level of burst suppression, an EEG marker of profound brain inactivation in which bursts of electrical activity alternate with periods of quiescence or suppression. The medical coma is often required for several days. A more rational approach would be to implement a brain-machine interface (BMI) that monitors the EEG and adjusts the anesthetic infusion rate in real time to maintain the specified target level of burst suppression. We used a stochastic control framework to develop a BMI to control medically-induced coma in a rodent model. The BMI controlled an EEG-guided closed-loop infusion of the anesthetic propofol to maintain precisely specified dynamic target levels of burst suppression. We used as the control signal the burst suppression probability (BSP), the brain's instantaneous probability of being in the suppressed state. We characterized the EEG response to propofol using a two-dimensional linear compartment model and estimated the model parameters specific to each animal prior to initiating control. We derived a recursive Bayesian binary filter algorithm to compute the BSP from the EEG and controllers using a linear-quadratic-regulator and a model-predictive control strategy. Both controllers used the estimated BSP as feedback. The BMI accurately controlled burst suppression in individual rodents across dynamic target trajectories, and enabled prompt transitions between target levels while avoiding both undershoot and overshoot. The median performance error for the BMI was 3.6%, the median bias was -1.4% and the overall posterior probability of reliable control was 1 (95% Bayesian credibility interval of [0.87, 1.0]). A BMI can maintain reliable and accurate real-time control of medically-induced coma in a rodent model suggesting this strategy could be applied in patient care.

Bone Factors Regulating the Osteotropism of Metastatic Breast Cancer

DTIC Science & Technology

1998-10-01

growth factors and rapid angiogenesis occurs in the immediate vicinity of an active osteoclast. 4,5 Osteoblast-derived bone sialoprotein (BSP...Cells Antigenic Marker Cells Cultured Alone Cells Co-Cultured (2d) MCF-7 MC3T3 MCF-7 MC3T3 human cytokeratin-+ -1 bone sialoprotein (BSP...proteins. Osteonectin, osteopontin and bone sialoprotein have been studied in a series of human breast cancers. 3,15-3 0 Immunohistochemical evaluation

Bone Sialoproteins and Breast Cancer Detection

DTIC Science & Technology

2005-07-01

Fig. 8 shows (DSPP) gene within the critical dentinogenesis imperfecta type 11 and BSP with an intact RGD bridging MMP-2 to its cell-surface dentin...sialoprotein (BSP) and the pivotal transcriptional oebter Gasy seler I Freedma NcWe of BiselarMa.tMatix regulator of osteogenesis , Cbfal/Runx2, in malignant...potential the pathogenesis of dentinogenesis imperfecta type II. Genomics 1997; diagnostic biomarker for ovarian cancer. JAMA 2002;287:1671-9. 42:38-45

Directed Evolution and Structural Analysis of Alkaline Pectate Lyase from the Alkaliphilic Bacterium Bacillus sp. Strain N16-5 To Improve Its Thermostability for Efficient Ramie Degumming.

PubMed

Zhou, Cheng; Ye, Jintong; Xue, Yanfen; Ma, Yanhe

2015-09-01

Thermostable alkaline pectate lyases have potential applications in the textile industry as an alternative to chemical-based ramie degumming processes. In particular, the alkaline pectate lyase from Bacillus sp. strain N16-5 (BspPelA) has potential for enzymatic ramie degumming because of its high specific activity under extremely alkaline conditions without the requirement for additional Ca(2+). However, BspPelA displays poor thermostability and is inactive after incubation at 50°C for only 30 min. Here, directed evolution was used to improve the thermostability of BspPelA for efficient and stable degumming. After two rounds of error-prone PCR and screening of >12,000 mutants, 10 mutants with improved thermostability were obtained. Sequence analysis and site-directed mutagenesis revealed that single E124I, T178A, and S271G substitutions were responsible for improving thermostability. Structural and molecular dynamic simulation analysis indicated that the formation of a hydrophobic cluster and new H-bond networks was the key factor contributing to the improvement in thermostability with these three substitutions. The most thermostable combined mutant, EAET, exhibited a 140-fold increase in the t50 (time at which the enzyme loses 50% of its initial activity) value at 50°C, accompanied by an 84.3% decrease in activity compared with that of wild-type BspPelA, while the most advantageous combined mutant, EA, exhibited a 24-fold increase in the t50 value at 50°C, with a 23.3% increase in activity. Ramie degumming with the EA mutant was more efficient than that with wild-type BspPelA. Collectively, our results suggest that the EA mutant, exhibiting remarkable improvements in thermostability and activity, has the potential for applications in ramie degumming in the textile industry. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Directed Evolution and Structural Analysis of Alkaline Pectate Lyase from the Alkaliphilic Bacterium Bacillus sp. Strain N16-5 To Improve Its Thermostability for Efficient Ramie Degumming

PubMed Central

Zhou, Cheng; Ye, Jintong; Xue, Yanfen

2015-01-01

Thermostable alkaline pectate lyases have potential applications in the textile industry as an alternative to chemical-based ramie degumming processes. In particular, the alkaline pectate lyase from Bacillus sp. strain N16-5 (BspPelA) has potential for enzymatic ramie degumming because of its high specific activity under extremely alkaline conditions without the requirement for additional Ca2+. However, BspPelA displays poor thermostability and is inactive after incubation at 50°C for only 30 min. Here, directed evolution was used to improve the thermostability of BspPelA for efficient and stable degumming. After two rounds of error-prone PCR and screening of >12,000 mutants, 10 mutants with improved thermostability were obtained. Sequence analysis and site-directed mutagenesis revealed that single E124I, T178A, and S271G substitutions were responsible for improving thermostability. Structural and molecular dynamic simulation analysis indicated that the formation of a hydrophobic cluster and new H-bond networks was the key factor contributing to the improvement in thermostability with these three substitutions. The most thermostable combined mutant, EAET, exhibited a 140-fold increase in the t50 (time at which the enzyme loses 50% of its initial activity) value at 50°C, accompanied by an 84.3% decrease in activity compared with that of wild-type BspPelA, while the most advantageous combined mutant, EA, exhibited a 24-fold increase in the t50 value at 50°C, with a 23.3% increase in activity. Ramie degumming with the EA mutant was more efficient than that with wild-type BspPelA. Collectively, our results suggest that the EA mutant, exhibiting remarkable improvements in thermostability and activity, has the potential for applications in ramie degumming in the textile industry. PMID:26070675

Cover cropping alters the diet of arthropods in a banana plantation: a metabarcoding approach.

PubMed

Mollot, Gregory; Duyck, Pierre-François; Lefeuvre, Pierre; Lescourret, Françoise; Martin, Jean-François; Piry, Sylvain; Canard, Elsa; Tixier, Philippe

2014-01-01

Plant diversification using cover crops may promote natural regulation of agricultural pests by supporting alternative prey that enable the increase of arthropod predator densities. However, the changes in the specific composition of predator diet induced by cover cropping are poorly understood. Here, we hypothesized that the cover crop can significantly alter the diet of predators in agroecosystems. The cover crop Brachiaria decumbens is increasingly used in banana plantations to control weeds and improve physical soil properties. In this paper, we used a DNA metabarcoding approach for the molecular analysis of the gut contents of predators (based on mini-COI) to identify 1) the DNA sequences of their prey, 2) the predators of Cosmopolites sordidus (a major pest of banana crops), and 3) the difference in the specific composition of predator diets between a bare soil plot (BSP) and a cover cropped plot (CCP) in a banana plantation. The earwig Euborellia caraibea, the carpenter ant Camponotus sexguttatus, and the fire ant Solenopsis geminata were found to contain C. sordidus DNA at frequencies ranging from 1 to 7%. While the frequencies of predators positive for C. sordidus DNA did not significantly differ between BSP and CCP, the frequency at which E. caraibea was positive for Diptera was 26% in BSP and 80% in CCP; the frequency at which C. sexguttatus was positive for Jalysus spinosus was 14% in BSP and 0% in CCP; and the frequency at which S. geminata was positive for Polytus mellerborgi was 21% in BSP and 3% in CCP. E. caraibea, C. sexguttatus and S. geminata were identified as possible biological agents for the regulation of C. sordidus. The detection of the diet changes of these predators when a cover crop is planted indicates the possible negative effects on pest regulation if predators switch to forage on alternative prey.

Cover Cropping Alters the Diet of Arthropods in a Banana Plantation: A Metabarcoding Approach

PubMed Central

Mollot, Gregory; Duyck, Pierre-François; Lefeuvre, Pierre; Lescourret, Françoise; Martin, Jean-François; Piry, Sylvain; Canard, Elsa; Tixier, Philippe

2014-01-01

Plant diversification using cover crops may promote natural regulation of agricultural pests by supporting alternative prey that enable the increase of arthropod predator densities. However, the changes in the specific composition of predator diet induced by cover cropping are poorly understood. Here, we hypothesized that the cover crop can significantly alter the diet of predators in agroecosystems. The cover crop Brachiaria decumbens is increasingly used in banana plantations to control weeds and improve physical soil properties. In this paper, we used a DNA metabarcoding approach for the molecular analysis of the gut contents of predators (based on mini-COI) to identify 1) the DNA sequences of their prey, 2) the predators of Cosmopolites sordidus (a major pest of banana crops), and 3) the difference in the specific composition of predator diets between a bare soil plot (BSP) and a cover cropped plot (CCP) in a banana plantation. The earwig Euborellia caraibea, the carpenter ant Camponotus sexguttatus, and the fire ant Solenopsis geminata were found to contain C. sordidus DNA at frequencies ranging from 1 to 7%. While the frequencies of predators positive for C. sordidus DNA did not significantly differ between BSP and CCP, the frequency at which E. caraibea was positive for Diptera was 26% in BSP and 80% in CCP; the frequency at which C. sexguttatus was positive for Jalysus spinosus was 14% in BSP and 0% in CCP; and the frequency at which S. geminata was positive for Polytus mellerborgi was 21% in BSP and 3% in CCP. E. caraibea, C. sexguttatus and S. geminata were identified as possible biological agents for the regulation of C. sordidus. The detection of the diet changes of these predators when a cover crop is planted indicates the possible negative effects on pest regulation if predators switch to forage on alternative prey. PMID:24695585

Sexual Well-Being in Patients with Blepharospasm, Spasmodic Torticollis, and Hemifacial Spasm: A Pilot Study

PubMed Central

Perozzo, Paola; Salatino, Adriana; Cerrato, Paolo; Ricci, Raffaella

2016-01-01

Mood, anxiety, and other psychological symptoms are common in dystonic patients suffering from blepharospasm (BSP) and spasmodic torticollis (ST). Since sexual well-being is an important aspect of mental health, here, we investigated whether these patients may also experience a worsening of their sexual life. In particular, quality of sexual life was evaluated in patients suffering from BSP (N = 30), ST (N = 30), and in a control group of patient with Hemifacial spasm (HFS; N = 30), undergoing botulinum toxin type A therapy. A group of 30 age-matched healthy volunteers constituted an additional control group. Patients were evaluated just before the periodic injection of botulinum toxin. Sexual functioning was assessed using the Sexual Functioning Inventory, a reduced form of the Golombok Rust Inventory, previously employed in patients with Parkinson’s disease. Depression (Beck Depression Inventory) and anxiety (STAI-X1/X2) were also assessed. Results revealed that sexual functioning was significantly affected in patients with BSP, ST, and HFS with respect to healthy controls. Dystonic patients manifested more sexual dysfunction than patients with HFS. Overall, females had a poorer quality of sexual life than males and, among females, women with BSP were the most dysfunctional. Psychological symptoms were present in patients with dystonia, but not in patients with HFS. As discussed in the paper, several factors might be taken into account to explain worse quality of sexual life in patients with dystonia compared to patients with hemifacial spasm. Among them an important role might be played by the central origin of dystonia pathophysiology (i.e., altered activity of cortico-striato-thalamic-cortical circuits). Future investigations are necessary to further explore these preliminary findings, considering that this is the first time that sexual well-being is evaluated in patients with BSP, ST, and HFS, and comparable data are not available. PMID:27761118

A pilot randomised trial of induced blood-stage Plasmodium falciparum infections in healthy volunteers for testing efficacy of new antimalarial drugs.

PubMed

McCarthy, James S; Sekuloski, Silvana; Griffin, Paul M; Elliott, Suzanne; Douglas, Nanette; Peatey, Chris; Rockett, Rebecca; O'Rourke, Peter; Marquart, Louise; Hermsen, Cornelius; Duparc, Stephan; Möhrle, Jörg; Trenholme, Katharine R; Humberstone, Andrew J

2011-01-01

Critical to the development of new drugs for treatment of malaria is the capacity to safely evaluate their activity in human subjects. The approach that has been most commonly used is testing in subjects with natural malaria infection, a methodology that may expose symptomatic subjects to the risk of ineffective treatment. Here we describe the development and pilot testing of a system to undertake experimental infection using blood stage Plasmodium falciparum parasites (BSP). The objectives of the study were to assess the feasibility and safety of induced BSP infection as a method for assessment of efficacy of new drug candidates for the treatment of P. falciparum infection. A prospective, unblinded, Phase IIa trial was undertaken in 19 healthy, malaria-naïve, male adult volunteers who were infected with BSP and followed with careful clinical and laboratory observation, including a sensitive, quantitative malaria PCR assay. Volunteers were randomly allocated to treatment with either of two licensed antimalarial drug combinations, artemether-lumefantrine (A/L) or atovaquone-proguanil (A/P). In the first cohort (n = 6) where volunteers received ∼360 BSP, none reached the target parasitemia of 1,000 before the day designated for antimalarial treatment (day 6). In the second and third cohorts, 13 volunteers received 1,800 BSP, with all reaching the target parasitemia before receiving treatment (A/L, n = 6; A/P, n = 7) The study demonstrated safety in the 19 volunteers tested, and a significant difference in the clearance kinetics of parasitemia between the drugs in the 13 evaluable subjects, with mean parasite reduction ratios of 759 for A/L and 17 for A/P (95% CI 120-4786 and 7-40 respectively; p<0.01). This system offers a flexible and safe approach to testing the in vivo activity of novel antimalarials. ClinicalTrials.gov NCT01055002.

Beta 2-Microglobulin: A Novel Therapeutic Target for the Treatment of Human Prostate Cancer Bone Metastasis

DTIC Science & Technology

2009-03-14

H, Sodek J, Zhau HE, Chung LW. Human osteocalcin and bone sialoprotein mediating osteomimicry of prostate cancer cells: role of cAMP-dependent...with mesenchymal phenotype b2-m b2-Microglobulin BSP Bone sialoprotein C4-2 Lineage derivative cells from LNCaP C4-2B C4-2 cells metastasized to bone...OPN) and bone sialoprotein (BSP), and RANKL, collectively allow- ing cancer cells to survive and thrive in the bone microenvironment [7–9]. Previous

An Investigation of IBM’s Business Systems Planning (BSP) as a Suitable Methodology for Strategic Information Systems Planning for the Naval Reserve.

DTIC Science & Technology

1986-09-01

determine information systems (IS) needs. This thesis is limited to an evaluation of BSP as a :ethodology for understanding information flow in the Naval...external. The information systems of the organization are also evaluated in this chapter. The purpose of Chapter II is to familiarize the reader with...Wide Military Command and Control System (WWMCCS) .p *The general way in which the sources or end users of different categories of information are

Behavioral Signal Processing: Deriving Human Behavioral Informatics From Speech and Language

PubMed Central

Narayanan, Shrikanth; Georgiou, Panayiotis G.

2013-01-01

The expression and experience of human behavior are complex and multimodal and characterized by individual and contextual heterogeneity and variability. Speech and spoken language communication cues offer an important means for measuring and modeling human behavior. Observational research and practice across a variety of domains from commerce to healthcare rely on speech- and language-based informatics for crucial assessment and diagnostic information and for planning and tracking response to an intervention. In this paper, we describe some of the opportunities as well as emerging methodologies and applications of human behavioral signal processing (BSP) technology and algorithms for quantitatively understanding and modeling typical, atypical, and distressed human behavior with a specific focus on speech- and language-based communicative, affective, and social behavior. We describe the three important BSP components of acquiring behavioral data in an ecologically valid manner across laboratory to real-world settings, extracting and analyzing behavioral cues from measured data, and developing models offering predictive and decision-making support. We highlight both the foundational speech and language processing building blocks as well as the novel processing and modeling opportunities. Using examples drawn from specific real-world applications ranging from literacy assessment and autism diagnostics to psychotherapy for addiction and marital well being, we illustrate behavioral informatics applications of these signal processing techniques that contribute to quantifying higher level, often subjectively described, human behavior in a domain-sensitive fashion. PMID:24039277

Efficient Mobility Management Signalling in Network Mobility Supported PMIPV6

PubMed Central

Jebaseeli Samuelraj, Ananthi; Jayapal, Sundararajan

2015-01-01

Proxy Mobile IPV6 (PMIPV6) is a network based mobility management protocol which supports node's mobility without the contribution from the respective mobile node. PMIPV6 is initially designed to support individual node mobility and it should be enhanced to support mobile network movement. NEMO-BSP is an existing protocol to support network mobility (NEMO) in PMIPV6 network. Due to the underlying differences in basic protocols, NEMO-BSP cannot be directly applied to PMIPV6 network. Mobility management signaling and data structures used for individual node's mobility should be modified to support group nodes' mobility management efficiently. Though a lot of research work is in progress to implement mobile network movement in PMIPV6, it is not yet standardized and each suffers with different shortcomings. This research work proposes modifications in NEMO-BSP and PMIPV6 to achieve NEMO support in PMIPV6. It mainly concentrates on optimizing the number and size of mobility signaling exchanged while mobile network or mobile network node changes its access point. PMID:26366431

USGS Blind Sample Project: monitoring and evaluating laboratory analytical quality

USGS Publications Warehouse

Ludtke, Amy S.; Woodworth, Mark T.

1997-01-01

The U.S. Geological Survey (USGS) collects and disseminates information about the Nation's water resources. Surface- and ground-water samples are collected and sent to USGS laboratories for chemical analyses. The laboratories identify and quantify the constituents in the water samples. Random and systematic errors occur during sample handling, chemical analysis, and data processing. Although all errors cannot be eliminated from measurements, the magnitude of their uncertainty can be estimated and tracked over time. Since 1981, the USGS has operated an independent, external, quality-assurance project called the Blind Sample Project (BSP). The purpose of the BSP is to monitor and evaluate the quality of laboratory analytical results through the use of double-blind quality-control (QC) samples. The information provided by the BSP assists the laboratories in detecting and correcting problems in the analytical procedures. The information also can aid laboratory users in estimating the extent that laboratory errors contribute to the overall errors in their environmental data.

Binary-space-partitioned images for resolving image-based visibility.

PubMed

Fu, Chi-Wing; Wong, Tien-Tsin; Tong, Wai-Shun; Tang, Chi-Keung; Hanson, Andrew J

2004-01-01

We propose a novel 2D representation for 3D visibility sorting, the Binary-Space-Partitioned Image (BSPI), to accelerate real-time image-based rendering. BSPI is an efficient 2D realization of a 3D BSP tree, which is commonly used in computer graphics for time-critical visibility sorting. Since the overall structure of a BSP tree is encoded in a BSPI, traversing a BSPI is comparable to traversing the corresponding BSP tree. BSPI performs visibility sorting efficiently and accurately in the 2D image space by warping the reference image triangle-by-triangle instead of pixel-by-pixel. Multiple BSPIs can be combined to solve "disocclusion," when an occluded portion of the scene becomes visible at a novel viewpoint. Our method is highly automatic, including a tensor voting preprocessing step that generates candidate image partition lines for BSPIs, filters the noisy input data by rejecting outliers, and interpolates missing information. Our system has been applied to a variety of real data, including stereo, motion, and range images.

Efficient Mobility Management Signalling in Network Mobility Supported PMIPV6.

PubMed

Samuelraj, Ananthi Jebaseeli; Jayapal, Sundararajan

2015-01-01

Proxy Mobile IPV6 (PMIPV6) is a network based mobility management protocol which supports node's mobility without the contribution from the respective mobile node. PMIPV6 is initially designed to support individual node mobility and it should be enhanced to support mobile network movement. NEMO-BSP is an existing protocol to support network mobility (NEMO) in PMIPV6 network. Due to the underlying differences in basic protocols, NEMO-BSP cannot be directly applied to PMIPV6 network. Mobility management signaling and data structures used for individual node's mobility should be modified to support group nodes' mobility management efficiently. Though a lot of research work is in progress to implement mobile network movement in PMIPV6, it is not yet standardized and each suffers with different shortcomings. This research work proposes modifications in NEMO-BSP and PMIPV6 to achieve NEMO support in PMIPV6. It mainly concentrates on optimizing the number and size of mobility signaling exchanged while mobile network or mobile network node changes its access point.

Effects of inorganic polyphosphate on bone sialoprotein gene expression.

PubMed

Wang, Zhitao; Li, Xinyue; Li, Zhengyang; Yang, Li; Sasaki, Yoko; Wang, Shuang; Zhou, Liming; Araki, Shouta; Mezawa, Masaru; Takai, Hideki; Ogata, Yorimasa

2010-03-01

Inorganic polyphosphate (poly(P)) is a biopolymer existing in almost all cells and tissues. The biological functions of poly(P) in micro-organisms have been extensively investigated in studies of poly(P) in eukaryotic cells, especially osteoblasts, and are increasing. Bone sialoprotein (BSP) is thought to function in bone mineralization, and is selectively expressed by differentiated osteoblasts. In this study, application of sodium phosphate glass type 25 (SPG25, 12.5 and 125 microM) increased BSP mRNA levels at 12 h in osteoblast-like ROS 17/2.8 cells. In transient transfection assay, 12.5 and 125 microM SPG25 increased luciferase activities of the constructs pLUC3 (-116 to +60), pLUC4 (-425 to +60), pLUC5 (-801 to +60) and pLUC6 (-938 to +60). Introduction of 2 bp mutations to the luciferase constructs showed that the effects of SPG25 were mediated by a FGF2 response element (FRE) and a homeodomain protein binding site (HOX). Luciferase activities induced by SPG25 were blocked by tyrosine kinase inhibitor herbimycine A, MAP kinase kinase inhibitor U0126, PI3-kinase/Akt inhibitor LY249002 and inorganic phosphate transport inhibitor foscarnet. Gel shift analyses showed that both 12.5 and 125 microM SPG25 increased nuclear protein binding to FRE and HOX elements. These studies demonstrate that SPG25 stimulates BSP transcription by targeting FRE and HOX elements in the proximal promoter of the rat BSP gene. Copyright 2010 Elsevier B.V. All rights reserved.

Aerosol chemical composition and light scattering during a winter season in Beijing

NASA Astrophysics Data System (ADS)

Tao, Jun; Zhang, Leiming; Gao, Jian; Wang, Han; Chai, Faihe; Wang, Shulan

2015-06-01

To evaluate PM2.5 contributions to light scattering under different air pollution levels, PM2.5 and its major chemical components, PM10, size-segregated water-soluble ions, and aerosol scattering coefficient (bsp) under dry conditions were measured at an urban site in Beijing in January 2013 when heavy pollution events frequently occurred. Measurements were categorized into three pollution levels including heavy-polluted (Air Quality Index (AQI) ≥ 200), light-polluted (200 > AQI ≥ 100) and clean periods (AQI < 100). The average PM2.5 mass concentration was 248 μg m-3 during the heavy-polluted period, which was 2.4 and 5.6 times of those during the light-polluted (104 μg m-3) and clean (44 μg m-3) periods, respectively. The concentrations of SO42-, NO3- and NH4+ increased much more than those of OC and EC during the heavy-polluted period compared with those during the light-polluted and clean periods. Good correlations between PM2.5 and bsp were found (R2 > 0.95) during the different pollution levels. The mass scattering efficiency (MSE) of PM2.5 was 4.9 m2 g-1 during the heavy-polluted period, which was higher than those during the light-polluted (4.3 m2 g-1) and clean periods (3.6 m2 g-1). To further evaluate the impact of individual chemical components of PM2.5 on light scattering, a multiple linear regression equation of measured bsp against the mass concentration of (NH4)2SO4, NH4NO3, Organic Matter (OM), EC, Fine Soil (FS), Coarse Matter (CM) and Other chemical compounds were performed. (NH4)2SO4, NH4NO3 and OM were the dominant species contributing to bsp under both dry and ambient conditions. OM contributed more to bsp than the sum of (NH4)2SO4 and NH4NO3 did under the dry condition during all the pollution periods and this was also the case under the ambient condition during the light-polluted and clean periods. However, the total contributions of (NH4)2SO4 and NH4NO3 to bsp under the ambient condition was 55%, much more than the 29% contribution from OM during the heavy-polluted period. High (NH4)2SO4 and NH4NO3 concentrations and their hygroscopicity were the main reasons causing visibility degradation during the heavy-polluted period, and the effect can be enhanced under high RH conditions.

Family variation in photosynthesis of 22-year-old black spruce: a test of two models of physiological response to water stress

Treesearch

John E. Major; Kurt H. Johnsen

1996-01-01

Gas exchange and water potential were measured in 22-year-old black spruce (Piceamariana (Mill.) BSP) trees from four full-sib families on two sites (one drier and one wetter) at the Petawawa National Forestry Institute, Ontario. Based on an observed genotype × environment interaction and earlier work with seedlings, a...

A closed-loop anesthetic delivery system for real-time control of burst suppression

NASA Astrophysics Data System (ADS)

Liberman, Max Y.; Ching, ShiNung; Chemali, Jessica; Brown, Emery N.

2013-08-01

Objective. There is growing interest in using closed-loop anesthetic delivery (CLAD) systems to automate control of brain states (sedation, unconsciousness and antinociception) in patients receiving anesthesia care. The accuracy and reliability of these systems can be improved by using as control signals electroencephalogram (EEG) markers for which the neurophysiological links to the anesthetic-induced brain states are well established. Burst suppression, in which bursts of electrical activity alternate with periods of quiescence or suppression, is a well-known, readily discernible EEG marker of profound brain inactivation and unconsciousness. This pattern is commonly maintained when anesthetics are administered to produce a medically-induced coma for cerebral protection in patients suffering from brain injuries or to arrest brain activity in patients having uncontrollable seizures. Although the coma may be required for several hours or days, drug infusion rates are managed inefficiently by manual adjustment. Our objective is to design a CLAD system for burst suppression control to automate management of medically-induced coma. Approach. We establish a CLAD system to control burst suppression consisting of: a two-dimensional linear system model relating the anesthetic brain level to the EEG dynamics; a new control signal, the burst suppression probability (BSP) defining the instantaneous probability of suppression; the BSP filter, a state-space algorithm to estimate the BSP from EEG recordings; a proportional-integral controller; and a system identification procedure to estimate the model and controller parameters. Main results. We demonstrate reliable performance of our system in simulation studies of burst suppression control using both propofol and etomidate in rodent experiments based on Vijn and Sneyd, and in human experiments based on the Schnider pharmacokinetic model for propofol. Using propofol, we further demonstrate that our control system reliably tracks changing target levels of burst suppression in simulated human subjects across different epidemiological profiles. Significance. Our results give new insights into CLAD system design and suggest a control-theory framework to automate second-to-second control of burst suppression for management of medically-induced coma.

Modelling of three long-periodic magnetic CP-stars: HD 2453, HD 12288, and HD 200311

NASA Astrophysics Data System (ADS)

Glagolevskij, Yurij V.; Gerth, Ewald

2004-12-01

Using observational data published as phase curves of the effective magnetic field strength Be(P) and the surface field Bs(P), magnetic models of three stars with long rotational periods are calculated by the Magnetic Charge Distribution method. For two of these stars (HD 2453 and HD 12288), the structure of the magnetic field can be described well by a central dipole model. The third star (HD 200311) is better fitted by a model of a displaced dipole, being decentered by triangle r = 0.08 R along the dipole axis.

Algal extracellular release in river-floodplain dissolved organic matter: response of extracellular enzymatic activity during a post-flood period

PubMed Central

Sieczko, Anna; Maschek, Maria; Peduzzi, Peter

2015-01-01

River-floodplain systems are susceptible to rapid hydrological events. Changing hydrological connectivity of the floodplain generates a broad range of conditions, from lentic to lotic. This creates a mixture of allochthonously and autochthonously derived dissolved organic matter (DOM). Autochthonous DOM, including photosynthetic extracellular release (PER), is an important source supporting bacterial secondary production (BSP). Nonetheless, no details are available regarding microbial extracellular enzymatic activity (EEA) as a response to PER under variable hydrological settings in river-floodplain systems. To investigate the relationship between bacterial and phytoplankton components, we therefore used EEA as a tool to track the microbial response to non-chromophoric, but reactive and ecologically important DOM. The study was conducted in three floodplain subsystems with distinct hydrological regimes (Danube Floodplain National Park, Austria). The focus was on the post-flood period. Enhanced %PER (up to 48% of primary production) in a hydrologically isolated subsystem was strongly correlated with β-glucosidase, which was related to BSP. This shows that—in disconnected floodplain backwaters with high terrestrial input—BSP can also be driven by autochthonous carbon sources (PER). In a semi-isolated section, in the presence of fresh labile material from primary producers, enhanced activity of phenol oxidase was observed. In frequently flooded river-floodplain systems, BSP was mainly driven by enzymatic degradation of particulate primary production. Our research demonstrates that EEA measurements are an excellent tool to describe the coupling between bacteria and phytoplankton, which cannot be deciphered when focusing solely on chromophoric DOM. PMID:25741326

Region of interest methylation analysis: a comparison of MSP with MS-HRM and direct BSP.

PubMed

Akika, Reem; Awada, Zainab; Mogharbil, Nahed; Zgheib, Nathalie K

2017-07-01

The aim of this study was to compare and contrast three DNA methylation methods of a specific region of interest (ROI): methylation-specific PCR (MSP), methylation-sensitive high resolution melting (MS-HRM) and direct bisulfite sequencing (BSP). The methylation of a CpG area in the promoter region of Estrogen receptor alpha (ESR1) was evaluated by these three methods with samples and standards of different methylation percentages. MSP data were neither reproducible nor sensitive, and the assay was not specific due to non-specific binding of primers. MS-HRM was highly reproducible and a step forward into categorizing the methylation status of the samples as percent ranges. Direct BSP was the most informative method regarding methylation percentage of each CpG site. Though not perfect, it was reproducible and sensitive. We recommend the use of either method depending on the research question and target amplicon, and provided that the designed primers and expected amplicons are within recommendations. If the research question targets a limited number of CpG sites and simple yes/no results are enough, MSP may be attempted. For short amplicons that are crowded with CpG sites and of single melting domain, MS-HRM may be the method of choice though it only indicates the overall methylation percentage of the entire amplicon. Although the assay is highly reproducible, being semi-quantitative makes it of lesser interest to study ROI methylation of samples with little methylation differences. Direct BSP is a step forward as it gives information about the methylation percentage at each CpG site.

LDFT-based watermarking resilient to local desynchronization attacks.

PubMed

Tian, Huawei; Zhao, Yao; Ni, Rongrong; Qin, Lunming; Li, Xuelong

2013-12-01

Up to now, a watermarking scheme that is robust against desynchronization attacks (DAs) is still a grand challenge. Most image watermarking resynchronization schemes in literature can survive individual global DAs (e.g., rotation, scaling, translation, and other affine transforms), but few are resilient to challenging cropping and local DAs. The main reason is that robust features for watermark synchronization are only globally invariable rather than locally invariable. In this paper, we present a blind image watermarking resynchronization scheme against local transform attacks. First, we propose a new feature transform named local daisy feature transform (LDFT), which is not only globally but also locally invariable. Then, the binary space partitioning (BSP) tree is used to partition the geometrically invariant LDFT space. In the BSP tree, the location of each pixel is fixed under global transform, local transform, and cropping. Lastly, the watermarking sequence is embedded bit by bit into each leaf node of the BSP tree by using the logarithmic quantization index modulation watermarking embedding method. Simulation results show that the proposed watermarking scheme can survive numerous kinds of distortions, including common image-processing attacks, local and global DAs, and noninvertible cropping.

Spatial variation in automated burst suppression detection in pharmacologically induced coma.

PubMed

An, Jingzhi; Jonnalagadda, Durga; Moura, Valdery; Purdon, Patrick L; Brown, Emery N; Westover, M Brandon

2015-01-01

Burst suppression is actively studied as a control signal to guide anesthetic dosing in patients undergoing medically induced coma. The ability to automatically identify periods of EEG suppression and compactly summarize the depth of coma using the burst suppression probability (BSP) is crucial to effective and safe monitoring and control of medical coma. Current literature however does not explicitly account for the potential variation in burst suppression parameters across different scalp locations. In this study we analyzed standard 19-channel EEG recordings from 8 patients with refractory status epilepticus who underwent pharmacologically induced burst suppression as medical treatment for refractory seizures. We found that although burst suppression is generally considered a global phenomenon, BSP obtained using a previously validated algorithm varies systematically across different channels. A global representation of information from individual channels is proposed that takes into account the burst suppression characteristics recorded at multiple electrodes. BSP computed from this representative burst suppression pattern may be more resilient to noise and a better representation of the brain state of patients. Multichannel data integration may enhance the reliability of estimates of the depth of medical coma.

Systematic nomenclature for the PLUNC/PSP/BSP30/SMGB proteins as a subfamily of the BPI fold-containing superfamily.

PubMed

Bingle, Colin D; Seal, Ruth L; Craven, C Jeremy

2011-08-01

We present the BPIFAn/BPIFBn systematic nomenclature for the PLUNC (palate lung and nasal epithelium clone)/PSP (parotid secretory protein)/BSP30 (bovine salivary protein 30)/SMGB (submandibular gland protein B) family of proteins, based on an adaptation of the SPLUNCn (short PLUNCn)/LPLUNCn (large PLUNCn) nomenclature. The nomenclature is applied to a set of 102 sequences which we believe represent the current reliable data for BPIFA/BPIFB proteins across all species, including marsupials and birds. The nomenclature will be implemented by the HGNC (HUGO Gene Nomenclature Committee).

Behavioral Signal Processing: Deriving Human Behavioral Informatics From Speech and Language: Computational techniques are presented to analyze and model expressed and perceived human behavior-variedly characterized as typical, atypical, distressed, and disordered-from speech and language cues and their applications in health, commerce, education, and beyond.

PubMed

Narayanan, Shrikanth; Georgiou, Panayiotis G

2013-02-07

The expression and experience of human behavior are complex and multimodal and characterized by individual and contextual heterogeneity and variability. Speech and spoken language communication cues offer an important means for measuring and modeling human behavior. Observational research and practice across a variety of domains from commerce to healthcare rely on speech- and language-based informatics for crucial assessment and diagnostic information and for planning and tracking response to an intervention. In this paper, we describe some of the opportunities as well as emerging methodologies and applications of human behavioral signal processing (BSP) technology and algorithms for quantitatively understanding and modeling typical, atypical, and distressed human behavior with a specific focus on speech- and language-based communicative, affective, and social behavior. We describe the three important BSP components of acquiring behavioral data in an ecologically valid manner across laboratory to real-world settings, extracting and analyzing behavioral cues from measured data, and developing models offering predictive and decision-making support. We highlight both the foundational speech and language processing building blocks as well as the novel processing and modeling opportunities. Using examples drawn from specific real-world applications ranging from literacy assessment and autism diagnostics to psychotherapy for addiction and marital well being, we illustrate behavioral informatics applications of these signal processing techniques that contribute to quantifying higher level, often subjectively described, human behavior in a domain-sensitive fashion.

Establishing a Suitable Tactical Design Model for Clear-Hold-Build Counterinsurgency Operations

DTIC Science & Technology

2009-06-12

Vietnam capitol of Saigon. Cedar Falls was tactically designed to achieve this result through two measures . First, U.S. Army forces would separate...provide a higher force ratio for the operation. This tethering would mitigate risk for the Soldiers themselves. Because risk management is so integrated...Vietnam) BCT Brigade Combat Team BCTP Battle Command Training Program BN Battalion BSP Baghdad Security Plan CF Coalition Forces C-H-B Clear-Hold

The Effect of Prescribed Burns and Wildfire on Vegetation in Bastrop State Park, TX

NASA Astrophysics Data System (ADS)

Justice, C. J.

2014-12-01

In 2011, central Texas had its worst drought since the 1950's. This, in conjunction with the strong winds produced by Tropical Storm Lee created conditions that made possible the Bastrop County Complex Fire in September 2011. These record-breaking wildfires burned over 95% of the 6,565-acre Bastrop State Park (BSP). Since 2003, BSP had been using prescribed burns as a management practice to reduce fuel load and prevent high severity wildfires. Although these prescribed fires did not prevent the 2011 wildfires they may have mitigated their effects. This study considered the effect of prescribed burn history and wildfire burn severity on vegetation recovery in BSP since the 2011 wildfire. The hypotheses of this study are that prescribed burn history and wildfire burn severity separately and jointly have affected post wildfire vegetation. To test these hypotheses, data were collected in 2013 from 46 plots across BSP using the Fire Effects Monitoring and Inventory (FIREMON) protocol to determine herbaceous plant density, shrub density, overstory density, and midstory tree density. Data were analyzed using analyses of variance (ANOVA) to determine the effects of prescribed fire and wildfire severity on these vegetation measurements. It was found that more severely burned plots had more herbaceous plants, fewer midstory trees, and lower shrub densities than less severely burned plots. Contrary to an initial hypotheses, there were few relationships between prescribed burn history and wildfire effects. The only significant effect detected for prescribed burning was the positive effect of prescribed fire on midstory tree density, but only for plots that were not severely burned in the wildfire. In this system, burn severity had a greater effect on post-wildfire vegetation than prescribed burns.

THE MAGNETIC FIELD OF L1544. I. NEAR-INFRARED POLARIMETRY AND THE NON-UNIFORM ENVELOPE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Clemens, Dan P.; Tassis, K.; Goldsmith, Paul F., E-mail: clemens@bu.edu, E-mail: tassis@physics.uoc.gr, E-mail: paul.f.goldsmith@jpl.nasa.gov

2016-12-20

The magnetic field ( B -field) of the starless dark cloud L1544 has been studied using near-infrared (NIR) background starlight polarimetry (BSP) and archival data in order to characterize the properties of the plane-of-sky B -field. NIR linear polarization measurements of over 1700 stars were obtained in the H band and 201 of these were also measured in the K band. The NIR BSP properties are correlated with reddening, as traced using the Rayleigh–Jeans color excess ( H – M ) method, and with thermal dust emission from the L1544 cloud and envelope seen in Herschel maps. The NIR polarizationmore » position angles change at the location of the cloud and exhibit their lowest dispersion there, offering strong evidence that NIR polarization traces the plane-of-sky B -field of L1544. In this paper, the uniformity of the plane-of-sky B -field in the envelope region of L1544 is quantitatively assessed. This allows evaluation of the approach of assuming uniform field geometry when measuring relative mass-to-flux ratios in the cloud envelope and core based on averaging of the radio Zeeman observations in the envelope, as done by Crutcher et al. In L1544, the NIR BSP shows the envelope B -field to be significantly non-uniform and likely not suitable for averaging Zeeman properties without treating intrinsic variations. Deeper analyses of the NIR BSP and related data sets, including estimates of the B -field strength and testing how it varies with position and gas density, are the subjects of later papers in this series.« less

European Surveillance of Antimicrobial Consumption (ESAC): outpatient penicillin use in Europe (1997-2009).

PubMed

Versporten, Ann; Coenen, Samuel; Adriaenssens, Niels; Muller, Arno; Minalu, Girma; Faes, Christel; Vankerckhoven, Vanessa; Aerts, Marc; Hens, Niel; Molenberghs, Geert; Goossens, Herman

2011-12-01

Data on 13 years (1997-2009) of outpatient penicillin use were collected from 33 European countries within the European Surveillance of Antimicrobial Consumption (ESAC) project and analysed in detail. For the period 1997-2009, data on outpatient use of systemic penicillins aggregated at the level of the active substance were collected using the Anatomical Therapeutic Chemical (ATC)/defined daily dose (DDD) method (WHO, version 2011) and expressed in DDD per 1000 inhabitants per day (DID). For detailed analysis of trends over time, seasonal variation and composition of outpatient penicillin use in 33 European countries, we distinguished between narrow-spectrum penicillins (NSP), broad-spectrum penicillins (BSP), penicillinase-resistant penicillins (PRP) and combinations with β-lactamase inhibitors (COP). Total outpatient penicillin (ATC group J01C) use in 2009 varied by a factor of 3.8 between the countries with the highest (16.08 DID in France) and lowest (4.23 DID in the Russian Federation) use. COP represented 45.8%, BSP 40.7%, NSP 10.8% and PRP 2.6% of total European outpatient penicillin use. Total outpatient penicillin use significantly increased over time by 1.53 (SD 0.71) DID between 1997 and 2009. COP (mainly co-amoxiclav) increased by 2.17 (SD 0.40) DID, which was the result of its absolute increase as well as the observed shift from NSP and BSP towards COP. This increase exceeded 10% in 20 countries, where it coincided with a similar decrease in either BSP (15 countries) or NSP (5 countries). Penicillins represented the most widely used antibiotic subgroup in all 33 participating countries, albeit with considerable variation in their use patterns. For Europe, a continuous increase in overall penicillin use and of COP use was observed during the period 1997-2009.

The Role of Bone Sialoprotein in the Tendon-Bone Insertion

PubMed Central

Marinovich, Ryan; Soenjaya, Yohannes; Wallace, Gregory Q.; Zuskov, Andre; Dunkman, Andrew; Foster, Brian L.; Ao, Min; Bartman, Kevin; Lam, Vida; Rizkalla, Amin; Beier, Frank; Somerman, Martha J.; Holdsworth, David W.; Soslowsky, Louis J.; Lagugné-Labarthet, François; Goldberg, Harvey A.

2016-01-01

Tendons/ligaments insert into bone via a transitional structure, the enthesis, which is susceptible to injury and difficult to repair. Fibrocartilaginous entheses contain fibrocartilage in their transitional zone, part of which is mineralized. Mineral-associated proteins within this zone have not been adequately characterized. Members of the Small Integrin Binding Ligand N-Linked Glycoprotein (SIBLING) family are acidic phosphoproteins expressed in mineralized tissues. Here we show that two SIBLING proteins, bone sialoprotein (BSP) and osteopontin (OPN), are present in the mouse enthesis. Histological analyses indicate that the calcified zone of the quadriceps tendon enthesis is longer in Bsp−/− mice, however no difference is apparent in the supraspinatus tendon enthesis. In an analysis of mineral content within the calcified zone, micro-CT and Raman spectroscopy reveal that the mineral content in the calcified fibrocartilage of the quadriceps tendon enthesis are similar between wild type and Bsp−/− mice. Mechanical testing of the patellar tendon shows that while the tendons fail under similar loads, the Bsp−/− patellar tendon is 7.5% larger in cross sectional area than wild type tendons, resulting in a 16.5% reduction in failure stress. However, picrosirius red staining shows no difference in collagen organization. Data collected here indicate that BSP is present in the calcified fibrocartilage of murine entheses and suggest that BSP plays a regulatory role in this structure, influencing the growth of the calcified fibrocartilage in addition to the weakening of the tendon mechanical properties. Based on the phenotype of the Bsp−/− mouse enthesis, and the known in vitro functional properties of the protein, BSP may be a useful therapeutic molecule in the reattachment of tendons and ligaments to bone. PMID:26826499

Robust control of burst suppression for medical coma

NASA Astrophysics Data System (ADS)

Westover, M. Brandon; Kim, Seong-Eun; Ching, ShiNung; Purdon, Patrick L.; Brown, Emery N.

2015-08-01

Objective. Medical coma is an anesthetic-induced state of brain inactivation, manifest in the electroencephalogram by burst suppression. Feedback control can be used to regulate burst suppression, however, previous designs have not been robust. Robust control design is critical under real-world operating conditions, subject to substantial pharmacokinetic and pharmacodynamic parameter uncertainty and unpredictable external disturbances. We sought to develop a robust closed-loop anesthesia delivery (CLAD) system to control medical coma. Approach. We developed a robust CLAD system to control the burst suppression probability (BSP). We developed a novel BSP tracking algorithm based on realistic models of propofol pharmacokinetics and pharmacodynamics. We also developed a practical method for estimating patient-specific pharmacodynamics parameters. Finally, we synthesized a robust proportional integral controller. Using a factorial design spanning patient age, mass, height, and gender, we tested whether the system performed within clinically acceptable limits. Throughout all experiments we subjected the system to disturbances, simulating treatment of refractory status epilepticus in a real-world intensive care unit environment. Main results. In 5400 simulations, CLAD behavior remained within specifications. Transient behavior after a step in target BSP from 0.2 to 0.8 exhibited a rise time (the median (min, max)) of 1.4 [1.1, 1.9] min; settling time, 7.8 [4.2, 9.0] min; and percent overshoot of 9.6 [2.3, 10.8]%. Under steady state conditions the CLAD system exhibited a median error of 0.1 [-0.5, 0.9]%; inaccuracy of 1.8 [0.9, 3.4]%; oscillation index of 1.8 [0.9, 3.4]%; and maximum instantaneous propofol dose of 4.3 [2.1, 10.5] mg kg-1. The maximum hourly propofol dose was 4.3 [2.1, 10.3] mg kg-1 h-1. Performance fell within clinically acceptable limits for all measures. Significance. A CLAD system designed using robust control theory achieves clinically acceptable performance in the presence of realistic unmodeled disturbances and in spite of realistic model uncertainty, while maintaining infusion rates within acceptable safety limits.

Robust control of burst suppression for medical coma

PubMed Central

Westover, M Brandon; Kim, Seong-Eun; Ching, ShiNung; Purdon, Patrick L; Brown, Emery N

2015-01-01

Objective Medical coma is an anesthetic-induced state of brain inactivation, manifest in the electroencephalogram by burst suppression. Feedback control can be used to regulate burst suppression, however, previous designs have not been robust. Robust control design is critical under real-world operating conditions, subject to substantial pharmacokinetic and pharmacodynamic parameter uncertainty and unpredictable external disturbances. We sought to develop a robust closed-loop anesthesia delivery (CLAD) system to control medical coma. Approach We developed a robust CLAD system to control the burst suppression probability (BSP). We developed a novel BSP tracking algorithm based on realistic models of propofol pharmacokinetics and pharmacodynamics. We also developed a practical method for estimating patient-specific pharmacodynamics parameters. Finally, we synthesized a robust proportional integral controller. Using a factorial design spanning patient age, mass, height, and gender, we tested whether the system performed within clinically acceptable limits. Throughout all experiments we subjected the system to disturbances, simulating treatment of refractory status epilepticus in a real-world intensive care unit environment. Main results In 5400 simulations, CLAD behavior remained within specifications. Transient behavior after a step in target BSP from 0.2 to 0.8 exhibited a rise time (the median (min, max)) of 1.4 [1.1, 1.9] min; settling time, 7.8 [4.2, 9.0] min; and percent overshoot of 9.6 [2.3, 10.8]%. Under steady state conditions the CLAD system exhibited a median error of 0.1 [−0.5, 0.9]%; inaccuracy of 1.8 [0.9, 3.4]%; oscillation index of 1.8 [0.9, 3.4]%; and maximum instantaneous propofol dose of 4.3 [2.1, 10.5] mg kg−1. The maximum hourly propofol dose was 4.3 [2.1, 10.3] mg kg−1 h−1. Performance fell within clinically acceptable limits for all measures. Significance A CLAD system designed using robust control theory achieves clinically acceptable performance in the presence of realistic unmodeled disturbances and in spite of realistic model uncertainty, while maintaining infusion rates within acceptable safety limits. PMID:26020243

Burst suppression probability algorithms: state-space methods for tracking EEG burst suppression

NASA Astrophysics Data System (ADS)

Chemali, Jessica; Ching, ShiNung; Purdon, Patrick L.; Solt, Ken; Brown, Emery N.

2013-10-01

Objective. Burst suppression is an electroencephalogram pattern in which bursts of electrical activity alternate with an isoelectric state. This pattern is commonly seen in states of severely reduced brain activity such as profound general anesthesia, anoxic brain injuries, hypothermia and certain developmental disorders. Devising accurate, reliable ways to quantify burst suppression is an important clinical and research problem. Although thresholding and segmentation algorithms readily identify burst suppression periods, analysis algorithms require long intervals of data to characterize burst suppression at a given time and provide no framework for statistical inference. Approach. We introduce the concept of the burst suppression probability (BSP) to define the brain's instantaneous propensity of being in the suppressed state. To conduct dynamic analyses of burst suppression we propose a state-space model in which the observation process is a binomial model and the state equation is a Gaussian random walk. We estimate the model using an approximate expectation maximization algorithm and illustrate its application in the analysis of rodent burst suppression recordings under general anesthesia and a patient during induction of controlled hypothermia. Main result. The BSP algorithms track burst suppression on a second-to-second time scale, and make possible formal statistical comparisons of burst suppression at different times. Significance. The state-space approach suggests a principled and informative way to analyze burst suppression that can be used to monitor, and eventually to control, the brain states of patients in the operating room and in the intensive care unit.

Are We Listening to Music or Noise? Use of the Lyapunov Exponent for Comprehensive Assessment of Heart Rate Complexity During Hemorrhage in Sedated Conscious Miniature Swine

DTIC Science & Technology

2009-09-01

physiologic mechanisms underlying experimental observations: a practical example☆ Sven Zenker, Andreas Hoeft Department of Anaesthesiology and...to describe experi - mental data (goodness of fit) and its complexity (number of parameters). Their use in macroscopic physiologic investigations...BSP, and BRS could either be identical or vary across interventions, resulting in models with 4 to 12 parameters. After digitizing the experimental data

World Antibody-Drug Conjugate Summit, October 15-16, 2013, San Francisco, CA.

PubMed

Klinguer-Hamour, Christine; Strop, Pavel; Shah, Dhaval K; Ducry, Laurent; Xu, April; Beck, Alain

2014-01-01

The World Antibody-Drug Conjugate (WADC) Summits organized by Hanson Wade are currently the largest meetings fully dedicated to ADCs. The first global ADC Summit was organized in Boston in October 2010. Since 2011, two WADC are held every year in Frankfurt and San Francisco, respectively. The 2013 WADC San Francisco event was structured around plenary sessions with keynote speakers from AbbVie, Agensys, ImmunoGen, Immunomedics, Genentech, Pfizer and Seattle Genetics. Parallel tracks were also organized addressing ADC discovery, development and optimization of chemistry, manufacturing and control (CMC) issues. Discovery and process scientists, regulatory experts (US Food and Drug Administration), academics and clinicians were present, including representatives from biotechnology firms (Concortis, CytomX Therapeutics, Glykos, Evonik, Igenica, Innate Pharma, Mersana Therapeutics, Polytherics, Quanta Biodesign, Redwood Bioscience, Sutro Biopharma, SynAffix), pharmaceutical companies (Amgen, Genmab, Johnson and Johnson, MedImmune, Novartis, Progenics, Takeda) and contract research or manufacturing organizations (Baxter, Bayer, BSP Pharmaceuticals, Fujifilm/Diosynth, Lonza, Pierre Fabre Contract Manufacturing, Piramal, SAFC, SafeBridge).

EEG entropy measures in anesthesia

PubMed Central

Liang, Zhenhu; Wang, Yinghua; Sun, Xue; Li, Duan; Voss, Logan J.; Sleigh, Jamie W.; Hagihira, Satoshi; Li, Xiaoli

2015-01-01

Highlights: ► Twelve entropy indices were systematically compared in monitoring depth of anesthesia and detecting burst suppression.► Renyi permutation entropy performed best in tracking EEG changes associated with different anesthesia states.► Approximate Entropy and Sample Entropy performed best in detecting burst suppression. Objective: Entropy algorithms have been widely used in analyzing EEG signals during anesthesia. However, a systematic comparison of these entropy algorithms in assessing anesthesia drugs' effect is lacking. In this study, we compare the capability of 12 entropy indices for monitoring depth of anesthesia (DoA) and detecting the burst suppression pattern (BSP), in anesthesia induced by GABAergic agents. Methods: Twelve indices were investigated, namely Response Entropy (RE) and State entropy (SE), three wavelet entropy (WE) measures [Shannon WE (SWE), Tsallis WE (TWE), and Renyi WE (RWE)], Hilbert-Huang spectral entropy (HHSE), approximate entropy (ApEn), sample entropy (SampEn), Fuzzy entropy, and three permutation entropy (PE) measures [Shannon PE (SPE), Tsallis PE (TPE) and Renyi PE (RPE)]. Two EEG data sets from sevoflurane-induced and isoflurane-induced anesthesia respectively were selected to assess the capability of each entropy index in DoA monitoring and BSP detection. To validate the effectiveness of these entropy algorithms, pharmacokinetic/pharmacodynamic (PK/PD) modeling and prediction probability (Pk) analysis were applied. The multifractal detrended fluctuation analysis (MDFA) as a non-entropy measure was compared. Results: All the entropy and MDFA indices could track the changes in EEG pattern during different anesthesia states. Three PE measures outperformed the other entropy indices, with less baseline variability, higher coefficient of determination (R2) and prediction probability, and RPE performed best; ApEn and SampEn discriminated BSP best. Additionally, these entropy measures showed an advantage in computation efficiency compared with MDFA. Conclusion: Each entropy index has its advantages and disadvantages in estimating DoA. Overall, it is suggested that the RPE index was a superior measure. Investigating the advantages and disadvantages of these entropy indices could help improve current clinical indices for monitoring DoA. PMID:25741277

Centrifugal Modelling of Soil Structures. Part III. The Stability of River Banks and Flood Embankments.

DTIC Science & Technology

1978-10-01

mode Plate 3.6, and also electrically using a strain gauged diaphragm transducer. This transducer was mounted in a I" BSP plug and installed in a...manufactured by Druck Ltd of Leicester and have been described by Hird, 1974. The membrane is a single silicon crystal into which is diffused a strain gauge ...diaphragm strain gauge on the back. The transducers were very small and gave excellent results in the water line to the reservoir. In the soil, however

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rajalin, Ann-Marie; Pollock, Hanna; Aarnisalo, Piia, E-mail: piia.aarnisalo@helsinki.fi

The orphan nuclear receptor estrogen-related receptor-{alpha} (ERR{alpha}) has been reported to have both a positive and a negative regulatory role in osteoblastic and adipocytic differentiation. We have studied the role of ERR{alpha} in osteoblastic and adipogenic differentiation of mesenchymal stem cells. Bone marrow mesenchymal stem cells were isolated from ERR{alpha} deficient mice and their differentiation capacities were compared to that of the wild-type cells. ERR{alpha} deficient cultures displayed reduced cellular proliferation, osteoblastic differentiation, and mineralization. In the complementary experiment, overexpression of ERR{alpha} in MC3T3-E1 cells increased the expression of osteoblastic markers and mineralization. Alterations in the expression of bone sialoproteinmore » (BSP) may at least partially explain the effects on mineralization as BSP expression was reduced in ERR{alpha} deficient MSCs and enhanced upon ERR{alpha} overexpression in MC3T3-E1 cells. Furthermore, a luciferase reporter construct driven by the BSP promoter was efficiently transactivated by ERR{alpha}. Under adipogenic conditions, ERR{alpha} deficient cultures displayed reduced adipocytic differentiation. Our data thus propose a positive role for ERR{alpha} in osteoblastic and adipocytic differentiation. The variability in the results yielded in the different studies implies that ERR{alpha} may play different roles in bone under different physiological conditions.« less

Serum bile acid concentrations in dairy cattle with hepatic lipidosis.

PubMed

Garry, F B; Fettman, M J; Curtis, C R; Smith, J A

1994-01-01

This study was designed to evaluate serum bile acid measurements as indicatory, of liver function and/or hepatic fat infiltration in dairy cattle. Serum bile acid concentrations were measured in healthy dairy cattle at different stages of lactation after fasting or feeding. Bile acid concentrations were compared with liver fat content and sulfobromophthalein (BSP) half-life (T 1/2). Serum bile acid concentrations were higher in cows in early lactation and with higher daily milk production. Compared with prefasting values, bile acid concentrations were decreased at 8, 14, and 24 hours of fasting. Blood samples from fed cows at 1- to 2-hour intervals had wide and inconsistent variations in bile acid concentration. Because serum bile acids correlated well with BSP T 1/2, it is suggested that both measurements evaluate a similar aspect of liver function. Neither bile acids nor BSP T 1/2 correlated with differences in liver fat content among cows. Because of large variability in serum bile acid concentrations in fed cows and the lack of correlation of measured values with liver fat content, bile acid determinations do not appear useful for showing changes in hepatic function in fed cows with subclinical hepatic lipidosis nor serve as a screening test for this condition.

A comparative trial of psychotherapy and pharmacotherapy for "pure" dysthymic patients.

PubMed

Markowitz, John C; Kocsis, James H; Bleiberg, Kathryn L; Christos, Paul J; Sacks, Michael

2005-12-01

Psychotherapy of "pure" dysthymic disorder remains understudied. This article reports outcomes of an acute randomized trial of 94 subjects treated for 16 weeks with either interpersonal psychotherapy (IPT), brief supportive psychotherapy (BSP), sertraline, or sertraline plus IPT. Recruited by clinical referral and advertising, subjects met DSM-IV criteria for early onset dysthymic disorder, with no episode of major depression in the prior six months. They were randomly assigned to one of four 16-week treatments, with options for crossover or continuation treatment. Results were analyzed from the intention-to-treat sample by ANCOVA, controlling for baseline depressive severity. Subjects improved in all conditions over time, with the cells including sertraline pharmacotherapy showing superiority over psychotherapy alone for response and remission. Response rates were 58% for sertraline alone, 57% for combined treatment, 35% for IPT, and 31% for BSP. The study was underpowered and may have employed too "active" a control condition. Follow-up data were unobtainable. In this acute trial for "pure" dysthymic disorder, sertraline with or without IPT showed advantages relative to IPT and BSP. Methodological difficulties may have limited differential outcome findings. This study bolsters a small but growing literature on the treatment of dysthymic disorder, suggesting that pharmacotherapy may acutely benefit patients more than psychotherapy.

Computing volume potentials for noninvasive imaging of cardiac excitation.

PubMed

van der Graaf, A W Maurits; Bhagirath, Pranav; van Driel, Vincent J H M; Ramanna, Hemanth; de Hooge, Jacques; de Groot, Natasja M S; Götte, Marco J W

2015-03-01

In noninvasive imaging of cardiac excitation, the use of body surface potentials (BSP) rather than body volume potentials (BVP) has been favored due to enhanced computational efficiency and reduced modeling effort. Nowadays, increased computational power and the availability of open source software enable the calculation of BVP for clinical purposes. In order to illustrate the possible advantages of this approach, the explanatory power of BVP is investigated using a rectangular tank filled with an electrolytic conductor and a patient specific three dimensional model. MRI images of the tank and of a patient were obtained in three orthogonal directions using a turbo spin echo MRI sequence. MRI images were segmented in three dimensional using custom written software. Gmsh software was used for mesh generation. BVP were computed using a transfer matrix and FEniCS software. The solution for 240,000 nodes, corresponding to a resolution of 5 mm throughout the thorax volume, was computed in 3 minutes. The tank experiment revealed that an increased electrode surface renders the position of the 4 V equipotential plane insensitive to mesh cell size and reduces simulated deviations. In the patient-specific model, the impact of assigning a different conductivity to lung tissue on the distribution of volume potentials could be visualized. Generation of high quality volume meshes and computation of BVP with a resolution of 5 mm is feasible using generally available software and hardware. Estimation of BVP may lead to an improved understanding of the genesis of BSP and sources of local inaccuracies. © 2014 Wiley Periodicals, Inc.

Alkaline Phosphatase Activity : an overlooked player on the phosphate behavior in macrotidal estuaries

NASA Astrophysics Data System (ADS)

Delmas, Daniel; Labry, Claire; Youenou, Agnes; Quere, Julien; Auguet, Jean Christophe; Montanie, Helene

2014-05-01

The non-conservative behavior of phosphate within the estuarine salinity gradient is essentially assigned to physico-chemical processes, such as desorption at low salinity and to benthic exchanges. Microbial phosphatase activity (APA), generally related to phosphate deficiency, is seldom studied in phosphate rich estuarine waters. In order to address the impact of microbial activity (bacterial abundance, production BSP, APA) on phosphate behavior, we studied these activities on a seasonal basis within the salinity gradient of two macrotidal estuaries presenting different levels of suspended solids. Whatever the season the Charente estuary is characterized by high levels of Suspended Particulate Matter (SPM > 1g.L-1), particularly in the Maximum Turbidity Zone (MTZ) located at the 5-10 psu. In this area characterized by high BSP and APA there is a significant increase of PO4 levels especially during summer. In the Aulne estuary the particle load is significantly lower (1/10) but high BSP and APA are equally recorded. In the highly turbid waters of the Charente estuary, active phytoplankton is virtually absent as pheopigments constitute up to 80% of the total pigments, particularly in the MTZ, therefore APA may essentially have a bacterial origin. In the Aulne estuary attached bacteria are dominant, both in numbers and production, and their distribution along the haline gradient perfectly follows those of APA and phosphate levels. These observations, associated with the very close relationships observed between APA, SPM and BSP, suggest that APA derive mainly from bacterial (attached) origin and operate at the expense of particulate phosphorus and hence contribute to PO4 regeneration, especially in spring and summer. Finally, as APA increased as PO4, whereas the reverse is observed in both fresh and marine waters, an original scheme for APA regulation, related to the large dominance of attached bacteria can be described for the estuarine waters.

The resolved star formation history of M51a through successive Bayesian marginalization

NASA Astrophysics Data System (ADS)

Martínez-García, Eric E.; Bruzual, Gustavo; Magris C., Gladis; González-Lópezlira, Rosa A.

2018-02-01

We have obtained the time and space-resolved star formation history (SFH) of M51a (NGC 5194) by fitting Galaxy Evolution Explorer (GALEX), Sloan Digital Sky Survey and near-infrared pixel-by-pixel photometry to a comprehensive library of stellar population synthesis models drawn from the Synthetic Spectral Atlas of Galaxies (SSAG). We fit for each space-resolved element (pixel) an independent model where the SFH is averaged in 137 age bins, each one 100 Myr wide. We used the Bayesian Successive Priors (BSP) algorithm to mitigate the bias in the present-day spatial mass distribution. We test BSP with different prior probability distribution functions (PDFs); this exercise suggests that the best prior PDF is the one concordant with the spatial distribution of the stellar mass as inferred from the near-infrared images. We also demonstrate that varying the implicit prior PDF of the SFH in SSAG does not affect the results. By summing the contributions to the global star formation rate of each pixel, at each age bin, we have assembled the resolved SFH of the whole galaxy. According to these results, the star formation rate of M51a was exponentially increasing for the first 10 Gyr after the big bang, and then turned into an exponentially decreasing function until the present day. Superimposed, we find a main burst of star formation at t ≈ 11.9 Gyr after the big bang.

Identification of PDC-109-like protein(s) in buffalo seminal plasma.

PubMed

Harshan, Hiron M; Sankar, Surya; Singh, L P; Singh, Manish Kumar; Sudharani, S; Ansari, M R; Singh, S K; Majumdar, A C; Joshi, P

2009-10-01

The FN-2 family of seminal plasma proteins represents the major protein fraction of bovine seminal plasma. These proteins also constitute the major seminal plasma proteins fraction in horse, goat and bison seminal plasma and are present in pig, rat, mouse, hamster and human seminal plasma. BSP-A1 and BSP-A2, the predominant proteins of the FN-2 family, are collectively termed as PDC-109. Fn-2 proteins play an important role in fertilization, including sperm capacitation and formation of oviductal sperm reservoirs. Significantly, BSP proteins were also shown to have negative effects in the context of sperm storage. No conclusive evidence for the presence of buffalo seminal plasma protein(s) similar to PDC-109 exists. Studies with buffalo seminal plasma indicated that isolation and identification of PDC-109-like protein(s) from buffalo seminal plasma by conventional methods might be difficult. Thus, antibodies raised against PDC-109 isolated, and purified from cattle seminal plasma, were used for investigating the presence of PDC-109-like protein(s) in buffalo seminal plasma. Buffalo seminal plasma proteins were resolved on SDS-PAGE, blotted to nitro cellulose membranes and probed for the presence of PDC-109-like protein(s) using the PDC-109 antisera raised in rabbits. A distinct immunoreactive band well below the 20-kDa regions indicated the presence of PDC-109-like protein(s) in buffalo seminal plasma.

Robust broad spectral photodetection (UV-NIR) and ultra high responsivity investigated in nanosheets and nanowires of Bi2Te3 under harsh nano-milling conditions.

PubMed

Sharma, Alka; Srivastava, A K; Senguttuvan, T D; Husale, Sudhir

2017-12-20

Due to miniaturization of device dimensions, the next generation's photodetector based devices are expected to be fabricated from robust nanostructured materials. Hence there is an utmost requirement of investigating exotic optoelectronic properties of nanodevices fabricated from new novel materials and testing their performances at harsh conditions. The recent advances on 2D layered materials indicate exciting progress on broad spectral photodetection (BSP) but still there is a great demand for fabricating ultra-high performance photodetectors made from single material sensing broad electromagnetic spectrum since the detection range 325 nm-1550 nm is not covered by the conventional Si or InGaAs photodetectors. Alternatively, Bi 2 Te 3 is a layered material, possesses exciting optoelectronic, thermoelectric, plasmonics properties. Here we report robust photoconductivity measurements on Bi 2 Te 3 nanosheets and nanowires demonstrating BSP from UV to NIR. The nanosheets of Bi 2 Te 3 show the best ultra-high photoresponsivity (~74 A/W at 1550 nm). Further these nanosheets when transform into nanowires using harsh FIB milling conditions exhibit about one order enhancement in the photoresponsivity without affecting the performance of the device even after 4 months of storage at ambient conditions. An ultra-high photoresponsivity and BSP indicate exciting robust nature of topological insulator based nanodevices for optoelectronic applications.

Human mesenchymal stem cell osteoblast differentiation, ECM deposition, and biomineralization on PAH/PAA polyelectrolyte multilayers.

PubMed

Pattabhi, Sudhakara Rao; Lehaf, Ali M; Schlenoff, Joseph B; Keller, Thomas C S

2015-05-01

Polyelectrolyte multilayer (PEMU) coatings built layer by layer with alternating pairs of polyelectrolytes can be tuned to improve cell interactions with surfaces and may be useful as biocompatible coatings to improve fixation between implants and tissues. Here, we show that human mesenchymal stromal cells (hMSCs) induced with bone differentiation medium (BDM) to become osteoblasts biomineralize crosslinked PEMUs built with the polycation poly(allylamine hydrochloride) (PAH) and the polyanion poly(acrylic acid) (PAA). Degrees of hMSC osteoblast differentiation and surface biomineralization on the smooth PAH-terminated PEMUs (PAH-PEMUs) and microstructured PAA-terminated PEMUs (PAA-PEMUs) reflect differences in cell-deposited extracellular matrix (ECM). BDM-induced hMSCs expressed higher levels of the early osteoblast differentiation marker alkaline phosphatase and collagen 1 (COL1) sooner on PAA-PEMUs than on PAH-PEMUs. Cells on both types of PEMUs proceeded to express the later stage osteoblast differentiation marker bone sialoprotein (BSP), but the BDM-induced cells organized a more amorphous Collagen I and denser BSP localization on PAA-PEMUs than on PAH-PEMUs. These ECM properties correlated with greater biomineralization on the PAA-PEMUs than on PAH-PEMUs. Together, these results confirm the suitability of PAH/PAA PEMUs as a substrate for hMSC osteogenesis and highlight the importance of substrate effects on ECM organization and BSP presentation on biomineralization. © 2014 Wiley Periodicals, Inc.

Broken symmetry phase transition in solid p-H 2, o-D 2 and HD: crystal field effects

NASA Astrophysics Data System (ADS)

Freiman, Yu. A.; Hemley, R. J.; Jezowski, A.; Tretyak, S. M.

1999-04-01

We report the effect of the crystal field (CF) on the broken symmetry phase transition (BSP) in solid parahydrogen, orthodeuterium, and hydrogen deuteride. The CF was calculated taking into account a distortion from the ideal HCP structure. We find that, in addition to the molecular field generated by the coupling terms in the intermolecular potential, the Hamiltonian of the system contains a crystal-field term, originating from single-molecular terms in the intermolecular potential. Ignoring the CF is the main cause of the systematic underestimation of the transition pressure, characteristic of published theories of the BSP transition. The distortion of the lattice that gives rise to the negative CF in response to the applied pressure is in accord with the general Le Chatelier-Braun principle.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nikolić, Hrvoje, E-mail: hnikolic@irb.hr

An argument by Banks, Susskind and Peskin (BSP), according to which violation of unitarity would violate either locality or energy-momentum conservation, is widely believed to be a strong argument against non-unitarity of Hawking radiation. We find that the whole BSP argument rests on the crucial assumption that the Hamiltonian is not highly degenerate, and point out that this assumption is not satisfied for systems with many degrees of freedom. Using Lindblad equation, we show that high degeneracy of the Hamiltonian allows local non-unitary evolution without violating energy-momentum conservation. Moreover, since energy-momentum is the source of gravity, we argue that energy-momentummore » is necessarily conserved for a large class of non-unitary systems with gravity. Finally, we explicitly calculate the Lindblad operators for non-unitary Hawking radiation and show that they conserve energy-momentum.« less

Structural Analysis of Alkaline β-Mannanase from Alkaliphilic Bacillus sp. N16-5: Implications for Adaptation to Alkaline Conditions

PubMed Central

Zhao, Yueju; Zhang, Yunhua; Cao, Yang; Qi, Jianxun; Mao, Liangwei; Xue, Yanfen; Gao, Feng; Peng, Hao; Wang, Xiaowei; Gao, George F.; Ma, Yanhe

2011-01-01

Significant progress has been made in isolating novel alkaline β-mannanases, however, there is a paucity of information concerning the structural basis for alkaline tolerance displayed by these β-mannanases. We report the catalytic domain structure of an industrially important β-mannanase from the alkaliphilic Bacillus sp. N16-5 (BSP165 MAN) at a resolution of 1.6 Å. This enzyme, classified into subfamily 8 in glycosyl hydrolase family 5 (GH5), has a pH optimum of enzymatic activity at pH 9.5 and folds into a classic (β/α)8-barrel. In order to gain insight into molecular features for alkaline adaptation, we compared BSP165 MAN with previously reported GH5 β-mannanases. It was revealed that BSP165 MAN and other subfamily 8 β-mannanases have significantly increased hydrophobic and Arg residues content and decreased polar residues, comparing to β-mannanases of subfamily 7 or 10 in GH5 which display optimum activities at lower pH. Further, extensive structural comparisons show alkaline β-mannanases possess a set of distinctive features. Position and length of some helices, strands and loops of the TIM barrel structures are changed, which contributes, to a certain degree, to the distinctly different shaped (β/α)8-barrels, thus affecting the catalytic environment of these enzymes. The number of negatively charged residues is increased on the molecular surface, and fewer polar residues are exposed to the solvent. Two amino acid substitutions in the vicinity of the acid/base catalyst were proposed to be possibly responsible for the variation in pH optimum of these homologous enzymes in subfamily 8 of GH5, identified by sequence homology analysis and pK a calculations of the active site residues. Mutational analysis has proved that Gln91 and Glu226 are important for BSP165 MAN to function at high pH. These findings are proposed to be possible factors implicated in the alkaline adaptation of GH5 β-mannanases and will help to further understanding of alkaline adaptation mechanism. PMID:21436878

Microbial Activity Response to Solar Radiation across Contrasting Environmental Conditions in Salar de Huasco, Northern Chilean Altiplano.

PubMed

Hernández, Klaudia L; Yannicelli, Beatriz; Olsen, Lasse M; Dorador, Cristina; Menschel, Eduardo J; Molina, Verónica; Remonsellez, Francisco; Hengst, Martha B; Jeffrey, Wade H

2016-01-01

In high altitude environments, extreme levels of solar radiation and important differences of ionic concentrations over narrow spatial scales may modulate microbial activity. In Salar de Huasco, a high-altitude wetland in the Andean mountains, the high diversity of microbial communities has been characterized and associated with strong environmental variability. Communities that differed in light history and environmental conditions, such as nutrient concentrations and salinity from different spatial locations, were assessed for bacterial secondary production (BSP, 3 H-leucine incorporation) response from short-term exposures to solar radiation. We sampled during austral spring seven stations categorized as: (a) source stations, with recently emerged groundwater (no-previous solar exposure); (b) stream running water stations; (c) stations connected to source waters but far downstream from source points; and (d) isolated ponds disconnected from ground sources or streams with a longer isolation and solar exposure history. Very high values of 0.25 μE m -2 s -1 , 72 W m -2 and 12 W m -2 were measured for PAR, UVA, and UVB incident solar radiation, respectively. The environmental factors measured formed two groups of stations reflected by principal component analyses (near to groundwater sources and isolated systems) where isolated ponds had the highest BSP and microbial abundance (35 microalgae taxa, picoeukaryotes, nanoflagellates, and bacteria) plus higher salinities and PO 4 3- concentrations. BSP short-term response (4 h) to solar radiation was measured by 3 H-leucine incorporation under four different solar conditions: full sun, no UVB, PAR, and dark. Microbial communities established in waters with the longest surface exposure (e.g., isolated ponds) had the lowest BSP response to solar radiation treatments, and thus were likely best adapted to solar radiation exposure contrary to ground source waters. These results support our light history (solar exposure) hypothesis where the more isolated the community is from ground water sources, the better adapted it is to solar radiation. We suggest that factors other than solar radiation (e.g., salinity, PO 4 3- , NO 3 - ) are also important in determining microbial productivity in heterogeneous environments such as the Salar de Huasco.

A batch assay to measure microbial hydrogen sulfide production from sulfur-containing solid wastes.

PubMed

Sun, Mei; Sun, Wenjie; Barlaz, Morton A

2016-05-01

Large volumes of sulfur-containing wastes enter municipal solid waste landfills each year. Under the anaerobic conditions that prevail in landfills, oxidized forms of sulfur, primarily sulfate, are converted to sulfide. Hydrogen sulfide (H2S) is corrosive to landfill gas collection and treatment systems, and its presence in landfill gas often necessitates the installation of expensive removal systems. For landfill operators to understand the cost of managing sulfur-containing wastes, an estimate of the H2S production potential is needed. The objective of this study was to develop and demonstrate a biochemical sulfide potential (BSP) test to measure the amount of H2S produced by different types of sulfur-containing wastes in a relatively fast (30days) and inexpensive (125mL serum bottles) batch assay. This study confirmed the toxic effect of H2S on both sulfate reduction and methane production in batch systems, and demonstrated that removing accumulated H2S by base adsorption was effective for mitigating inhibition. H2S production potentials of coal combustion fly ash, flue gas desulfurization residual, municipal solid waste combustion ash, and construction and demolition waste were determined in BSP assays. After 30days of incubation, most of the sulfate in the wastes was converted to gaseous or aqueous phase sulfide, with BSPs ranging from 0.8 to 58.8mLH2S/g waste, depending on the chemical composition of the samples. Selected samples contained solid phase sulfide which contributed to the measured H2S yield. A 60day incubation in selected samples resulted in 39-86% additional sulfide production. H2S production measured in BSP assays was compared with that measured in simulated landfill reactors and that calculated from chemical analyses. H2S production in BSP assays and in reactors was lower than the stoichiometric values calculated from chemical composition for all wastes tested, demonstrating the importance of assays to estimate the microbial sulfide production potential of sulfur-containing wastes. Copyright © 2016 Elsevier B.V. All rights reserved.

Microbial Activity Response to Solar Radiation across Contrasting Environmental Conditions in Salar de Huasco, Northern Chilean Altiplano

PubMed Central

Hernández, Klaudia L.; Yannicelli, Beatriz; Olsen, Lasse M.; Dorador, Cristina; Menschel, Eduardo J.; Molina, Verónica; Remonsellez, Francisco; Hengst, Martha B.; Jeffrey, Wade H.

2016-01-01

In high altitude environments, extreme levels of solar radiation and important differences of ionic concentrations over narrow spatial scales may modulate microbial activity. In Salar de Huasco, a high-altitude wetland in the Andean mountains, the high diversity of microbial communities has been characterized and associated with strong environmental variability. Communities that differed in light history and environmental conditions, such as nutrient concentrations and salinity from different spatial locations, were assessed for bacterial secondary production (BSP, 3H-leucine incorporation) response from short-term exposures to solar radiation. We sampled during austral spring seven stations categorized as: (a) source stations, with recently emerged groundwater (no-previous solar exposure); (b) stream running water stations; (c) stations connected to source waters but far downstream from source points; and (d) isolated ponds disconnected from ground sources or streams with a longer isolation and solar exposure history. Very high values of 0.25 μE m-2 s-1, 72 W m-2 and 12 W m-2 were measured for PAR, UVA, and UVB incident solar radiation, respectively. The environmental factors measured formed two groups of stations reflected by principal component analyses (near to groundwater sources and isolated systems) where isolated ponds had the highest BSP and microbial abundance (35 microalgae taxa, picoeukaryotes, nanoflagellates, and bacteria) plus higher salinities and PO43- concentrations. BSP short-term response (4 h) to solar radiation was measured by 3H-leucine incorporation under four different solar conditions: full sun, no UVB, PAR, and dark. Microbial communities established in waters with the longest surface exposure (e.g., isolated ponds) had the lowest BSP response to solar radiation treatments, and thus were likely best adapted to solar radiation exposure contrary to ground source waters. These results support our light history (solar exposure) hypothesis where the more isolated the community is from ground water sources, the better adapted it is to solar radiation. We suggest that factors other than solar radiation (e.g., salinity, PO43-, NO3-) are also important in determining microbial productivity in heterogeneous environments such as the Salar de Huasco. PMID:27920763

Cognitive Behavioral Analysis System of Psychotherapy and Brief Supportive Psychotherapy for Augmentation of Antidepressant Nonresponse in Chronic Depression

PubMed Central

Kocsis, James H.; Gelenberg, Alan J.; Rothbaum, Barbara O.; Klein, Daniel N.; Trivedi, Madhukar H.; Manber, Rachel; Keller, Martin B.; Leon, Andrew C.; Wisniewski, Steven R.; Arnow, Bruce A.; Markowitz, John C.; Thase, Michael E.

2012-01-01

Context Previous studies have found that few chronically depressed patients remit with antidepressant medications alone. Objective To determine the role of adjunctive psychotherapy in the treatment of chronically depressed patients with less than complete response to an initial medication trial. Design This trial compared 12 weeks of (1) continued pharmacotherapy and augmentation with cognitive behavioral analysis system of psychotherapy (CBASP), (2) continued pharmacotherapy and augmentation with brief supportive psychotherapy (BSP), and (3) continued optimized pharmacotherapy (MEDS) alone. We hypothesized that adding CBASP would produce higher rates of response and remission than adding BSP or continuing MEDS alone. Setting Eight academic sites. Participants Chronically depressed patients with a current DSM-IV–defined major depressive episode and persistent depressive symptoms for more than 2 years. Interventions Phase 1 consisted of open-label, algorithm-guided treatment for 12 weeks based on a history of antidepressant response. Patients not achieving remission received next-step pharmacotherapy options with or without adjunctive psychotherapy (phase 2). Individuals undergoing psychotherapy were randomized to receive either CBASP or BSP stratified by phase 1 response, ie, as nonresponders (NRs) or partial responders (PRs). Main Outcome Measures Proportions of remitters, PRs, and NRs and change on Hamilton Scale for Depression (HAM-D) scores. Results In all, 808 participants entered phase 1, of which 491 were classified as NRs or PRs and entered phase 2 (200 received CBASP and MEDS, 195 received BSP and MEDS, and 96 received MEDS only). Mean HAM-D scores dropped from 25.9 to 17.7 in NRs and from 15.2 to 9.9 in PRs. No statistically significant differences emerged among the 3 treatment groups in the proportions of phase 2 remission (15.0%), partial response (22.5%), and non-response (62.5%) or in changes on HAM-D scores. Conclusions Although 37.5% of the participants experienced partial response or remitted in phase 2, neither form of adjunctive psychotherapy significantly improved outcomes over that of a flexible, individualized pharmacotherapy regimen alone. A longitudinal assessment of later-emerging benefits is ongoing. Trial Registration clinicaltrials.gov Identifier: NCT00057551 PMID:19884606

Short communication: phylodynamics analysis of the human immunodeficiency virus type 1 envelope gene in mother and child pairs.

PubMed

Santos, Luciane Amorim; Gray, Rebecca R; Monteiro-Cunha, Joana Paixão; Strazza, Evandra; Kashima, Simone; Santos, Edson de Souza; Araújo, Thessika Hialla Almeida; Gonçalves, Marilda de Souza; Salemi, Marco; Alcantara, Luiz Carlos Junior

2015-09-01

Characterizing the impact of HIV transmission routes on viral genetic diversity can improve the understanding of the mechanisms of virus evolution and adaptation. HIV vertical transmission can occur in utero, during delivery, or while breastfeeding. The present study investigated the phylodynamics of the HIV-1 env gene in mother-to-child transmission by analyzing one chronically infected pair from Brazil and three acutely infected pairs from Zambia, with three to five time points. Sequences from 25 clones from each sample were obtained and aligned using Clustal X. ML trees were constructed in PhyML using the best evolutionary model. Bayesian analyses testing the relaxed and strict molecular clock were performed using BEAST and a Bayesian Skyline Plot (BSP) was construed. The genetic variability of previously described epitopes was investigated and compared between each individual time point and between mother and child sequences. The relaxed molecular clock was the best-fitted model for all datasets. The tree topologies did not show differentiation in the evolutionary dynamics of the virus circulating in the mother from the viral population in the child. In the BSP, the effective population size was more constant in time in the chronically infected patients while in the acute patients it was possible to detect bottlenecks. The genetic variability within viral epitopes recognized by the human immune system was considerably higher among the chronically infected pair in comparison with acutely infected pairs. These results contribute to a better understanding of HIV-1 evolutionary dynamics in mother-to-child transmission.

Critical-Size Calvarial Bone Defects Healing in a Mouse Model with Silk Scaffolds and SATB2- Modified iPSCs

PubMed Central

Ye, Jin-Hai; Xu, Yuan-Jin; Gao, Jun; Yan, Shi-Guo; Zhao, Jun; Tu, Qisheng; Zhang, Jin; Duan, Xue-Jing; Sommer, Cesar A.; Mostoslavsky, Gustavo; Kaplan, David; Wu, Yu-Nong; Zhang, Chen-Ping; Wang, Lin; Chen, Jake

2011-01-01

Induced pluripotent stem cells (iPSCs) can differentiate into mineralizing cells and thus have a great potential in application in engineered bone substitutes with bioactive scaffolds in regeneration medicine. In the current study we characterized and demonstrated the pluripotency and osteogenic differentiation of mouse iPSCs. To enhance the osteogenic differentiation of iPSCs, we then transduced the iPSCs with the potent transcription factor, nuclear matrix protein SATB2. We observed that in SATB2-overexpressing iPSCs there were increased mineral nodule formation and elevated mRNA levels of key osteogenic genes, osterix (OSX), Runx2, bone sialoprotein (BSP) and osteocalcin (OCN). Moreover, the mRNA levels of HoxA2 was reduced after SATB2 overexpression in iPSCs. The SATB2-overexpressing iPSCs were then combined with silk scaffolds and transplanted into critical-size calvarial bone defects created in nude mice. Five weeks post-surgery, radiological and micro-CT analysis revealed enhanced new bone formation in calvarial defects in SATB2 group. Histological analysis also showed increased new bone formation and mineralization in the SATB2 group. In conclusion, the results demonstrate that SATB2 facilitates the differentiation of iPSCs towards osteoblast-lineage cells by repressing HoxA2 and augmenting the functions of the osteoblast determinants Runx2, BSP and OCN. PMID:21492931

Increased serum cartilage oligomeric matrix protein levels and decreased patellar bone mineral density in patients with chondromalacia patellae

PubMed Central

Murphy, E; FitzGerald, O; Saxne, T; Bresnihan, B

2002-01-01

Background: Chondromalacia patellae is a potentially disabling disorder characterised by features of patellar cartilage degradation. Objective: To evaluate markers of cartilage and bone turnover in patients with chondromalacia patellae. Methods: 18 patients with chondromalacia patellae were studied. Serum cartilage oligomeric matrix protein (s-COMP) and bone sialoprotein (s-BSP) levels were measured by enzyme linked immunosorbent assay (ELISA) and compared with those of age and sex matched healthy control subjects. Periarticular bone mineral density (BMD) of both knee joints was assessed by dual energy x ray absorptiometry (DXA). Results: s-COMP levels were significantly raised in all patients with chondromalacia patellae compared with healthy control subjects (p=0.0001). s-BSP levels did not differ significantly between the groups (p=0.41). BMD of the patella was significantly reduced in patients with chondromalacia patellae compared with the control subjects (p=0.016). In patients with bilateral chondromalacia patellae, BMD of the patella was lower in the more symptomatic knee joint (p=0.005). Changes in periarticular BMD were localised to the patella and were not present in femoral regions. Neither s-COMP (p=0.18) nor s-BSP (p=0.40) levels correlated with patellar BMD. Conclusions: Increased s-COMP levels, reflecting cartilage degradation, and reduced BMD localised to the patella may represent clinically useful markers in the diagnosis and monitoring of patients with chondromalacia patellae. Measures of cartilage degradation did not correlate with loss of patellar bone density, suggesting dissociated pathophysiological mechanisms. PMID:12379520

Increased serum cartilage oligomeric matrix protein levels and decreased patellar bone mineral density in patients with chondromalacia patellae.

PubMed

Murphy, E; FitzGerald, O; Saxne, T; Bresnihan, B

2002-11-01

Chondromalacia patellae is a potentially disabling disorder characterised by features of patellar cartilage degradation. To evaluate markers of cartilage and bone turnover in patients with chondromalacia patellae. 18 patients with chondromalacia patellae were studied. Serum cartilage oligomeric matrix protein (s-COMP) and bone sialoprotein (s-BSP) levels were measured by enzyme linked immunosorbent assay (ELISA) and compared with those of age and sex matched healthy control subjects. Periarticular bone mineral density (BMD) of both knee joints was assessed by dual energy x ray absorptiometry (DXA). s-COMP levels were significantly raised in all patients with chondromalacia patellae compared with healthy control subjects (p=0.0001). s-BSP levels did not differ significantly between the groups (p=0.41). BMD of the patella was significantly reduced in patients with chondromalacia patellae compared with the control subjects (p=0.016). In patients with bilateral chondromalacia patellae, BMD of the patella was lower in the more symptomatic knee joint (p=0.005). Changes in periarticular BMD were localised to the patella and were not present in femoral regions. Neither s-COMP (p=0.18) nor s-BSP (p=0.40) levels correlated with patellar BMD. Increased s-COMP levels, reflecting cartilage degradation, and reduced BMD localised to the patella may represent clinically useful markers in the diagnosis and monitoring of patients with chondromalacia patellae. Measures of cartilage degradation did not correlate with loss of patellar bone density, suggesting dissociated pathophysiological mechanisms.

Acute and chronic toxicity studies with monochlorobenzene in rainbow trout

USGS Publications Warehouse

Dahlich, G.M.; Larson, R.E.; Gingerich, W.H.

1982-01-01

The toxicity of monochlorobenzene (CB) was investigated in rainbow trout following acute intraperitoneal (i.p.) administration and chronic exposure via the water in a continuously flowing system for 15 or 30 days. In the acute study overt toxicity and hepatotoxicity were monitored over a 96-h time period. Variables measured to assess toxicity included weight changes, liver weight to body weight ratios, behavioral changes, alanine aminotransferase activity (GPT), sulfobromophthalein (BSP) retention, total plasma protein concentration and liver histopathology. In the chronic study the same measures of toxicity were followed as well as food consumption and alkaline phosphatase (AP) activity. Upon acute i.p. exposure the toxicant (9.8 mmol/kg) caused behavioral changes in the fish which were consistent with the known anesthetic properties of CB in mammals. Elevations in BSP retention and GPT activity, and histopathology indicated that CB was hepatotoxic in fish. The LC50 of CB in trout exposed via the water for 96 h was 4.7 mg/l. Chronic exposure of trout to 2 or 3 mg/l CB resulted in similar behavioral changes as seen in the acute study. Liver toxicity was evident from elevations in GPT activity. BSP retention and AP activity appeared to be affected by the nutritional status of the trout as much as by the CB treatment. After 30 days of exposure to 3 mg/l CB, trout appeared to have developed some tolerance to the toxic effects.

Automated Monitoring with a BSP Fault-Detection Test

NASA Technical Reports Server (NTRS)

Bickford, Randall L.; Herzog, James P.

2003-01-01

The figure schematically illustrates a method and procedure for automated monitoring of an asset, as well as a hardware- and-software system that implements the method and procedure. As used here, asset could signify an industrial process, power plant, medical instrument, aircraft, or any of a variety of other systems that generate electronic signals (e.g., sensor outputs). In automated monitoring, the signals are digitized and then processed in order to detect faults and otherwise monitor operational status and integrity of the monitored asset. The major distinguishing feature of the present method is that the fault-detection function is implemented by use of a Bayesian sequential probability (BSP) technique. This technique is superior to other techniques for automated monitoring because it affords sensitivity, not only to disturbances in the mean values, but also to very subtle changes in the statistical characteristics (variance, skewness, and bias) of the monitored signals.

Violation of unitarity by Hawking radiation does not violate energy-momentum conservation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nikolić, Hrvoje

2015-04-02

An argument by Banks, Susskind and Peskin (BSP), according to which violation of unitarity would violate either locality or energy-momentum conservation, is widely believed to be a strong argument against non-unitarity of Hawking radiation. We find that the whole BSP argument rests on the crucial assumption that the Hamiltonian is not highly degenerate, and point out that this assumption is not satisfied for systems with many degrees of freedom. Using Lindblad equation, we show that high degeneracy of the Hamiltonian allows local non-unitary evolution without violating energy-momentum conservation. Moreover, since energy-momentum is the source of gravity, we argue that energy-momentummore » is necessarily conserved for a large class of non-unitary systems with gravity. Finally, we explicitly calculate the Lindblad operators for non-unitary Hawking radiation and show that they conserve energy-momentum.« less

Bosonic-seesaw portal dark matter

NASA Astrophysics Data System (ADS)

Ishida, Hiroyuki; Matsuzaki, Shinya; Yamaguchi, Yuya

2017-10-01

We discuss a new type of Higgs-portal dark matter (DM) production mechanism, called the bosonic-seesaw portal (BSP) scenario. The BS provides the dynamical origin of the electroweak symmetry breaking, triggered by mixing between the elementary Higgs and a composite Higgs generated by a new-color strong dynamics, hypercolor (HC). At the HC strong coupling scale, the classical-scale invariance assumed in the model is dynamically broken, as well as the "chiral" symmetry present in the HC sector. In addition to the composite Higgs, HC baryons emerge to potentially be stable because of the unbroken HC baryon number symmetry. Hence the lightest HC baryon can be a DM candidate. Of interest in the present scenario is that HC pions can be as heavy as the HC baryon due to the possibly enhanced explicit "chiral"-breaking effect triggered after the BS mechanism, so the HC baryon pair cannot annihilate into HC pions. As in the standard setup of the freeze-in scenario, it is assumed that the DM was never in the thermal equilibrium, which ends up with no thermal abundance. It is then the non-thermal BSP process that crucially comes into the game below the HC scale: the HC baryon significantly couples to the standard-model Higgs via the BS mechanism, and can non-thermally be produced from the thermal plasma below the HC scale, which turns out to allow the TeV mass scale for the composite baryonic DM, much smaller than the generic bound placed in the conventional thermal freeze-out scenario, to account for the observed relic abundance. Thus the DM can closely be related to the mechanism of the electroweak symmetry breaking.

Experimental non-alcoholic fatty liver disease results in decreased hepatic uptake transporter expression and function in rats

PubMed Central

Fisher, Craig D.; Lickteig, Andrew J.; Augustine, Lisa M.; Oude Elferink, Ronald P.J.; Besselsen, David G.; Erickson, Robert P.; Cherrington, Nathan J.

2009-01-01

Non-alcoholic fatty liver disease (NAFLD) encompasses a spectrum of diagnoses ranging from simple fatty liver (SFL), to non-alcoholic steatohepatitis (NASH). This study aimed to determine the effect of moderate and severe NAFLD on hepatic transporter expression and function in vivo. Rats were fed a high-fat diet (SFL model) or a methionine-choline-deficient diet (NASH model) for eight weeks. Hepatic uptake transporter function was determined by bromosulfophthalein (BSP) disposition. Transporter expression was determined by branched DNA signal amplification assay and western blotting; inflammation was identified by immunostaining of liver slices for interleukin 1 beta (IL-1β). MC- rats showed significant retention of BSP in the plasma when compared to control rats. Hepatic NTCP, OATP1a1, 1a4, 1b2 and 2b1; and OAT 2 and 3 mRNA levels were significantly decreased in high-fat and MC- diet rats when compared to control. Protein expression of OATP1a1 was significantly decreased in high-fat animals, while OATP1a1 and OATP1b2 expression was significantly lower in MC- rats when compared to control. Liver tissue from high-fat and MC- rats stained positive for IL-1β, a pro-inflammatory cytokine known to decrease expression of NTCP, OATP and OAT transporters, suggesting a plausible mechanism for the observed transporter alterations. These data suggest that different stages of NAFLD result in altered hepatic uptake transporter expression that can lead to a functional impairment of xenobiotic uptake from the blood. Furthermore, NAFLD may alter the plasma retention time of clinically relevant drugs that are reliant on these transporters and may increase the potential drug toxicity. PMID:19358839

Mineralization induction effects of osteopontin, bone sialoprotein, and dentin phosphoprotein on a biomimetic collagen substrate.

PubMed

Zurick, Kevin M; Qin, Chunlin; Bernards, Matthew T

2013-06-01

Native bone tissue is composed of a matrix of collagen, noncollagenous proteins, and calcium phosphate minerals, which are primarily hydroxyapatite. The SIBLING (small integrin-binding ligand, N-linked glycoprotein) family of proteins is the primary noncollagenous protein group found in mineralized tissues. In this work, the mineralization induction capabilities of three of the SIBLING members, bone sialoprotein (BSP), osteopontin (OPN), and the calcium-binding subdomain of dentin sialophosphoprotein, dentin phosphoprotein (DPP), are directly compared on a biomimetic collagen substrate. A self-assembled, loosely aligned collagen fibril substrate was prepared, and then (125) I-radiolabeled adsorption isotherms were developed for BSP, OPN, and DPP. The results showed that BSP exhibited the highest binding capacity for collagen at lower concentrations, followed by DPP and OPN. However, at the highest concentrations, all three proteins had similar adsorption levels. The adsorption isotherms were then used to identify conditions that resulted in identical amounts of adsorbed protein. These substrates were prepared and placed in simulated body fluid for 5, 10, and 24 h at 37°C. The resulting mineral morphology was assessed by atomic force microscopy, and the composition was determined using photochemical assays. Mineralization was seen in the presence of all the proteins. However, DPP was seen to be the only protein that formed individual mineral nodules similar to those seen in developing bone. This suggests that DPP plays a significant role in the biomineralization process and that the incorporation of DPP into tissue engineering constructs may facilitate the induction of biomimetic mineral formation. Copyright © 2012 Wiley Periodicals, Inc.

Mineralization Induction Effects of Osteopontin, Bone Sialoprotein, and Dentin Phosphoprotein on a Biomimetic Collagen Substrate

PubMed Central

Zurick, Kevin M.; Qin, Chunlin; Bernards, Matthew T.

2012-01-01

Native bone tissue is composed of a matrix of collagen, non-collagenous proteins, and calcium phosphate minerals, which are primarily hydroxyapatite (HA). The SIBLING (small integrin-binding ligand, N-linked glycoprotein) family of proteins is the primary non-collagenous protein group found in mineralized tissues. In this work, the mineralization induction capabilities of three of the SIBLING members, bone sialoprotein (BSP), osteopontin (OPN), and the calcium binding subdomain of dentin sialophosphoprotein, dentin phosphoprotein (DPP), are directly compared on a biomimetic collagen substrate. A self-assembled, loosely aligned collagen fibril substrate was prepared and then 125I radiolabeled adsorption isotherms were developed for BSP, OPN, and DPP. The results showed that BSP exhibited the highest binding capacity for collagen at lower concentrations, followed by DPP and OPN. However, at the highest concentrations all three proteins had similar adsorption levels. The adsorption isotherms were then used to identify conditions that resulted in identical amounts of adsorbed protein. These substrates were prepared and placed in simulated body fluid for 5 hours, 10 hours, and 24 hours at 37°C. The resulting mineral morphology was assessed by atomic force microscopy and the composition was determined using photochemical assays. Mineralization was seen in the presence of all of the proteins. However, DPP was seen to be the only protein that formed individual mineral nodules similar to those seen in developing bone. This suggests that DPP plays a significant role in the biomineralization process and that the incorporation of DPP into tissue engineering constructs may facilitate the induction of biomimetic mineral formation. PMID:23161527

Direct comparison of regulators of calcification between bone and vessels in humans.

PubMed

Schweighofer, N; Aigelsreiter, A; Trummer, O; Graf-Rechberger, M; Hacker, N; Kniepeiss, D; Wagner, D; Stiegler, P; Trummer, C; Pieber, T; Obermayer-Pietsch, B; Müller, H

2016-07-01

Calcification is not only physiologically present in bone but is a main pathophysiological process in vasculature, favouring cardiovascular diseases. Our aim was to investigate changes in the expression of calcification regulators during vascular calcification in bone and vasculature. Levels of gene expression of osteoprotegerin (OPG), receptor activator of NF-κB ligand (RANKL), osteopontin (OPN), matrix gla protein (MGP), bone sialoprotein (BSP), SMAD6, and runt-related transcription factor 2 (RUNX2) were determined in bone, aorta, and external iliac artery tissue samples of transplant donors. Histological stages of atherosclerosis (AS) in vessels are defined as "no changes", "intima thickening", or "intima calcification". Patients' bone samples were subgrouped accordingly. We demonstrate that in vessels BSP and OPN expression significantly increased during intima thickening and decreased during intima calcification, whereas the expression of regulators of calcification did not significantly change in bone during intima thickening and intima calcification. At the stage of intima thickening, MGP, OPG, and SMAD6 expression and at stage of intima calcification only MGP expression was lower in bone than in vessel. The expression of BSP and RANKL was regulated in opposite ways in bone and vessels, whereas the expression of MGP, OC, RUNX2, and OPN was regulated in a tissue-specific manner. Our study is the first direct comparison of gene expression changes during AS progression in bone and vessels. Our results indicate that changes in the expression of regulators of calcification in the vessel wall as well as in bone occur early in the calcification process, even prior to deposition of calcium/phosphate precipitation. Copyright © 2016. Published by Elsevier Inc.

Two-dimensional polyacrylamide gel electrophoresis of bovine semen after cryopreservation in half-milliliter straws.

PubMed

Frazer, G S; Bucci, D M; Brooks, C L

1996-11-01

One of the problems encountered with two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) is the streaking of proteins so that individual spot identification is compromised. This study was conducted to determine whether a low loading dose (50 microg) of protein would permit resolution of more discrete protein spots using megapixel camera technology, and if so, to present a nomenclature for future comparisons of the identified proteins. If the major proteins could be identified in a 50-microg sample we aimed to determine whether they could be identified in the supernatant (seminal plasma plus extender) of cryopreserved semen. Two ejaculates were obtained from each of 6 bulls and bovine seminal plasma (BSP) protein concentration was standardized to 50 microg/10 microl. Isoelectric points (pI) and molecular weights (MWt) of BSP proteins were determined by measuring spot mobility on 2-D PAGE (15% polyacrylamide). Three distinct protein spot constellations (a,b,c) could be readily seen by the naked eye and a faintly stained constellation "d" was identified by the megapixel camera. The image analysis software located 6 protein spots in both constellation "a" (MWt 26 kDa; pI 4.2 to 4.8) and "b" ( MWt 27 kDa; pI 6.6 to 8.0). Constellation "c" contained 13 protein spots distributed in a right-angled triangle with its base towards the acidic end of the gel (MWt 14.7 to 18.8 kDa; pI 5.3 to 7.4). Only spots c(2), c(3), c(5), c(8), and c(13) were present in all 12 samples. Streaking can be eliminated by using 50 microg protein for 2-D PAGE, and the major protein spots are readily identified by megapixel camera technology. Protein spots c(3), c(5), c(13) and constellation "a" appear to correspond with Manjunath's proteins (BSP-A(1), -A(2); -A(3); -30 kDa). Killian's 2 low fertility proteins may lie in the "c" constellation, and 1 of the high fertility proteins may lie in the "b" constellation. The 3 major BSP proteins can be visualized in the supernatant of cryopreserved semen. We believe that the technique may prove useful for retrospective analysis of processed semen batches that achieve less than satisfactory results in the field.

Collaborative study for the validation of an improved HPLC assay for recombinant IFN-alfa-2.

PubMed

Jönsson, K H; Daas, A; Buchheit, K H; Terao, E

2016-01-01

The current European Pharmacopoeia (Ph. Eur.) texts for Interferon (IFN)-alfa-2 include a nonspecific photometric protein assay using albumin as calibrator and a highly variable cell-based assay for the potency determination of the protective effects. A request was expressed by the Official Medicines Control Laboratories (OMCLs) for improved methods for the batch control of recombinant interferon alfa-2 bulk and market surveillance testing of finished products, including those formulated with Human Serum Albumin (HSA). A HPLC method was developed at the Medical Products Agency (MPA, Sweden) for the testing of IFN-alfa-2 products. An initial collaborative study run under the Biological Standardisation Programme (BSP; study code BSP039) revealed the need for minor changes to improve linearity of the calibration curves, assay reproducibility and robustness. The goal of the collaborative study, coded BSP071, was to transfer and further validate this improved HPLC method. Ten laboratories participated in the study. Four marketed IFN-alfa-2 preparations (one containing HSA) together with the Ph. Eur. Chemical Reference Substance (CRS) for IFN-alfa-2a and IFN-alfa-2b, and in-house reference standards from two manufacturers were used for the quantitative assay. The modified method was successfully transferred to all laboratories despite local variation in equipment. The resolution between the main and the oxidised forms of IFN-alfa-2 was improved compared to the results from the BSP039 study. The improved method even allowed partial resolution of an extra peak after the principal peak. Symmetry of the main IFN peak was acceptable for all samples in all laboratories. Calibration curves established with the Ph. Eur. IFN-alfa-2a and IFN-alfa-2b CRSs showed excellent linearity with intercepts close to the origin and coefficients of determination greater than 0.9995. Assay repeatability, intermediate precision and reproducibility varied with the tested sample within acceptable ranges. Test accuracy estimated by comparing the values obtained by the participants to the declared contents determined by the manufacturers was good despite the absence of a common reference preparation. In conclusion, the present study showed that the new method is suitable, reproducible and transferable. Proposals for the revision of Ph. Eur. texts are presented.

Senior Computational Scientist | Center for Cancer Research

Cancer.gov

The Basic Science Program (BSP) pursues independent, multidisciplinary research in basic and applied molecular biology, immunology, retrovirology, cancer biology, and human genetics. Research efforts and support are an integral part of the Center for Cancer Research (CCR) at the Frederick National Laboratory for Cancer Research (FNLCR). The Cancer & Inflammation Program (CIP), Basic Science Program, HLA Immunogenetics Section, under the leadership of Dr. Mary Carrington, studies the influence of human leukocyte antigens (HLA) and specific KIR/HLA genotypes on risk of and outcomes to infection, cancer, autoimmune disease, and maternal-fetal disease. Recent studies have focused on the impact of HLA gene expression in disease, the molecular mechanism regulating expression levels, and the functional basis for the effect of differential expression on disease outcome. The lab’s further focus is on the genetic basis for resistance/susceptibility to disease conferred by immunogenetic variation. KEY ROLES/RESPONSIBILITIES The Senior Computational Scientist will provide research support to the CIP-BSP-HLA Immunogenetics Section performing bio-statistical design, analysis and reporting of research projects conducted in the lab. This individual will be involved in the implementation of statistical models and data preparation. Successful candidate should have 5 or more years of competent, innovative biostatistics/bioinformatics research experience, beyond doctoral training Considerable experience with statistical software, such as SAS, R and S-Plus Sound knowledge, and demonstrated experience of theoretical and applied statistics Write program code to analyze data using statistical analysis software Contribute to the interpretation and publication of research results

Biology Curriculum Reform in Venezuela.

ERIC Educational Resources Information Center

Rondon, Leonor Mariasole

2001-01-01

Describes science in the Venezuelan school system which reflects on the process of development followed to design and validate the Biology Study Programs (BSP) with the emphasis on the relevance of curricular changes proposed in biological science for secondary education. (Contains 19 references.) (ASK)

Wnt/β-Catenin Pathway Regulates Cementogenic Differentiation of Adipose Tissue-Deprived Stem Cells in Dental Follicle Cell-Conditioned Medium

PubMed Central

Nie, Xin; Zhang, Bo; Zhou, Xia; Deng, Manjing

2014-01-01

The formation and attachment of new cementum is crucial for periodontium regeneration. Tissue engineering is currently explored to achieve complete, reliable and reproducible regeneration of the periodontium. The capacity of multipotency and self-renewal makes adipose tissue-deprived stem cells (ADSCs) an excellent cell source for tissue regeneration and repair. After rat ADSCs were cultured in dental follicle cell-conditioned medium (DFC-CM) supplemented with DKK-1, an inhibitor of the Wnt pathway, followed by 7 days of induction, they exhibited several phenotypic characteristics of cementoblast lineages, as indicated by upregulated expression levels of CAP, ALP, BSP and OPN mRNA, and accelerated expression of BSP and CAP proteins. The Wnt/β-catenin signaling pathway controls differentiation of stem cells by regulating the expression of target genes. Cementoblasts share phenotypical features with osteoblasts. In this study, we demonstrated that culturing ADSCs in DFC-CM supplemented with DKK-1 results in inhibition of β-catenin nuclear translocation and down-regulates TCF-4 and LEF-1 mRNA expression levels. We also found that DKK-1 could promote cementogenic differentiation of ADSCs, which was evident by the up-regulation of CAP, ALP, BSP and OPN gene expressions. On the other hand, culturing ADSCs in DFC-CM supplemented with 100 ng/mL Wnt3a, which activates the Wnt/β-catenin pathway, abrogated this effect. Taken together, our study indicates that the Wnt/β-catenin signaling pathway plays an important role in regulating cementogenic differentiation of ADSCs cultured in DFC-CM. These results raise the possibility of using ADSCs for periodontal regeneration by modifying the Wnt/β-catenin pathway. PMID:24806734

Doxorubicin-loaded aromatic imine-contained amphiphilic branched star polymer micelles: synthesis, self-assembly, and drug delivery

PubMed Central

Qiu, Liang; Hong, Chun-Yan; Pan, Cai-Yuan

2015-01-01

Redox-and pH-sensitive branched star polymers (BSPs), BP(DMAEMA-co-MAEBA-co-DTDMA)(PMAIGP)ns, have been successively prepared by two steps of reversible addition–fragmentation chain transfer (RAFT) polymerization. The first step is RAFT polymerization of 2-(N,N-dimethylaminoethyl)methacrylate (DMAEMA) and p-(methacryloxyethoxy) benzaldehyde (MAEBA) in the presence of divinyl monomer, 2,2′-dithiodiethoxyl dimethacrylate (DTDMA). The resultant branched polymers were used as a macro-RAFT agent in the subsequent RAFT polymerization. After hydrolysis of the BSPs to form BP(DMAEMA-co-MAEBA-co-DTDMA)(PMAGP)ns (BSP-H), the anticancer drug doxorubicin (DOX) was covalently linked to branched polymer chains by reaction of primary amine of DOX and aldehyde groups in the polymer chains. Their compositions, structures, molecular weights, and molecular weight distributions were respectively characterized by nuclear magnetic resonance spectra and gel permeation chromatography measurements. The DOX-loaded micelles were fabricated by self-assembly of DOX-containing BSPs in water, which were characterized by transmission electron microscopy and dynamic light scattering. Aromatic imine linkage is stable in neutral water, but is acid-labile; controlled release of DOX from the BSP-H-DOX micelles was realized at pH values of 5 and 6, and at higher acidic solution, fast release of DOX was observed. In vitro cytotoxicity experiment results revealed low cytotoxicity of the BSPs and release of DOX from micelles in HepG2 and HeLa cells. Confocal laser fluorescence microscopy observations showed that DOX-loaded micelles have specific interaction with HepG2 cells. Thus, this type of BSP micelle is an efficient drug delivery system. PMID:26056444

Origin, enzymatic response and fate of dissolved organic matter during flood and non-flood conditions in a river-floodplain system of the Danube (Austria).

PubMed

Sieczko, Anna; Peduzzi, Peter

2014-01-01

Spectroscopic techniques and extracellular enzyme activity measurements were combined with assessments of bacterial secondary production (BSP) to elucidate flood-pulse-linked differences in carbon (C) sources and related microbial processes in a river-floodplain system near Vienna (Austria). Surface connection with the main channel significantly influenced the quantity and quality of dissolved organic matter (DOM) in floodplain backwaters. The highest values of dissolved organic carbon (DOC) and chromophoric DOM (CDOM) were observed during the peak of the flood, when DOC increased from 1.36 to 4.37 mg l -1 and CDOM from 2.94 to 14.32 m -1 . The flood introduced DOC which consisted of more allochthonously-derived, aromatic compounds. Bacterial enzymatic activity, as a proxy to track the response to changes in DOM, indicated elevated utilization of imported allochthonous material. Based on the enzyme measurements, new parameters were calculated: metabolic effort and enzymatic indices (EEA 1 and EEA 2). During connection, bacterial glucosidase and protease activity were dominant, whereas during disconnected phases a switch to lignin degradation (phenol oxidase) occurred. The enzymatic activity analysis revealed that flooding mobilized reactive DOM, which then supported bacterial metabolism. No significant differences in overall BSP between the two phases were detected, indicating that heterogeneous sources of C sufficiently support BSP. The study demonstrates that floods are important for delivering DOM, which, despite its allochthonous origin, is reactive and can be effectively utilized by aquatic bacteria in this river-floodplain systems. The presence of active floodplains, characterized by hydrological connectivity with the main channel, creates the opportunity to process allochthonous DOC. This has potential consequences for carbon flux, enhancing C sequestration and mineralization processes in this river-floodplain system.

Validity of Wearable Activity Monitors during Cycling and Resistance Exercise.

PubMed

Boudreaux, Benjamin D; Hebert, Edward P; Hollander, Daniel B; Williams, Brian M; Cormier, Corinne L; Naquin, Mildred R; Gillan, Wynn W; Gusew, Emily E; Kraemer, Robert R

2018-03-01

The use of wearable activity monitors has seen rapid growth; however, the mode and intensity of exercise could affect the validity of heart rate (HR) and caloric (energy) expenditure (EE) readings. There is a lack of data regarding the validity of wearable activity monitors during graded cycling regimen and a standard resistance exercise. The present study determined the validity of eight monitors for HR compared with an ECG and seven monitors for EE compared with a metabolic analyzer during graded cycling and resistance exercise. Fifty subjects (28 women, 22 men) completed separate trials of graded cycling and three sets of four resistance exercises at a 10-repetition-maximum load. Monitors included the following: Apple Watch Series 2, Fitbit Blaze, Fitbit Charge 2, Polar H7, Polar A360, Garmin Vivosmart HR, TomTom Touch, and Bose SoundSport Pulse (BSP) headphones. HR was recorded after each cycling intensity and after each resistance exercise set. EE was recorded after both protocols. Validity was established as having a mean absolute percent error (MAPE) value of ≤10%. The Polar H7 and BSP were valid during both exercise modes (cycling: MAPE = 6.87%, R = 0.79; resistance exercise: MAPE = 6.31%, R = 0.83). During cycling, the Apple Watch Series 2 revealed the greatest HR validity (MAPE = 4.14%, R = 0.80). The BSP revealed the greatest HR accuracy during resistance exercise (MAPE = 6.24%, R = 0.86). Across all devices, as exercise intensity increased, there was greater underestimation of HR. No device was valid for EE during cycling or resistance exercise. HR from wearable devices differed at different exercise intensities; EE estimates from wearable devices were inaccurate. Wearable devices are not medical devices, and users should be cautious when using these devices for monitoring physiological responses to exercise.

Sexual Polyploidization in Medicago sativa L.: Impact on the Phenotype, Gene Transcription, and Genome Methylation

PubMed Central

Rosellini, Daniele; Ferradini, Nicoletta; Allegrucci, Stefano; Capomaccio, Stefano; Zago, Elisa Debora; Leonetti, Paola; Balech, Bachir; Aversano, Riccardo; Carputo, Domenico; Reale, Lara; Veronesi, Fabio

2016-01-01

Polyploidization as the consequence of 2n gamete formation is a prominent mechanism in plant evolution. Studying its effects on the genome, and on genome expression, has both basic and applied interest. We crossed two diploid (2n = 2x = 16) Medicago sativa plants, a subsp. falcata seed parent, and a coerulea × falcata pollen parent that form a mixture of n and 2n eggs and pollen, respectively. Such a cross produced full-sib diploid and tetraploid (2n = 4x = 32) hybrids, the latter being the result of bilateral sexual polyploidization (BSP). These unique materials allowed us to investigate the effects of BSP, and to separate the effect of intraspecific hybridization from those of polyploidization by comparing 2x with 4x full sib progeny plants. Simple sequence repeat marker segregation demonstrated tetrasomic inheritance for all chromosomes but one, demonstrating that these neotetraploids are true autotetraploids. BSP brought about increased biomass, earlier flowering, higher seed set and weight, and larger leaves with larger cells. Microarray analyses with M. truncatula gene chips showed that several hundred genes, related to diverse metabolic functions, changed their expression level as a consequence of polyploidization. In addition, cytosine methylation increased in 2x, but not in 4x, hybrids. Our results indicate that sexual polyploidization induces significant transcriptional novelty, possibly mediated in part by DNA methylation, and phenotypic novelty that could underpin improved adaptation and reproductive success of tetraploid M. sativa with respect to its diploid progenitor. These polyploidy-induced changes may have promoted the adoption of tetraploid alfalfa in agriculture. PMID:26858330

Sexual Polyploidization in Medicago sativa L.: Impact on the Phenotype, Gene Transcription, and Genome Methylation.

PubMed

Rosellini, Daniele; Ferradini, Nicoletta; Allegrucci, Stefano; Capomaccio, Stefano; Zago, Elisa Debora; Leonetti, Paola; Balech, Bachir; Aversano, Riccardo; Carputo, Domenico; Reale, Lara; Veronesi, Fabio

2016-04-07

Polyploidization as the consequence of 2n gamete formation is a prominent mechanism in plant evolution. Studying its effects on the genome, and on genome expression, has both basic and applied interest. We crossed two diploid (2n = 2x = 16) Medicago sativa plants, a subsp. falcata seed parent, and a coerulea × falcata pollen parent that form a mixture of n and 2n eggs and pollen, respectively. Such a cross produced full-sib diploid and tetraploid (2n = 4x = 32) hybrids, the latter being the result of bilateral sexual polyploidization (BSP). These unique materials allowed us to investigate the effects of BSP, and to separate the effect of intraspecific hybridization from those of polyploidization by comparing 2x with 4x full sib progeny plants. Simple sequence repeat marker segregation demonstrated tetrasomic inheritance for all chromosomes but one, demonstrating that these neotetraploids are true autotetraploids. BSP brought about increased biomass, earlier flowering, higher seed set and weight, and larger leaves with larger cells. Microarray analyses with M. truncatula gene chips showed that several hundred genes, related to diverse metabolic functions, changed their expression level as a consequence of polyploidization. In addition, cytosine methylation increased in 2x, but not in 4x, hybrids. Our results indicate that sexual polyploidization induces significant transcriptional novelty, possibly mediated in part by DNA methylation, and phenotypic novelty that could underpin improved adaptation and reproductive success of tetraploid M. sativa with respect to its diploid progenitor. These polyploidy-induced changes may have promoted the adoption of tetraploid alfalfa in agriculture. Copyright © 2016 Rosellini et al.

Cloning and Characterization of the Lactococcal Plasmid-Encoded Type II Restriction/Modification System, LlaDII

PubMed Central

Madsen, Annette; Josephsen, Jytte

1998-01-01

The LlaDII restriction/modification (R/M) system was found on the naturally occurring 8.9-kb plasmid pHW393 in Lactococcus lactis subsp. cremoris W39. A 2.4-kb PstI-EcoRI fragment inserted into the Escherichia coli-L. lactis shuttle vector pCI3340 conferred to L. lactis LM2301 and L. lactis SMQ86 resistance against representatives of the three most common lactococcal phage species: 936, P335, and c2. The LlaDII endonuclease was partially purified and found to recognize and cleave the sequence 5′-GC↓NGC-3′, where the arrow indicates the cleavage site. It is thus an isoschizomer of the commercially available restriction endonuclease Fnu4HI. Sequencing of the 2.4-kb PstI-EcoRI fragment revealed two open reading frames arranged tandemly and separated by a 105-bp intergenic region. The endonuclease gene of 543 bp preceded the methylase gene of 954 bp. The deduced amino acid sequence of the LlaDII R/M system showed high homology to that of its only sequenced isoschizomer, Bsp6I from Bacillus sp. strain RFL6, with 41% identity between the endonucleases and 60% identity between the methylases. The genetic organizations of the LlaDII and Bsp6I R/M systems are identical. Both methylases have two recognition sites (5′-GCGGC-3′ and 5′-GCCGC-3′) forming a putative stem-loop structure spanning part of the presumed −35 sequence and part of the intervening region between the −35 and −10 sequences. Alignment of the LlaDII and Bsp6I methylases with other m5C methylases showed that the protein primary structures possessed the same organization. PMID:9647810

Variations in the management of the axilla in screen-detected ductal carcinoma in situ: evidence from the UK NHS breast screening programme audit of screen detected DCIS.

PubMed

Nicholson, S; Hanby, A; Clements, K; Kearins, O; Lawrence, G; Dodwell, D; Bishop, H; Thompson, A

2015-01-01

The diagnosis and surgical management of screen-detected Ductal Carcinoma In Situ (DCIS) remains controversial including a range of axillary approaches and consequent morbidity. This study examined the management of the axilla in all patients with DCIS presenting through the United Kingdom National Health Service Breast Screening Programme (UK NHS BSP). Retrospective analysis of the UK NHS BSP identified 26,696 women initially diagnosed with DCIS over the 8 years 1 April 2003-31 March 2011. The final breast pathology of these women was upgraded to invasive ductal cancer in 5564 (20.8%) women or micro-invasive cancer in 1031 (3.9%) women. At first operation, 5290 (26.3%) of the 20,094 women who had a final post-operative diagnosis of DCIS only underwent axillary surgery (72.4% at the time of mastectomy, 23.8% breast conservation surgery, 3.8% axillary surgery alone). Performance of axillary surgery reflected increasing tumour size, micro-invasion or increasing nuclear grade for the final diagnosis of DCIS. More extensive nodal surgery was performed in those undergoing mastectomy; 10.8% of women had more than 8 nodes removed. Overall, 12.0% of women with invasive cancer, 1.7% with micro-invasion, and 0.2% with DCIS alone, were ultimately node positive. Improved pre-operative sampling of DCIS, axillary assessment by ultrasound with needle biopsy for suspected metastases, risk stratification for sentinel node biopsy (for high grade or extensive DCIS) and avoiding axillary clearance for a pre-operative diagnosis of DCIS alone should reduce unnecessary axillary surgery. Standards using such criteria for axillary surgery in screen-detected DCIS should be integrated into the NHS BSP. Crown Copyright © 2014. Published by Elsevier Ltd. All rights reserved.

17β-estradiol regulates the differentiation of cementoblasts via Notch signaling cascade

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liao, Jing; Zhou, Zeyuan; Huang, Li

Estrogen has been well recognized as a key factor in the homeostasis of bone and periodontal tissue, but the way it regulates the activities of cementoblasts, the cell population maintaining cementum has not been fully understood. In this study, we examined the expression of estrogen receptor in OCCM-30 cells and the effect of 17β-estradiol (E2) on the proliferation and differentiation of OCCM-30 cells. We found that both estrogen receptor α and β were expressed in OCCM-30 cells. E2 exerted no significant influence on the proliferation of OCCM-30 cells, but inhibited the transcription and translation of BSP and Runx2 in the early phase of osteogenicmore » induction except the BSP mRNA. Afterwards in the late phase of osteogenic induction, E2 enhanced the transcription and translation of BSP and Runx2 and promoted the calcium deposition. In addition, the expression level of Notch1, NICD and Hey1 mRNAs responded to exogenous E2 in a pattern similar to that of the osteoblastic markers. DAPT could attenuate the effect of E2 on the expression of osteoblastic markers. These findings indicated that E2 might regulate the differentiation of cementoblasts via Notch signaling. - Highlights: • 17β-estradiol showed no significant effect on the proliferation of cementoblasts. • 17β-estradiol promoted the osteoblastic differentiation of cementoblasts despite of an early transient inhibition. • Notch signaling was regulated by 17β-estradiol and was responsible for mediating the effect of E2 on cementoblasts. • Hey1 might display an opposite expression pattern to Notch signaling in certain circumstances.« less

Inferring the global phylodynamics of influenza A/H3N2 viruses in Taiwan.

PubMed

Gong, Yu-Nong; Tsao, Kuo-Chien; Chen, Guang-Wu

2018-02-20

Influenza A/H3N2 viruses are characterized by highly mutated RNA genomes. In this study, we focused on tracing the phylodynamics of Taiwanese strains over the past four decades. All Taiwanese H3N2 HA1 sequences and references were downloaded from public database. A Bayesian skyline plot (BSP) and phylogenetic tree were used to analyze the evolutionary history, and Bayesian phylogeographic analysis was applied to predict the spatiotemporal migrations of influenza outbreaks. Genetic diversity was found to have peaked near the summer of 2009 in BSP, in addition to the two earlier reported ones in summer of 2005 and 2007. We predicted their spatiotemporal migrations and found the summer epidemic of 2005 from Korea, and 2007 and 2009 from the Western United States. BSP also predicted an elevated genetic diversity in 2015-2017. Quasispecies were found over approximately 20% of the strains included in this time span. In addition, a first-time seen N31S mutation was noted in Taiwan in 2016-2017. We comprehensively investigated the evolutionary history of Taiwanese strains in 1979-2017. An epidemic caution could thus be raised if genetic diversity was found to have peaked. An example showed a newly-discovered cluster in 2016-2017 strains featuring a mutation N31S together with HA-160 quasispecies. Phylogeographic analysis, moreover, provided useful insights in tracing the possible source and migrations of these epidemics around the world. We demonstrated that Asian destinations including Taiwan were the immediate followers, while U.S. continent was predicted the origin of two summer epidemics in 2007 and 2009. Copyright © 2018. Published by Elsevier B.V.

Isolation and Preliminary Screening of a Weissella confusa Strain from Giant Panda (Ailuropoda melanoleuca).

PubMed

Xiong, Lvchen; Ni, Xueqin; Niu, Lili; Zhou, Yi; Wang, Qiang; Khalique, Abdul; Liu, Qian; Zeng, Yan; Shu, Gang; Pan, Kangcheng; Jing, Bo; Zeng, Dong

2018-04-13

Weissella confusa has recently received attention for its probiotic potential. Some W. confusa and Weissella cibaria strains isolated from fermented foods show favorable probiotic effects. However, the probiotic properties of W. confusa isolated from giant panda remain unreported to date. Thus, this study isolated a W. confusa strain from giant panda feces and then investigated its characteristics and probiotic properties. A lactic acid bacteria strain was isolated from giant panda fecal samples. The isolated strain was screened by in vitro probiotic property tests, including in vitro antimicrobial test, antioxidant test, surface hydrophobicity, and stress resistance. On the basis of biochemical identification and 16S rDNA sequencing, the W. confusa strain was identified as BSP201703. This Weissella confusa strain can survive at pH 2 and 0.3% (w/v) concentration of bile salt environment and inhibit common intestinal pathogens. It also possesses an in vitro antioxidant capacity, a high auto-aggregation ability, and a high surface hydrophobicity. BSP201703 might serve as a probiotic to giant pandas.

Microbial transformation of pharmaceuticals naproxen, bisoprolol, and diclofenac in aerobic and anaerobic environments.

PubMed

Lahti, Marja; Oikari, Aimo

2011-08-01

Although biotransformation is generally considered to be the main process by which to remove pharmaceuticals, both in sewage treatment plants and in aquatic environments, quantitative information on specific compounds is scarce. In this study, the transformations of diclofenac (DCF), naproxen (NPX), and bisoprolol (BSP) were studied under aerobic and anaerobic conditions using inocula taken from activated and digested sludge processes, respectively. Whereas concentration decays were monitored by LC-tandem mass spectrometry, oxygen consumption and methane production were used for the evaluation of the performance of overall conditions. DCF was recalcitrant against both aerobic and anaerobic biotransformation. More than one third of the BSP disappeared under aerobic conditions, whereas only 14% was anaerobically biotransformed in 161 days. Under aerobic conditions, complete removal of NPX was evident within 14 days, but anaerobic transformation was also efficient. Formation of 6-O-desmethylnaproxen, a previously reported aerobic metabolite, was also detected under anaerobic conditions and persisted for 161 days.

MethPrimer: designing primers for methylation PCRs.

PubMed

Li, Long-Cheng; Dahiya, Rajvir

2002-11-01

DNA methylation is an epigenetic mechanism of gene regulation. Bisulfite- conversion-based PCR methods, such as bisulfite sequencing PCR (BSP) and methylation specific PCR (MSP), remain the most commonly used techniques for methylation mapping. Existing primer design programs developed for standard PCR cannot handle primer design for bisulfite-conversion-based PCRs due to changes in DNA sequence context caused by bisulfite treatment and many special constraints both on the primers and the region to be amplified for such experiments. Therefore, the present study was designed to develop a program for such applications. MethPrimer, based on Primer 3, is a program for designing PCR primers for methylation mapping. It first takes a DNA sequence as its input and searches the sequence for potential CpG islands. Primers are then picked around the predicted CpG islands or around regions specified by users. MethPrimer can design primers for BSP and MSP. Results of primer selection are delivered through a web browser in text and in graphic view.

Aberrant Expression of Xist in Aborted Porcine Fetuses Derived from Somatic Cell Nuclear Transfer Embryos

PubMed Central

Yuan, Lin; Wang, Anfeng; Yao, Chaogang; Huang, Yongye; Duan, Feifei; Lv, Qinyan; Wang, Dongxu; Ouyang, Hongsheng; Li, Zhanjun; Lai, Liangxue

2014-01-01

Cloned pigs generated by somatic cell nuclear transfer (SCNT) show a greater ratio of early abortion during mid-gestation than normal controls. X-linked genes have been demonstrated to be important for the development of cloned embryos. To determine the relationship between the expression of X-linked genes and abortion of cloned porcine fetuses, the expression of X-linked genes were investigated by quantitative real-time polymerase chain reaction (q-PCR) and the methylation status of Xist DMR was performed by bisulfate-specific PCR (BSP). q-PCR analysis indicated that there was aberrant expression of X-linked genes, especially the upregulated expression of Xist in both female and male aborted fetuses compared to control fetuses. Results of BSP suggested that hypomethylation of Xist occurred in aborted fetuses, whether male or female. These results suggest that the abnormal expression of Xist may be associated with the abortion of fetuses derived from somatic cell nuclear transfer embryos. PMID:25429426

LIVER DAMAGE IN MICE TREATED WITH 4-(p-DIMETHYLAMINOSTYRYL) QUINOLINE, A RADIOMIMETIC AGENT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davis, M.L.; Gude, W.D.; Asano, M.

1963-10-01

The effects of intravenous injections of the radiomimetic agent 4-(p- dimethylaminostyryl)quinoline on the liver were studied in mice of the RF/Up and (101 x C3H) F/sub 1/ strains. The effects were assessed by use of the Bromsulphalcin (BSP) liver function test and histologic examimation of liver sections. Liver cell lipoid vacuolation was noted within 1 hour after injection of 4 mg of the drug and was very severe before 24 hours had elapsed. BSP testing on succeeding days indicated progressive liver damage that reached a peak on the sixth day in the RF/Up mice and on the third day inmore » the (101 x C3H) F/sub 1/ mice. This was accompanied by extensive liver cell necrosis, especially in the central part of the lobule. Resolution of the lesions occurred gradually over the 17-day observation period, but residual cytologic changes were still present at the end of this time. (P.C.H.)« less

BSP-01: Full Four-Digit Typing for Class I and II HLA Genes | Frederick National Laboratory for Cancer Research

Cancer.gov

The Basic Science Program will receive genomic DNA at a concentration of 50 ng/ul.Human leukocyte antigen (HLA) typing will be performed using atargeted next-generation sequencing (NGS) method.Briefly, locus-specific primers are use

Senior Computational Scientist | Center for Cancer Research

Cancer.gov

The Basic Science Program (BSP) pursues independent, multidisciplinary research in basic and applied molecular biology, immunology, retrovirology, cancer biology, and human genetics. Research efforts and support are an integral part of the Center for Cancer Research (CCR) at the Frederick National Laboratory for Cancer Research (FNLCR). The Cancer & Inflammation Program (CIP),

Structure and resilience of fungal communities in Alaskan boreal forest soils

Treesearch

D. Lee Taylor; Ian C. Herriott; Kelsie E. Stone; Jack W. McFarland; Michael G. Booth; Mary Beth Leigh

2010-01-01

This paper outlines molecular analyses of soil fungi within the Bonanza Creek Long Term Ecological Research program. We examined community structure in three studies in mixed upland, black spruce (Picea mariana (Mill.) BSP), and white spruce (Picea glauca (Moench) Voss) forests and examined taxa involved in cellulose...

Meal Counting and Claiming Manual.

ERIC Educational Resources Information Center

Food and Nutrition Service (USDA), Washington, DC.

This manual contains information about the selection and implementation of a meal counting and claiming system for the National School Lunch Program (NSLP) and the School Breakfast Program (BSP). Federal reimbursement is provided for each meal that meets program requirements and is served to an eligible student. Part 1 explains the six elements of…

Reproductive barriers and hybridity in two spruces, Picea rubens and Picea mariana, sympatric in eastern North America

Treesearch

John E. Major; Alex Mosseler; Kurt H. Johnsen; Om P. Rajora; Debby C. Barsi; K.-H. Kim; J.-M. Park; Moira Campbell

2005-01-01

Hybridization between red spruce (Picea rubens Sarg.) and black spruce (Picea mariana (Mill.) BSP), lateand early-successional species, respectively, has resulted in identification and management problems. We investigated the nature and magnitude of reproductive and life-cycle success barriers in controlled intra- and inter-...

Climate-growth relationships along a black spruce toposequence in Interior Alaska

Treesearch

Jane M. Wolken; Daniel H. Mann; Thomas A. Grant; Andrea H. Lloyd; T. Scott Rupp; Teresa N. Hollingsworth

2016-01-01

Despite its wide geographic distribution and important role in boreal forest fire regimes, little is known about the climate-growth relationships of black spruce (Picea mariana [Mill.] B.S.P.). We used site- and tree-level analyses to evaluate the radial growth responses to climate of black spruce growing...

Growth, shoot phenology and physiology of diverse seed sources of black spruce: I Seedling responses to varied atmospheric CO2 concentrations and photoperiods

Treesearch

Kurt H. Johnsen; John R. Seiler

1996-01-01

We conducted a greenhouse experiment to determine: (1) if diverse provenances of black spruce (Picea mariana (Mill.) B.S.P.) respond similarly in growth, phenology and physiology to an approximately 300 ppm increase in atmospheric CO2...

JPRS Report, Soviet Union, Political Affairs

DTIC Science & Technology

1990-09-05

Latvian Balto-Slavic Party Considered 90UN2270B Riga SOVETSKAYA MOLODEZH in Russian 23 May 90 p 1 [Article by Oleg Ilenkov: "More About the BSP...freeing of the leaders of the Karabakh and Krunk committees, as well as the Sverd- lovsk journalist S. Kuznetsov . Nowadays "Memorial" is not merely

Allozyme variation in Picea mariana from Newfoundland: Discussion

Treesearch

William B. Critchfield

1987-01-01

In their recent paper describing the distribution of genetic variation in black spruce (Picea mariana (Mill.) B.S.P.) on the island of Newfoundland, Yeh et el. (1986) concluded that a center of variability in west-central Newfoundland derived from ancestral populations that persisted on the island during the last (Wisconsin) glaciation. They...

DNA methylation modulates H19 and IGF2 expression in porcine female eye

PubMed Central

Wang, Dongxu; Wang, Guodong; Yang, Hao; Liu, Haibo; Li, Cuie; Li, Xiaolan; Lin, Chao; Song, Yuning; Li, Zhanjun; Liu, Dianfeng

2017-01-01

Abstract The sexually dimorphic expression of H19/IGF2 is evolutionarily conserved. To investigate whether the expression of H19/IGF2 in the female porcine eye is sex-dependent, gene expression and methylation status were evaluated using quantitative real-time PCR (qPCR) and bisulfite sequencing PCR (BSP). We hypothesized that H19/IGF2 might exhibit a different DNA methylation status in the female eye. In order to evaluate our hypothesis, parthenogenetic (PA) cells were used for analysis by qPCR and BSP. Our results showed that H19 and IGF2 were over-expressed in the female eye compared with the male eye (3-fold and 2-fold, respectively). We observed a normal monoallelic methylation pattern for H19 differentially methylated regions (DMRs). Compared with H19 DMRs, IGF2 DMRs showed a different methylation pattern in the eye. Taken together, these results suggest that elevated expression of H19/IGF2 is caused by a specific chromatin structure that is regulated by the DNA methylation status of IGF2 DMRs in the female eye. PMID:28266684

Low-power wireless ECG acquisition and classification system for body sensor networks.

PubMed

Lee, Shuenn-Yuh; Hong, Jia-Hua; Hsieh, Cheng-Han; Liang, Ming-Chun; Chang Chien, Shih-Yu; Lin, Kuang-Hao

2015-01-01

A low-power biosignal acquisition and classification system for body sensor networks is proposed. The proposed system consists of three main parts: 1) a high-pass sigma delta modulator-based biosignal processor (BSP) for signal acquisition and digitization, 2) a low-power, super-regenerative on-off keying transceiver for short-range wireless transmission, and 3) a digital signal processor (DSP) for electrocardiogram (ECG) classification. The BSP and transmitter circuits, which are the body-end circuits, can be operated for over 80 days using two 605 mAH zinc-air batteries as the power supply; the power consumption is 586.5 μW. As for the radio frequency receiver and DSP, which are the receiving-end circuits that can be integrated in smartphones or personal computers, power consumption is less than 1 mW. With a wavelet transform-based digital signal processing circuit and a diagnosis control by cardiologists, the accuracy of beat detection and ECG classification are close to 99.44% and 97.25%, respectively. All chips are fabricated in TSMC 0.18-μm standard CMOS process.

Secretary | Center for Cancer Research

Cancer.gov

The Basic Science Program (BSP) pursues independent, multidisciplinary research programs in basic or applied molecular biology, immunology, retrovirology, cancer biology, or human genetics. Research efforts and support are an integral part of the Center for Cancer Research (CCR) at the Frederick national Laboratory for Cancer Research (FNLCR). The BSP Office provides procurement and logistical assistance in support of the research activities of the Center for Cancer Research.KEY ROLES/RESPONSIBILITIES The Secretary III will: Provide heavy-volume procurement support to a large customer base of laboratory staff, both Leidos Biomed and CCR (gov’t), using blanket orders, purchase requisitions, credit card, and online warehouse system Data entry into appropriate financial system component (CostPoint, Cor360), status checks on orders, maintenance of orders log, reconciliation of credit card transactions, maintenance of electronic filing systems Providing logistical support for the facilitation of travel packages (both pre-travel and post travel) for Leidos Biomed employees, as well as the coordination of seminar speakers and subsequent reimbursements Composing and answering emails/correspondence Communicating with all levels of personnel, both verbally and in writing, to gather and clearly convey information

In vitro bioactivity of Bioroot™ RCS, via A4 mouse pulpal stem cells.

PubMed

Dimitrova-Nakov, Sasha; Uzunoglu, Emel; Ardila-Osorio, Hector; Baudry, Anne; Richard, Gilles; Kellermann, Odile; Goldberg, Michel

2015-11-01

To evaluate the biocompatibility and osteoinductive properties of Bioroot™ RCS (BR, Septodont, France) compared to Kerr's Pulp Canal Sealer™ (PCS, Kerr, Italy) using the mouse pulp-derived stem cell line A4, which have an osteo/odontogenic potential in vitro and contribute to efficient bone repair in vivo. A4 cells were cultured at the stem cell stage in the presence of solid disks of BR or PCS, whereas untreated A4 cells were used as control. After 3, 7, 10 days of direct contact with the sealers, cell viability was quantified using Trypan Blue exclusion assay. Immunolabelings were performed to assess the expression of odontoblast markers i.e. type 1 collagen, DMP1 or BSP. Finally, sealer-treated cells were induced toward osteo/odontogenic differentiation to assess the impact of the sealers on mineralization by Von Kossa staining. Statistical significance was evaluated by one-way analysis of variance and t-test (p<0.05). BR did not alter the viability and morphology of A4 pulpal cells compared to control group (p>0.05); however, living cell percentage of PCS was significantly lower compared to control and BR groups (p<0.05). BR preserved the intrinsic ability of A4 cells to express type 1 collagen, DMP1 or BSP at the stem cell stage. It did not alter the integrity of collagen fibers surrounding the cells and promoted overexpression of BSP and DMP1 at the cell surface. In contrast to PCS, BR did not compromise the mineralization potential of pulpal A4 stem cells. Bioroot™ RCS was not as cytotoxic as PCS. It did not recruit the pulpal stem cells toward differentiation but preserve their osteo-odontogenic intrinsic properties. Bioroot™ RCS might provide more suitable environment to induce stem cells for hard tissue deposition. Copyright © 2015 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Sustained delivery and efficacy of polymeric nanoparticles containing osteopontin and bone sialoprotein antisenses in rats with breast cancer bone metastasis.

PubMed

Elazar, Victoria; Adwan, Hassan; Bäuerle, Tobias; Rohekar, Keren; Golomb, Gershon; Berger, Martin R

2010-04-01

Poor prognosis in mammary carcinoma is associated with a certain expression profile of a defined set of genes including osteopontin and bone sialoprotein. Efficient and specific delivery of antisenses (AS) and a protection of the sequences from degradation are the crucial conditions for AS therapeutic efficiency. We hypothesized that effective and safe AS delivery direceted against these genes could be achieved by polymeric nanoparticles (NP) fabricated from a biocompatible polymer. Due to their nano-size range and small negative charge, AS-NP can overcome the absorption barrier offering increased resistance to nuclease degradation, sustained duration of AS administration, and consequently, prolonged antisense action. The ASs designed against OPN and BSP-II were successfully encapsulated in NP composed of the biodegradable and biocompatible polylactide-co-glycolide polymer (PLGA), exhibiting sustained release and stability of the ASs. The therapeutic efficacy of the AS-NP delivery system was examined in vitro, and in a breast cancer bone metastasis animal model of MDA-MB-231 human breast cancer cells in nude rats. Treatment with OPN-AS or BSP-AS loaded NP in comparison with osmotic mini-pumps (locoregional injection and SC implants, respectively) resulted in a significant decrease in both, tumor bone metastasis incidence and in the size of the lesions in rats with metastases. Despite its smaller dose, AS-NP exhibited a better therapeutic efficacy than osmotic mini-pumps in terms of lesion ratio at later time periods (8-12 weeks). It may be concluded that AS delivery by NP is a promising therapeutic modality providing stability of the encapsulated AS and a sustained release.

Postglacial range shift and demographic expansion of the marine intertidal snail Batillaria attramentaria

PubMed Central

Ho, Phuong-Thao; Kwan, Ye-Seul; Kim, Boa; Won, Yong-Jin

2015-01-01

To address the impacts of past climate changes, particularly since the last glacial period, on the history of the distribution and demography of marine species, we investigated the evolutionary and demographic responses of the intertidal batillariid gastropod, Batillaria attramentaria, to these changes, using the snail as a model species in the northwest Pacific. We applied phylogeographic and divergence population genetic approaches to mitochondrial COI sequences from B. attramentaria. To cover much of its distributional range, 197 individuals collected throughout Korea and 507 publically available sequences (mostly from Japan) were used. Finally, a Bayesian skyline plot (BSP) method was applied to reconstruct the demographic history of this species. We found four differentiated geographic groups around Korea, confirming the presence of two distinct, geographically subdivided haplogroups on the Japanese coastlines along the bifurcated routes of the warm Tsushima and Kuroshio Currents. These two haplogroups were estimated to have begun to split approximately 400,000 years ago. Population divergence analysis supported the hypothesis that the Yellow Sea was populated by a northward range expansion of a small fraction of founders that split from a southern ancestral population since the last glacial maximum (LGM: 26,000–19,000 years ago), when the southern area became re-submerged. BSP analyses on six geographically and genetically defined groups in Korea and Japan consistently demonstrated that each group has exponentially increased approximately since the LGM. This study resolved the phylogeography of B. attramentaria as a series of events connected over space and time; while paleoceanographic conditions determining the connectivity of neighboring seas in East Asia are responsible for the vicariance of this species, the postglacial sea-level rise and warming temperatures have played a crucial role in rapid range shifts and broad demographic expansions of its populations. PMID:25691968

Silvical characteristics of Atlantic white-cedar (Chamaecyparis thyoides)

Treesearch

S. Little

1959-01-01

Atlantic white-cedar ((Chamaecyparis thyoides (L.) B.S.P.) has been a highly prized species since Colonial times because of the durability and high quality of its wood. The wood has been used for many purposes: boat boards, shingles and lath, framing, house and boat finish, pails and tanks, cabin logs, posts, and poles. Good white-cedar has always...

Negative heterosis not apparent in 22-year-old hybrids of Picea mariana and Picea rubens

Treesearch

Kurt H. Johnsen; John E. Major; Judy Loo; Donald McPhee

1998-01-01

Abstract: Work from the 1970s indicated that, relative to either parent species, crosses between red spruce (Picea rubens Sarg.) and black spruce (Picea mariana (Mill.) B.S.P.) were inferior with respect to both growth and photosynthesis. We re-examined the hypothesis that there is negative heterosis in hybrids...

A Writing Template for Probing Students' Botanical Sense of Place

ERIC Educational Resources Information Center

Wandersee, James H.; Clary, Renee M.; Guzman, Sandra M.

2006-01-01

Writing can be a powerful tool for learning biology. Writing assignments in biology could help students personalize and understand the biology knowledge they are studying. In this article, the authors present the "Botanical Sense of Place" (BSP), a convenient and easy-to-use writing template that they developed to elicit and probe students' prior…

Contextualizing Earth Science Professional Development Courses for Geoscience Teachers in Boston

NASA Astrophysics Data System (ADS)

Chen, R. F.; Pelletier, P.; Dorsen, J.; Douglas, E. M.; Pringle, M. S.; Karp, J.

2009-12-01

Inquiry-based, hands-on, graduate content courses have been developed specifically for Boston Public School middle school teachers of Earth Science. Earth Science I: Weather and Water and Earth Science II: The Solid Earth--Earth History and Planetary Systems have been taught a total of seven times to over 120 teachers. Several key attributes to these successful courses have been identified, including co-instruction by a university professor and a high school and a middle school teacher that are familiar with the Boston curriculum, use of hands-on activities that are closed related to those used in the Boston curriculum, pre- and post-course local field trips, and identification of key learning objectives for each day. This model of professional development was developed over several years in all disciplines (Earth Science, Physics, Biology, Chemistry) by the Boston Science Partnership (BSP), an NSF-funded Math Science Partnership program. One of the core strategies of the BSP is these Contextualized Content Courses (CCC), graduate level, lab-based courses taught at either UMass Boston or Northeastern University during summer intensive or semester formats. Two of the eleven courses developed under the grant are Earth Science I & II. This presentation shares the model of the CCC, the impact on teacher participants, the value of these courses for the professor, and lessons learned for successful professional development. Findings about the courses’ impact and effectiveness come from our external evaluation by the Program Evaluation Research Group (PERG). The combination of content and modeling good instructional practices have many positive outcomes for teachers, including increased self-efficacy in science understanding and teaching, positive impacts on student achievement, and teacher shifts from more traditional, more lecture-based instructional models to more inquiry approaches. STEM faculty members become involved in science education and learn and practice new instructional strategies. The teacher co-instructors hold leadership roles for their peers and gain university teaching experience. The participants have a course that is content rich and tailored for their needs in the classroom. Earth scientists develop a “broader impact” for their science by increasing climate and earth science literacy for teachers who, in turn, reach 100s to 1000s of students every year, possibly stimulating interest for students becoming future earth scientists, but at the very least, increasing the public appreciation for earth science.

Female strobili incidence in a Minnesota population of black spruce: heritability and correlation with height growth

Treesearch

C. Dana Nelson; C. A. Mohn

1989-01-01

Significant family variation in female strobili incidence, ripeness-to-flower and production were found in a Minnesota black spruce (Picea mariana (Mill.) B.S.P.) population tested at four locations. Heritability estimates indicated that gain in early flowering from selection would be possible. Height growth through age 12 years was positively correlated (genetic and...

Proceedings: Atlantic white-cedar: ecology and management symposium; 1997 August 6-7; Newport News, VA.

Treesearch

Theodore H. Shear; K.O. Summerville; [Editors

1999-01-01

As the past decade has seen a resurgence of interest in Atlantic white-cedar (Chamaecyparis thyoides (L.) B.S.P.), a conference was convened in August 1997 to present the latest information in the research and management of the species. New information included, among other things: natural and artificial regeneration and growth after harvesting;...

Effects of trees on the burning of organic layers on permafrost terrain

Treesearch

Eric S. Kasischke; Merritt R. Turetsky; Evan S. Kane

2012-01-01

We collected data to estimate depth of the remaining (residual) organic layer as well as data to estimate total pre-fire organic layer depth in 99 plots located in mature black spruce (Picea mariana (Mill.) BSP) forests in interior Alaska that burned during the large fire seasons of 2004 and 2005. These data were collected immediately adjacent to...

A key for predicting postfire successional trajectories in black spruce stands of interior Alaska.

Treesearch

Jill F. Johnstone; Teresa N. Hollingsworth; F. Stuart Chapin

2008-01-01

Black spruce (Picea mariana (Mill) B.S.P) is the dominant forest cover type in interior Alaska and is prone to frequent, stand-replacing wildfires. Through impacts on tree recruitment, the degree of fire consumption of soil organic layers can act as an important determinant of whether black spruce forests regenerate to a forest composition similar...

Genetic variation in carbon isotope discrimination and its relationship to growth under field conditions in full-sib families of Picea mariana

Treesearch

Lawrence B. Flanagan; Kurt H. Johnsen

1995-01-01

Measurements of the stable carbon isotope composition of leaf tissue were made on Picea mariana (Mill.) B.S.P. trees from four full-sib families grown on three different field sites at the Petawawa National Forestry Institute, Ontario, Canada. The four families chosen exhibited genetic variation for growth characteristics. Genetic...

Selfing results in inbreeding depression of growth but not of gas exchange of surviving adult black spruce trees

Treesearch

Kurt Johnsen; John E. Major; Chris A. Maier

2003-01-01

Summary In most tree species, inbreeding greatly reduces seed production, seed viability, survival and growth. In a previous large-scale quantitative analysis of a black spruce (Picea mariana (Mill.) B.S.P.) diallel experiment, selfing had large deleterious effects on growth but no impact on stable carbon isotope discrimination (an...

Effect of an Invasive Grass on Ambient Rates of Decomposition and Microbial Community Structure: A Search for Causality

USDA-ARS?s Scientific Manuscript database

In sutu decomposition of above and below ground plant biomass of the native grass species Andropogon glmoeratus (Walt.) B.S.P and exotic Imperata cylindrica (L.) Beauv. (cogongrass) was investigated using litter bags over the course of a 12 month period. The above and below ground biomass of the inv...

You Can Help Every Provider Have a Better Understanding of Functional Behavior Assessment! A Review of the Website: Basic FBA to BSP

ERIC Educational Resources Information Center

Shultz, Gwendolyn Joy; Havens, Nathan; Gurney, Beth Newberry; Burt, Jon

2017-01-01

Managing problematic classroom behavior is a challenge for many teachers, regardless of population. The website, www.basicfba.com, designed by researchers at Portland State University, offers teachers and practitioners a wealth of materials to assist them in conducting and maintaining a functional behavior assessment and behavior support plan.…

Postfire seed rain of black spruce, a semiserotinous conifer, in forests of interior Alaska

Treesearch

Jill Johnstone; Leslie Boby; Emily Tissier; Michelle Mack; Dave Verbyla; Xanthe. Walker

2009-01-01

The availability of viable seed can act as an important constraint on plant regeneration following disturbance. This study presents data on seed quantity and quality for black spruce (Picea mariana (Mill.) B.S.P.), a semiserotinous conifer that dominates large areas of North American boreal forest. We sampled seed rain and viability for 2 years...

Silymarin-Loaded Nanoparticles Based on Stearic Acid-Modified Bletilla striata Polysaccharide for Hepatic Targeting.

PubMed

Ma, Yanni; He, Shaolong; Ma, Xueqin; Hong, Tongtong; Li, Zhifang; Park, Kinam; Wang, Wenping

2016-02-29

Silymarin has been widely used as a hepatoprotective drug in the treatment of various liver diseases, yet its effectiveness is affected by its poor water solubility and low bioavailability after oral administration, and there is a need for the development of intravenous products, especially for liver-targeting purposes. In this study, silymarin was encapsulated in self-assembled nanoparticles of Bletilla striata polysaccharide (BSP) conjugates modified with stearic acid and the physicochemical properties of the obtained nanoparticles were characterized. The silymarin-loaded micelles appeared as spherical particles with a mean diameter of 200 nm under TEM. The encapsulation of drug molecules was confirmed by DSC thermograms and XRD diffractograms, respectively. The nanoparticles exhibited a sustained-release profile for nearly 1 week with no obvious initial burst. Compared to drug solutions, the drug-loaded nanoparticles showed a lower viability and higher uptake intensity on HepG2 cell lines. After intravenous administration of nanoparticle formulation for 30 min to mice, the liver became the most significant organ enriched with the fluorescent probe. These results suggest that BSP derivative nanoparticles possess hepatic targeting capability and are promising nanocarriers for delivering silymarin to the liver.

Social Problem Solving and Depressive Symptoms Over Time: A Randomized Clinical Trial of Cognitive Behavioral Analysis System of Psychotherapy, Brief Supportive Psychotherapy, and Pharmacotherapy

PubMed Central

Klein, Daniel N.; Leon, Andrew C.; Li, Chunshan; D’Zurilla, Thomas J.; Black, Sarah R.; Vivian, Dina; Dowling, Frank; Arnow, Bruce A.; Manber, Rachel; Markowitz, John C.; Kocsis, James H.

2011-01-01

Objective Depression is associated with poor social problem-solving, and psychotherapies that focus on problem-solving skills are efficacious in treating depression. We examined the associations between treatment, social problem solving, and depression in a randomized clinical trial testing the efficacy of psychotherapy augmentation for chronically depressed patients who failed to fully respond to an initial trial of pharmacotherapy (Kocsis et al., 2009). Method Participants with chronic depression (n = 491) received Cognitive Behavioral Analysis System of Psychotherapy (CBASP), which emphasizes interpersonal problem-solving, plus medication; Brief Supportive Psychotherapy (BSP) plus medication; or medication alone for 12 weeks. Results CBASP plus pharmacotherapy was associated with significantly greater improvement in social problem solving than BSP plus pharmacotherapy, and a trend for greater improvement in problem solving than pharmacotherapy alone. In addition, change in social problem solving predicted subsequent change in depressive symptoms over time. However, the magnitude of the associations between changes in social problem solving and subsequent depressive symptoms did not differ across treatment conditions. Conclusions It does not appear that improved social problem solving is a mechanism that uniquely distinguishes CBASP from other treatment approaches. PMID:21500885

Reimplementation of the Biome-BGC model to simulate successional change.

PubMed

Bond-Lamberty, Ben; Gower, Stith T; Ahl, Douglas E; Thornton, Peter E

2005-04-01

Biogeochemical process models are increasingly employed to simulate current and future forest dynamics, but most simulate only a single canopy type. This limitation means that mixed stands, canopy succession and understory dynamics cannot be modeled, severe handicaps in many forests. The goals of this study were to develop a version of Biome-BGC that supported multiple, interacting vegetation types, and to assess its performance and limitations by comparing modeled results to published data from a 150-year boreal black spruce (Picea mariana (Mill.) BSP) chronosequence in northern Manitoba, Canada. Model data structures and logic were modified to support an arbitrary number of interacting vegetation types; an explicit height calculation was necessary to prioritize radiation and precipitation interception. Two vegetation types, evergreen needle-leaf and deciduous broadleaf, were modeled based on site-specific meteorological and physiological data. The new version of Biome-BGC reliably simulated observed changes in leaf area, net primary production and carbon stocks, and should be useful for modeling the dynamics of mixed-species stands and ecological succession. We discuss the strengths and limitations of Biome-BGC for this application, and note areas in which further work is necessary for reliable simulation of boreal biogeochemical cycling at a landscape scale.

Molecular evolution of respiratory syncytial virus subgroup A genotype NA1 and ON1 attachment glycoprotein (G) gene in central Vietnam.

PubMed

Yoshihara, Keisuke; Le, Minh Nhat; Nagasawa, Koo; Tsukagoshi, Hiroyuki; Nguyen, Hien Anh; Toizumi, Michiko; Moriuchi, Hiroyuki; Hashizume, Masahiro; Ariyoshi, Koya; Dang, Duc Anh; Kimura, Hirokazu; Yoshida, Lay-Myint

2016-11-01

We performed molecular evolutionary analyses of the G gene C-terminal 3rd hypervariable region of RSV-A genotypes NA1 and ON1 strains from the paediatric acute respiratory infection patients in central Vietnam during the 2010-2012 study period. Time-scaled phylogenetic analyses were performed using Bayesian Markov Chain Monte Carlo (MCMC) method, and pairwise distances (p-distances) were calculated. Bayesian Skyline Plot (BSP) was constructed to analyze the time-trend relative genetic diversity of central Vietnam RSV-A strains. We also estimated the N-glycosylation sites within G gene hypervariable region. Amino acid substitutions under positive and negative selection pressure were examined using Conservative Single Likelihood Ancestor Counting (SLAC), Fixed Effects Likelihood (FEL), Internal Fixed Effects Likelihood (IFEL) and Mixed Effects Model for Episodic Diversifying Selection (MEME) models. The majority of central Vietnam ON1 strains detected in 2012 were classified into lineage 1 with few positively selected substitutions. As for the Vietnamese NA1 strains, four lineages were circulating during the study period with a few positive selection sites. Shifting patterns of the predominantly circulating NA1 lineage were observed in each year during the investigation period. Median p-distance of central Vietnam NA1 strains was wider (p-distance=0.028) than that of ON1 (p-distance=0.012). The molecular evolutionary rate of central Vietnam ON1 strains was estimated to be 2.55×10 -2 (substitutions/site/year) and was faster than NA1 (7.12×10 -3 (substitutions/site/year)). Interestingly, the evolutionary rates of both genotypes ON1 and NA1 strains from central Vietnam were faster than the global strains respectively. Furthermore, the shifts of N-glycosylation pattern within the G gene 3rd hypervariable region of Vietnamese NA1 strains were observed in each year. BSP analysis indicated the rapid growth of RSV-A effective population size in early 2012. These results suggested that the molecular evolution of RSV-A G gene detected in central Vietnam was fast with unique evolutionary dynamics. Copyright © 2016 Elsevier B.V. All rights reserved.

Intestinal ischemia-reperfusion suppresses biliary excretion of hepatic organic anion transporting polypeptides substrate.

PubMed

Maruyama, Hajime; Ogura, Jiro; Fujikawa, Asuka; Terada, Yusuke; Tsujimoto, Takashi; Koizumi, Takahiro; Kuwayama, Kaori; Kobayashi, Masaki; Yamaguchi, Hiroaki; Iseki, Ken

2013-01-01

Intestinal ischemia-reperfusion (I/R) causes gut dysfunction and promotes multi-organ failure. The liver and kidney can be affected by multi-organ failure after intestinal I/R. Organic anion transporting polypeptides (OATPs) and organic anion transporters (OATs) are recognized in a broad spectrum from endogenous compounds to xenobiotics, including clinically important drugs. Therefore, it is important for understanding the pharmacokinetics to obtain evidence of alterations in OATPs and OATs expression and transport activities. In the present study, we investigated the expression of rat Oatps and Oats after intestinal I/R. We used intestinal ischemia-reperfusion (I/R) model rats. Real-time PCR and Western blotting were used to assess mRNA and protein expression levels. Plasma concentration and biliary excretion of sulfobromophthalein (BSP), which is used as a model compound of organic anion drugs, were measured after intravenous administration in intestinal I/R rats. Although Oat1 and Oat3 mRNA levels were not altered in the kidney, Oatp1a1, Oatp1b2 and Oatp2b1 mRNA levels in the liver were significantly decreased at 1-6 h after intestinal I/R. Moreover, Oatp1a1 and Oatp2b1 protein expression levels were decreased at 1 h after intestinal I/R. Plasma concentration of BSP, which is a typical substrate of Oatps, in intestinal I/R rats reperfused 1 h was increased than that in sham-operated rats. Moreover, the area under the concentration-time curve (AUC₀₋₉₀) in intestinal I/R rats reperfused 1 h was significantly increased than that in sham-operated rats. The total clearance (CL(tot)) and the biliary clearance (CL(bile)) in intestinal I/R rats reperfused 1 h were significantly decreased than those in sham-operated rats. Oatp1a1 and Oatp2b1 expression levels are decreased by intestinal I/R. The decreases in these transporters cause alteration of pharmacokinetics of organic anion compound. The newly found influence of intestinal I/R on the expression and function of Oatps may be a key to perform appropriate drug therapy.

Bone Sialoproteins and Breast Cancer Detection

DTIC Science & Technology

2006-07-01

DAMD17-02-1-0684 TITLE: Bone Sialoproteins and Breast Cancer Detection PRINCIPAL INVESTIGATOR: Neal S. Fedarko, Ph.D...DATES COVERED (From - To) 1 Jul 2002 – 30 Jun 2006 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Bone Sialoproteins and Breast Cancer Detection 5b...accomplish this goal we have developed competitive enzyme-linked immunosorbent assays (ELISAs) for the SIBLINGs bone sialoprotein (BSP), osteopontin (OPN

A System Approach to Navy Medical Education and Training. Appendix 6. Pharmacy Technician.

DTIC Science & Technology

1974-08-31

lz PREPARE BUFFER SOLUTIONS 13 ICOMPUTE AMOUNTS OF INGREDIENTS FOR CCMPOUNDING/PREPARING IPHARMACEUTICALS 14 IWEIGH/MEASURE CHEMICALS 15 ICHECK ...DOSAGE OF DIAGNOSTIC PHARMACEUTICAL, E.G. BSP DYE II 19 1PREPARE C02 SLUSH 20 PREPARE PATCH TEST SOLUTION USING PATIENTOS SUSPECTED ALLERGENS 21 ICHECK ...PRESCRIPTIONS FOR INCOMPATABILITY/IDIOSYNCRACIES OF ICONCURRENTLY PRESCRIBED MEDICATIONS 22 ICHECK PRESCRIPTIONS FOR COMPLETENESSE.Go DRUG, IDOSEFORMSIG

JPRS Report, East Europe.

DTIC Science & Technology

1991-05-31

Replaces BSP Deputy Gotsev in Parliament [DUMA 16 May] 5 KNSB Leadership Issues Statement on Property [TRUD 14 May] 5 Italian Journalist on...Communist Party. However, these problems are strictly his and those of the BSDP leader- ship. He personally sincerely acknowledges that "the most...strengthening of the united opposition and removing compromised or ineptly imposed members of national and regional SDS leaderships ) should be explained as

A Preliminary Investigation of the Utility of the "Behavior Support Plan Quality Evaluation Guide II" for Use in Australia

ERIC Educational Resources Information Center

Webber, Lynne S.; McVilly, Keith R.; Fester, Tarryn; Zazelis, Telly

2011-01-01

Background: The quality of behaviour support plans (BSPs) can be an important influence on the quality of the support provided to people with disability who show challenging behaviours. The Behavior Support Plan Quality Evaluation Guide II (BSP-QE II) is one tool that may be useful in assessing the quality of behaviour support plans. It has…

Physostigmine and Methylphenidate Induce Distinct Arousal States During Isoflurane General Anesthesia in Rats.

PubMed

Kenny, Jonathan D; Chemali, Jessica J; Cotten, Joseph F; Van Dort, Christa J; Kim, Seong-Eun; Ba, Demba; Taylor, Norman E; Brown, Emery N; Solt, Ken

2016-11-01

Although emergence from general anesthesia is clinically treated as a passive process driven by the pharmacokinetics of drug clearance, agents that hasten recovery from general anesthesia may be useful for treating delayed emergence, emergence delirium, and postoperative cognitive dysfunction. Activation of central monoaminergic neurotransmission with methylphenidate has been shown to induce reanimation (active emergence) from general anesthesia. Cholinergic neurons in the brainstem and basal forebrain are also known to promote arousal. The objective of this study was to test the hypothesis that physostigmine, a centrally acting cholinesterase inhibitor, induces reanimation from isoflurane anesthesia in adult rats. The dose-dependent effects of physostigmine on time to emergence from a standardized isoflurane general anesthetic were tested. It was then determined whether physostigmine restores righting during continuous isoflurane anesthesia. In a separate group of rats with implanted extradural electrodes, physostigmine was administered during continuous inhalation of 1.0% isoflurane, and the electroencephalogram changes were recorded. Finally, 2.0% isoflurane was used to induce burst suppression, and the effects of physostigmine and methylphenidate on burst suppression probability (BSP) were tested. Physostigmine delayed time to emergence from isoflurane anesthesia at doses ≥0.2 mg/kg (n = 9). During continuous isoflurane anesthesia (0.9% ± 0.1%), physostigmine did not restore righting (n = 9). Blocking the peripheral side effects of physostigmine with the coadministration of glycopyrrolate (a muscarinic antagonist that does not cross the blood-brain barrier) produced similar results (n = 9 each). However, during inhalation of 1.0% isoflurane, physostigmine shifted peak electroencephalogram power from δ (<4 Hz) to θ (4-8 Hz) in 6 of 6 rats. During continuous 2.0% isoflurane anesthesia, physostigmine induced large, statistically significant decreases in BSP in 6 of 6 rats, whereas methylphenidate did not. Unlike methylphenidate, physostigmine does not accelerate time to emergence from isoflurane anesthesia and does not restore righting during continuous isoflurane anesthesia. However, physostigmine consistently decreases BSP during deep isoflurane anesthesia, whereas methylphenidate does not. These findings suggest that activation of cholinergic neurotransmission during isoflurane anesthesia produces arousal states that are distinct from those induced by monoaminergic activation.

New Generation Energy Efficient Refractory Application in Soaking Pits of Bhilai Steel Plant, Sail

NASA Astrophysics Data System (ADS)

Roy, Indranil; Chintaiah, Perumetla; Bhattacharya, Ajoy Kr.; Garai, Swapan Kr.; Ray Choudhury, Pankaj Kr.; Tiwari, Laksman

In Bhilai Steel Plant (BSP), soaking pits are used for heating ingots for successive rolling into blooms. Pits are operated at a temperature of around 1350°C. Mixed gas (Mixture of Blast Furnace gas & Coke Oven gas) of calorific value around 2040 kcal/Nm3 is used as fuel. The walls of soaking pits were lined with traditional 38% Al2O3 firebricks and top 500mm was cast with 70% Al2O3 low cement castable (LCC). This type of lining results in frequent damages due to hitting by ingots while being lifted from pit by overhead cranes thus affecting the availability of pit. Life of pits was 2 to 2.5 years in BSP with 3-4 cold repairs and 3-4 hot repairs. Energy loss through the wall is also quite high in this type of lining. To triumph over the limitations of the conventional lining, a lining design was developed for the walls which consist of special 70% Al2O3 LCC having high hot strength (HMOR) in combination with specially design flexible SS-304 anchors. Ceramic fiber blanket and insulation bricks were provided between castable and the metallic shell of the pit to minimize the heat loss. A heating schedule was developed and introduced based on available infrastructure at BSP for proper curing of modified LCC based lining. After introduction of modified lining, pit no. 14/2 is running for more than 2.5 years without any repair. To capitalize the success, two more pits i.e. 12/1 and 9/2 were converted to modified lining. These pits are also running satisfactorily for more than 1.5 years. The modification has resulted in higher availability with substantial increase in production. Shell temperature of the modified pits reduced to 90° - 140°C from 120° - 200°C of conventional pits. This shows reduction in heat loss through walls, resulting less fuel consumption and energy saving of about 18%.

A Preliminary Study on the Effects of Training Using Behavior Support Plan Quality Evaluation Guide (BSP-QE) to Improve Positive Behavioral Support Plans

ERIC Educational Resources Information Center

Wright, Diana Browning; Mayer, G. Roy; Cook, Clayton R.; Crews, S. Dean; Kraemer, Bonnie Rawlings; Gale, Bruce

2007-01-01

The purpose of this research was to evaluate the effects of two trainings designed to increase the competencies of professionals to develop high quality positive behavior support plans for students that engage in problem behaviors that interfere with theirs and/or others' ability to learn. Training one consisted of training attendees on six key…

Western Balkans as Base for Radical Islamists

DTIC Science & Technology

2011-06-10

18_12_06fulleureport.pdf (accessed March 25, 2011). 11Tufyal Choudhury, Mohammed Aziz , Duaa Izzidien, Intissar Khreeji, and Dilwar Hussain, ―Perceptions of...Macedonia, the Chief Mufti of the Islamic community Suleyman Rexhepi claimed in March 2011 that Wahhabis controlled four mosques in the capital Skopje...shared/bsp/hi/pdfs/18_12_06fulleureport.pdf (accessed March 25, 2011) 27Tufyal Choudhury, Mohammed Aziz , Duaa Izzidien, Intissar Khreeji, Dilwar Hussain

Atlantic white cedar: ecology, restoration, and management: Proceedings of the Arlington Echo symposium

Treesearch

Philip Sheridan

2005-01-01

A symposium was held on the globally threatened and coastally restricted tree species, Atlantic white-cedar (Chamaecyparis thyoides (L) B.S.P.) at the Arlington Echo Outdoor Education Center, Millersville, MD, in June 2003. The theme of the symposium was “Uniting Forces for Action,” and participants in the symposium came from throughout the range of this species, from...

Reliability and Utility of the Behaviour Support Plan Quality Evaluation Tool (BSP-QEII) for Auditing and Quality Development in Services for Adults with Intellectual Disability and Challenging Behaviour

ERIC Educational Resources Information Center

McVilly, K.; Webber, L.; Paris, M.; Sharp, G.

2013-01-01

Background: Having an objective means of evaluating the quality of behaviour support plans (BSPs) could assist service providers and statutory authorities to monitor and improve the quality of support provided to people with intellectual disability (ID) who exhibit challenging behaviour. The Behaviour Support Plan Quality Evaluation Guide II…

Recovery of carbon pools a decade after wildfire in black spruce forests of interior Alaska: effects of soil texture and landscape position

Treesearch

Gregory P. Houle; Evan S. Kane; Eric S. Kasischke; Carolyn M. Gibson; Merritt R. Turetsky

2017-01-01

We measured organic-layer (OL) recovery and carbon stocks in dead woody debris a decade after wildfire in black spruce (Picea mariana (Mill.) B.S.P.) forests of interior Alaska. Previous study at these research plots has shown the strong role that landscape position plays in governing the proportion of OL consumed during fire and revegetation after...

CMOS Bit-Stream Band-Pass Beamforming

DTIC Science & Technology

2016-03-31

unlimited. with direct IF sampling, most of the signal processing, including digital down-conversion ( DDC ), is carried out in the digital domain, and I/Q...level digitized signals are directly processed without decimation filtering for I/Q DDC and phase shifting. This novel BSP approach replaces bulky...positive feedback. The resonator center frequency of fs/4 (260MHz) simplifies the design of DDC . 4b tunable capacitors adjust the center frequency

In-situ Raman microprobe studies of plant cell walls: macromolecular organization and compositional variability in the secondary wall of Picea mariana (Mill.) B.S.P.

Treesearch

U.P. Agarwal; R.H. Atalla

1986-01-01

Native-state organization and distribution of cell-wall components in the secondary wall of woody tissue from P. mariana (Black Spruce) have been investigated using polarized Raman microspectroscopy. Evidence for orientation is detected through Raman intensity variations resulting from rotations of the exciting electric vector with respect to cell-wall geometry....

Microbiological Control of Eurasian Watermilfoil

DTIC Science & Technology

1990-06-01

34 Plant Disease Reporter, Vol 60, pp 77-80. Coler, R. A., and Gunner, H. B. 1969. "The Rhizosphere of an Aquatic Plant ( Lemna minor )," Canadian...Common Name Scientific Name Visible Symptoms* Aquatic plants Corkscrew eelgrass Vallisneria sp. - Duckweed Lemna minor - Elodea EZodea (Anacharis) - Grass...xanthan as a car- rier for BSP8 inoculum appeared to exert only a minor influence on the popu- lation dynamics; however, as will be discussed more

A New Species of Megastigmus Dalman (Hymenoptera: Torymidae) Reared from Seeds of Atlantic White Cedar (Cupressaceae), with Notes on Infestation Rates

Treesearch

J.J. Turgeon; K. Kamijo; G. DeBarr

1997-01-01

A new species, Megastigmus thyoides Kamijo (Hymenoptera: Torymidae), which emerged from seeds of Atlantic white cedar, Chamaecyparis thyoides (L.) B.S.P., collected in eastern United States is described and illustrated. This is the first record of this genus exploiting seeds of Cupressaceae in the Nearctic region. An average of 7% of the seeds collected from five sites...

JPRS Report, East Europe.

DTIC Science & Technology

1991-01-25

Announced [NEPSZABADSAG 4 Dec] 40 UTC Explores Idea of Budapest Airline Hub [FIGYELO 22 Nov] 41 Chamber of Commerce, Industry Established [FIGYELO...regardless of whether it is the BSP [Bulgarian Socialist Party], a coalition of the type of the SDS [Union of Democratic Forces ], or other, that accepts...even suspect that there is some kind of an agreement that exists between the two principal forces . [Simeonova] Do you consider that the 1946

Proliferation and differentiation of osteoblastic cells on titanium modified by ammonia plasma immersion ion implantation

NASA Astrophysics Data System (ADS)

Liu, Fei; Li, Bin; Sun, Junying; Li, Hongwei; Wang, Bing; Zhang, Shailin

2012-03-01

We report here a new method of titanium surface modification through ammonia (NH3) plasma immersion ion implantation (PIII) technique and its effect on the cellular behaviors of MC3T3-E1 osteoblastic cells. The NH3 PIII-treated titanium substrates (NH3-Ti) were characterized by X-ray photoelectron (XPS), which showed that NH3-Ti had a nitrogen-rich surface. However, there was no significant difference between the surface morphology of NH3-Ti and unmodified Ti. When MC3T3-E1 cells were cultured on NH3-Ti substrates, it was found that cell proliferation was accelerated at 4 and 7 days of culture. Meanwhile, cell differentiation was evaluated using type I collagen (COL I), osteocalcin (OC) and bone sialoprotein (BSP) as differentiation markers. It was found that expression of COL I and OC genes was up-regulated on NH3-Ti substrates. However, no significant difference was found in BSP gene expression between NH3-Ti and unmodified Ti substrates. Therefore, findings from this study indicate that surface modification of titanium through NH3 PIII favors osteoblastic proliferation and differentiation and as a result, it may be used to improve the biocompatibility of Ti implants in vivo.

[Reconstructed ambient light extinction coefficient and its contribution factors in Beijing in January, 2010].

PubMed

Zhu, Li-Hua; Tao, Jun; Chen, Zhong-Ming; Zhao, Yue; Zhang, Ren-Jian; Cao, Jun-Ji

2012-01-01

Aerosol samples for PM2.5 were collected from 1st January to 31st January 2010, in Beijing. The concentrations of organic carbon, elemental carbon, water-solubile ions and soil elements of all particle samples were determined by thermal/optical carbon analyzer, ion chromatography and X-ray fluorescence spectrometer, respectively. The scattering coefficients (b(sp)), absorbing coefficients (b(ap)) and meteorological parameters for this period were also measured. Ambient light extinction coefficients were reconstructed by IMPROVE formula and were compared with measured light extinction coefficients. The results showed that the average mass concentration of PM2.5 was (144.3 +/- 89.1) microg x m(-3) during campaigning period. The average values of measured b(ap), b(sp) and extinction coefficient (b(ext)) were (67.4 +/- 54.3), (328.5 +/- 353.8) and (395.9 +/- 405.2) Mm(-1), respectively. IMPROVE formula is suitable for source apportionment of light extinction coefficient in campaign period. The average value of calculated b'(ext) was (611 +/- 503) Mm(-1) in January, 2010. The major contributors to ambient light extinction coefficients included (NH4) 2SO4 (24.6%), NH4NO3 (11.6%), OM (45.5%), EC (11.9%) and FS (6.4%), respectively.

Single genome retrieval of context-dependent variability in mutation rates for human germline.

PubMed

Sahakyan, Aleksandr B; Balasubramanian, Shankar

2017-01-13

Accurate knowledge of the core components of substitution rates is of vital importance to understand genome evolution and dynamics. By performing a single-genome and direct analysis of 39,894 retrotransposon remnants, we reveal sequence context-dependent germline nucleotide substitution rates for the human genome. The rates are characterised through rate constants in a time-domain, and are made available through a dedicated program (Trek) and a stand-alone database. Due to the nature of the method design and the imposed stringency criteria, we expect our rate constants to be good estimates for the rates of spontaneous mutations. Benefiting from such data, we study the short-range nucleotide (up to 7-mer) organisation and the germline basal substitution propensity (BSP) profile of the human genome; characterise novel, CpG-independent, substitution prone and resistant motifs; confirm a decreased tendency of moieties with low BSP to undergo somatic mutations in a number of cancer types; and, produce a Trek-based estimate of the overall mutation rate in human. The extended set of rate constants we report may enrich our resources and help advance our understanding of genome dynamics and evolution, with possible implications for the role of spontaneous mutations in the emergence of pathological genotypes and neutral evolution of proteomes.

Immunolocalization of markers for bone formation during guided bone regeneration in osteopenic rats

PubMed Central

TERA, Tábata de Mello; NASCIMENTO, Rodrigo Dias; do PRADO, Renata Falchete; SANTAMARIA, Mauro Pedrine; JARDINI, Maria Aparecida Neves

2014-01-01

Objective The aim of this paper was to evaluate the repair of onlay autogenous bone grafts covered or not covered by an expanded polytetrafluoroethylene (e-PTFE) membrane using immunohistochemistry in rats with induced estrogen deficiency. Material and Methods Eighty female rats were randomly divided into two groups: ovariectomized (OVX) and with a simulation of the surgical procedure (SHAM). Each of these groups was again divided into groups with either placement of an autogenous bone graft alone (BG) or an autogenous bone graft associated with an e-PTFE membrane (BGM). Animals were euthanized on days 0, 7, 21, 45, and 60. The specimens were subjected to immunohistochemistry for bone sialoprotein (BSP), osteonectin (ONC), and osteocalcin (OCC). Results All groups (OVX+BG, OVX+BMG, SHAM+BG, and SHAM+BMG) showed greater bone formation, observed between 7 and 21 days, when BSP and ONC staining were more intense. At the 45-day, the bone graft showed direct bonding to the recipient bed in all specimens. The ONC and OCC showed more expressed in granulation tissue, in the membrane groups, independently of estrogen deficiency. Conclusions The expression of bone forming markers was not negatively influenced by estrogen deficiency. However, the markers could be influenced by the presence of the e-PTFE membrane. PMID:25591022

Effects of titanium surface anodization with CaP incorporation on human osteoblastic response

PubMed Central

OLIVEIRA, Natássia Cristina Martins; MOURA, Camilla Christian Gomes; ZANETTA-BARBOSA, Darceny; MENDONÇA, Daniela Baccelli Silveira; MENDONÇA, Gustavo; DECHICHI, Paula

2015-01-01

In this study we investigated whether anodization with calcium phosphate (CaP) incorporation (Vulcano®) enhances growth factors secretion, osteoblast-specific gene expression, and cell viability, when compared to acid etched surfaces (Porous®) and machined surfaces (Screw®) after 3 and 7 days. Results showed significant cell viability for Porous and Vulcano at day 7, when compared with Screw (p=0.005). At the same time point, significant differences regarding runt-related transcription factor 2 (Runx2), alkaline phosphatase (ALP) and bone sialoprotein (BSP) expression were found for all surfaces (p<0.05), but with greater fold induction for Porous and Vulcano. The secretion of transforming growth factor β1 (TGF-β1) and bone morphogenetic protein 2 (BMP-2) was not significantly affected by surface treatment in any experimental time (p>0.05). Although no significant correlation was found for growth factors secretion and Runx2 expression, a significant positive correlation between this gene and ALP/BSP expression showed that their strong association is independent on the type of surface. The incorporation of CaP affected the biological parameters evaluated similar to surfaces just acid etched. The results presented here support the observations that roughness also may play an important role in determining cell response. PMID:23498218

Emerging paradigms in anti-infective drug design.

PubMed

Barrett, Michael P; Croft, Simon L

2014-01-01

The need for new drugs to treat microbial infections is pressing. The great progress made in the middle part of the twentieth Century was followed by a period of relative inactivity as the medical needs relating to infectious disease in the wealthier nations receded. Growing realisation that anti-infectives are needed in many parts of the world, to treat neglected diseases as well as to combat the burgeoning risk of resistance to existing drugs, has galvanised a new wave of research into anti-microbial drugs. The transfer of knowledge from the Pharmaceutical industry relating to the importance of understanding how to target drugs successfully within the body, and improved understanding of how pathogens interact with their hosts, is driving a series of new paradigms in anti-infective drug design. Here we provide an overview of those processes as an introduction to a series of articles from experts in this area that emerged from a meeting entitled "Emerging Paradigms in Anti-Infective Drug Design" held in London on the 17th and 18th September 2012. The symposium was organised jointly by British Society for Parasitology (BSP) and the Biological & Medicinal Chemistry sector of the Royal Society of Chemistry (RSC) and held at the London School of Hygiene & Tropical Medicine. The symposium set out to cover all aspects of the identification of new therapeutic modalities for the treatment of neglected and tropical diseases. We aimed to bring together leading scientists from all the disciplines working in this field and cover the pharmacology, medicinal chemistry and drug delivery of potential new medicines. Sessions were held on: "Target diseases and targets for drugs", "Target based medicinal chemistry", "Bioavailability and chemistry", "Targeting intracellular microbes", "Alternative approaches and models", and "New anti-infectives - how do we get there?" This symposium was organised by Simon Croft (LSHTM) and Mike Barrett (University of Glasgow) for the BSP, and David Alker (David Alker Associates) and Andrew Stachulski (University of Liverpool) for the Biological & Medicinal Chemistry sector of the RSC.

Multitasking TORT under UNICOS: Parallel performance models and measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barnett, A.; Azmy, Y.Y.

1999-09-27

The existing parallel algorithms in the TORT discrete ordinates code were updated to function in a UNICOS environment. A performance model for the parallel overhead was derived for the existing algorithms. The largest contributors to the parallel overhead were identified and a new algorithm was developed. A parallel overhead model was also derived for the new algorithm. The results of the comparison of parallel performance models were compared to applications of the code to two TORT standard test problems and a large production problem. The parallel performance models agree well with the measured parallel overhead.

Multitasking TORT Under UNICOS: Parallel Performance Models and Measurements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Azmy, Y.Y.; Barnett, D.A.

1999-09-27

The existing parallel algorithms in the TORT discrete ordinates were updated to function in a UNI-COS environment. A performance model for the parallel overhead was derived for the existing algorithms. The largest contributors to the parallel overhead were identified and a new algorithm was developed. A parallel overhead model was also derived for the new algorithm. The results of the comparison of parallel performance models were compared to applications of the code to two TORT standard test problems and a large production problem. The parallel performance models agree well with the measured parallel overhead.

Stem biomass, C and N partitioning and growth efficiency of mature pedigreed black spruce on both a wet and a dry site.

Treesearch

John Major; Kurt Johnsen; Debra Barsi; Moira Campbell; John Malcolm

2013-01-01

Worldwide, efforts to manage atmospheric CO2 are being explored both by reducing emissions and by sequestering more carbon (C). Stem biomass, C, and nitrogen (N) parameters were measured in plots of first-generation (F1), 32-year-old black spruce (Picea mariana (Mill.) B.S.P.) from four full-sib families studied previously for drought tolerance and differential...

Shoot water relations of mature black spruce families displaying a genotype x environment interaction in growth rate. II. Temporal trends and response to varying soil water conditions

Treesearch

John E. Major; Kurt H. Johnsen

1999-01-01

Pressure-volume curves and shoot water potentials were determined for black spruce (Picea mariana (Mill.) BSP) trees from four full-sib families at the Petawawa Research Forest, Ontario, Canada. Trees were sampled from a dry site in 1992 and from the dry site and a wet site in 1993. Modulus of elasticity (e ), osmotic potential at...

Shoot water relations of mature black spruce families displaying a genotype x environment interaction in growth rate. I. Family and site effects over three growing seasons

Treesearch

Kurt H. Johnsen; John E Major

1999-01-01

Pressure-volume curves were determined for black spruce (Picea mariana (Mill.) BSP) trees from four full-sib families. During the first two years, trees were measured from a plantation on a dry site. In the third year, trees were sampled from the dry site and a wet site. Diurnal measurements of shoot water potential allowed in situ ...

Black spruce family growth performance under ambient and elevated atmospheric CO2

Treesearch

Kurt H. Johnsen; John E. Major

1998-01-01

Abstract. Seedlings from 20 families of black spruce (Picea mariana (Mill.) B.S.P.), representing a large range in field productivity, were subjected to a greenhouse retrospective test under ambient (409 ppm – year 1, 384 ppm – year 2) and high (686 ppm – year 1, 711 ppm – year 2) atmospheric CO2 environments. After one and two...

MSP-HTPrimer: a high-throughput primer design tool to improve assay design for DNA methylation analysis in epigenetics.

PubMed

Pandey, Ram Vinay; Pulverer, Walter; Kallmeyer, Rainer; Beikircher, Gabriel; Pabinger, Stephan; Kriegner, Albert; Weinhäusel, Andreas

2016-01-01

Bisulfite (BS) conversion-based and methylation-sensitive restriction enzyme (MSRE)-based PCR methods have been the most commonly used techniques for locus-specific DNA methylation analysis. However, both methods have advantages and limitations. Thus, an integrated approach would be extremely useful to quantify the DNA methylation status successfully with great sensitivity and specificity. Designing specific and optimized primers for target regions is the most critical and challenging step in obtaining the adequate DNA methylation results using PCR-based methods. Currently, no integrated, optimized, and high-throughput methylation-specific primer design software methods are available for both BS- and MSRE-based methods. Therefore an integrated, powerful, and easy-to-use methylation-specific primer design pipeline with great accuracy and success rate will be very useful. We have developed a new web-based pipeline, called MSP-HTPrimer, to design primers pairs for MSP, BSP, pyrosequencing, COBRA, and MSRE assays on both genomic strands. First, our pipeline converts all target sequences into bisulfite-treated templates for both forward and reverse strand and designs all possible primer pairs, followed by filtering for single nucleotide polymorphisms (SNPs) and known repeat regions. Next, each primer pairs are annotated with the upstream and downstream RefSeq genes, CpG island, and cut sites (for COBRA and MSRE). Finally, MSP-HTPrimer selects specific primers from both strands based on custom and user-defined hierarchical selection criteria. MSP-HTPrimer produces a primer pair summary output table in TXT and HTML format for display and UCSC custom tracks for resulting primer pairs in GTF format. MSP-HTPrimer is an integrated, web-based, and high-throughput pipeline and has no limitation on the number and size of target sequences and designs MSP, BSP, pyrosequencing, COBRA, and MSRE assays. It is the only pipeline, which automatically designs primers on both genomic strands to increase the success rate. It is a standalone web-based pipeline, which is fully configured within a virtual machine and thus can be readily used without any configuration. We have experimentally validated primer pairs designed by our pipeline and shown a very high success rate of primer pairs: out of 66 BSP primer pairs, 63 were successfully validated without any further optimization step and using the same qPCR conditions. The MSP-HTPrimer pipeline is freely available from http://sourceforge.net/p/msp-htprimer.

Shoot water relations of mature black spruce families displaying a genotype × environment interaction in growth rate. III. Diurnal patterns as influenced by vapor pressure deficit and internal water status

Treesearch

John E. Major; Kurt H. Johnsen

2001-01-01

Pressure­volume curves were constructed and shoot water potentials measured for +20-year-old black spruce (Picea mariana (Mill.) BSP) trees from four full-sib families growing on a moist site and a dry site at the Petawawa Research Forest, Ontario, to determine whether differences in diurnal water relations traits were related to productivity. To...

Chronic Inhalation Toxicity of Unsymmetrical Dimethylhydrazine: Oncogenic Effects

DTIC Science & Technology

1984-10-01

maintained for various time periods postexposure as long as: hamsters, 17 months; mice and rats, 19 months; and dogs , 54 months. The lung was a target organ...Force Base, Ohio R. H. Bruner, Lt Col United States Army BLOCK 18. Subject Terms Peroral Dogs Rats Neoplastic Mice Non-Neoplastic Hamsters BLOCK 19...Abstract An indication of hepatotoxicity in dogs was revealed by transitory elevation in SGPT and BSP values for dogs exposed to 5 ppm. Since the UDMH

Bone sialoprotein keratan sulfate proteoglycan (BSP-KSPG) and FGF-23 are important physiological components of medullary bone.

PubMed

Hadley, Jill A; Horvat-Gordon, Maria; Kim, Woo-Kyun; Praul, Craig A; Burns, Dennis; Leach, Roland M

2016-04-01

Medullary bone is a specialized bone found in the marrow cavity of laying birds. It provides a significant contribution to the calcium supply for egg shell formation. Medullary bone is distinguished from cortical bone by the presence of large amounts of a keratan sulfate proteoglycan (KSPG). The aims of the present experiment are to confirm the identity of the core protein of KSPG, identify a marker of medullary bone metabolism, and determine whether changes in keratan sulfate (KS) concentration in blood are associated with the egg-laying cycle. Using two different isolation techniques- one specific for bone and another for blood- we have identified bone sialoprotein (BSP) to be the core protein of this KSPG. We also determined that the amount of keratan sulfate (KS) in laying hen blood fluctuates in synchrony with the egg-laying cycle, and thus can serve as a specific marker for medullary bone metabolism. During the course of this investigation, we also found FGF-23 (phosphatonin) to be expressed in medullary bone, in synchrony with the egg-laying cycle. Western blotting was used to demonstrate the presence of this peptide in both laying hen blood and medullary bone extracts. The importance of FGF-23 (phosphatonin) and parathyroid hormone in normalizing the dramatic changes in plasma calcium and phosphorus during the 24h egg-laying cycle is discussed. Copyright © 2016 Elsevier Inc. All rights reserved.

The effect of collagen coating on titanium with nanotopography on in vitro osteogenesis.

PubMed

Costa, Daniel G; Ferraz, Emanuela P; Abuna, Rodrigo P F; de Oliveira, Paulo T; Morra, Marco; Beloti, Marcio M; Rosa, Adalberto L

2017-10-01

Several studies have shown the positive effects of Ti either with nanotopography or coated with collagen on osteoblast differentiation. Thus, we hypothesized that the association of nanotopography with collagen may increase the in vitro osteogenesis on Ti surface. Ti discs with nanotopography with or without collagen coating were characterized by scanning electron microscopy and atomic force microscopy. Rat calvaria-derived osteoblastic cells were cultured on both Ti surfaces for up to 14 days and the following parameters were evaluated: cell proliferation, alkaline phosphatase (ALP) activity, extracellular matrix mineralization, protein expression of bone sialoprotein (BSP) and osteopontin (OPN), and gene expression of collagen type 1a (Coll1a), runt-related transcription factor 2 (Runx2), osterix (OSX), osteocalcin (OC), Ki67, Survivin, and Bcl2-associated X protein (BAX). Surface characterization evidenced that collagen coating did not alter the nanotopography. Collagen coating increased cell proliferation, ALP activity, extracellular matrix mineralization, and Coll1a, OSX, OC, and BAX gene expression. Also, OPN and BSP proteins were strongly detected in cultures grown on both Ti surfaces. In conclusion, our results showed that the combination of nanotopography with collagen coating stimulates the early, intermediate, and final events of the in vitro osteogenesis and may be considered a potential approach to promote osseointegration of Ti implants. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 2783-2788, 2017. © 2017 Wiley Periodicals, Inc.

Research Associate | Center for Cancer Research

Cancer.gov

The Basic Science Program (BSP) at the Frederick National Laboratory for Cancer Research (FNLCR) pursues independent, multidisciplinary research programs in basic or applied molecular biology, immunology, retrovirology, cancer biology or human genetics. As part of the BSP, the Microbiome and Genetics Core (the Core) characterizes microbiomes by next-generation sequencing to determine their composition and variation, as influenced by immune, genetic, and host health factors. The Core provides support across a spectrum of processes, from nucleic acid isolation through bioinformatics and statistical analysis. KEY ROLES/RESPONSIBILITIES The Research Associate II will provide support in the areas of automated isolation, preparation, PCR and sequencing of DNA on next generation platforms (Illumina MiSeq and NextSeq). An opportunity exists to join the Core’s team of highly trained experimentalists and bioinformaticians working to characterize microbiome samples. The following represent requirements of the position: A minimum of five (5) years related of biomedical experience. Experience with high-throughput nucleic acid (DNA/RNA) extraction. Experience in performing PCR amplification (including quantitative real-time PCR). Experience or familiarity with robotic liquid handling protocols (especially on the Eppendorf epMotion 5073 or 5075 platforms). Experience in operating and maintaining benchtop Illumina sequencers (MiSeq and NextSeq). Ability to evaluate experimental quality and to troubleshoot molecular biology protocols. Experience with sample tracking, inventory management and biobanking. Ability to operate and communicate effectively in a team-oriented work environment.

Decellularized bone extracellular matrix and human dental pulp stem cells as a construct for bone regeneration.

PubMed

Paduano, Francesco; Marrelli, Massimo; Alom, Noura; Amer, Mahetab; White, Lisa J; Shakesheff, Kevin M; Tatullo, Marco

2017-06-01

Dental pulp tissue represents a source of mesenchymal stem cells that have a strong differentiation potential towards the osteogenic lineage. The objective of the current study was to examine in vitro osteogenic induction of dental pulp stem cells (DPSCs) cultured on hydrogel scaffolds derived from decellularized bone extracellular matrix (bECM) compared to collagen type I (Col-I), the major component of bone matrix. DPSCs in combination with bECM hydrogels were cultured under three different conditions: basal medium, osteogenic medium and medium supplemented with growth factors (GFs) and cell growth, mineral deposition, gene and protein expression were investigated. The DPSCs/bECM hydrogel constructs cultured in basal medium showed that cells were viable after three weeks and that the expression of runt-related transcription factor 2 (RUNX-2) and bone sialoprotein (BSP) were significantly upregulated in the absence of extra osteogenic inducers compared to Col-I hydrogel scaffolds. In addition, the protein expression levels of BSP and osteocalcin were higher on bECM with respect to Col-I hydrogel scaffolds. Furthermore, DPSCs/bECM hydrogels cultured with osteogenic or GFs supplemented medium displayed a higher upregulation of the osteo-specific markers compared to Col-I hydrogels in identical media. Collectively, our results demonstrate that bECM hydrogels might be considered as suitable scaffolds to support osteogenic differentiation of DPSCs.

Validation of methylation-sensitive high-resolution melting (MS-HRM) for the detection of stool DNA methylation in colorectal neoplasms.

PubMed

Xiao, Zhujun; Li, Bingsheng; Wang, Guozhen; Zhu, Weisi; Wang, Zhongqiu; Lin, Jinfeng; Xu, Angao; Wang, Xinying

2014-04-20

Methylation-sensitive high-resolution melting (MS-HRM) is a new technique for assaying DNA methylation, but its feasibility for assaying stool in patients with colorectal cancer (CRC) is unknown. First, the MS-HRM and methylation-specific PCR (MSP) detection limits were tested. Second, the methylation statuses of SFRP2 and VIM were analyzed in stool samples by MS-HRM, and in matching tumor and normal colon tissues via bisulfite sequencing PCR (BSP). Third, a case-control study evaluated the diagnostic sensitivity and specificity of MS-HRM relative to results obtained with MSP and the fecal immunochemical test (FIT). Finally, the linearity and reproducibility of MS-HRM were assessed. The detection limits of MS-HRM and MSP were 1% and 5%, respectively. The diagnostic sensitivities of MS-HRM (87.3%, 55/63) in stool and BSP in matching tumor tissue (92.1%, 58/63) were highly consistent (κ=0.744). The MS-HRM assay detected 92.5% (37/40) methylation in CRCs, 94.4% (34/36) in advanced adenomas, and 8.8% (5/57) in normal controls. The results of MS-HRM analysis were stable and reliable and showed fairly good linearity for both SFRP2 (P<0.001, R(2)=0.957) and VIM (P<0.001, R(2)=0.954). MS-HRM shows potential for CRC screening. Copyright © 2014 Elsevier B.V. All rights reserved.

Real-time segmentation of burst suppression patterns in critical care EEG monitoring

PubMed Central

Westover, M. Brandon; Shafi, Mouhsin M.; Ching, ShiNung; Chemali, Jessica J.; Purdon, Patrick L.; Cash, Sydney S.; Brown, Emery N.

2014-01-01

Objective Develop a real-time algorithm to automatically discriminate suppressions from non-suppressions (bursts) in electroencephalograms of critically ill adult patients. Methods A real-time method for segmenting adult ICU EEG data into bursts and suppressions is presented based on thresholding local voltage variance. Results are validated against manual segmentations by two experienced human electroencephalographers. We compare inter-rater agreement between manual EEG segmentations by experts with inter-rater agreement between human vs automatic segmentations, and investigate the robustness of segmentation quality to variations in algorithm parameter settings. We further compare the results of using these segmentations as input for calculating the burst suppression probability (BSP), a continuous measure of depth-of-suppression. Results Automated segmentation was comparable to manual segmentation, i.e. algorithm-vs-human agreement was comparable to human-vs-human agreement, as judged by comparing raw EEG segmentations or the derived BSP signals. Results were robust to modest variations in algorithm parameter settings. Conclusions Our automated method satisfactorily segments burst suppression data across a wide range adult ICU EEG patterns. Performance is comparable to or exceeds that of manual segmentation by human electroencephalographers. Significance Automated segmentation of burst suppression EEG patterns is an essential component of quantitative brain activity monitoring in critically ill and anesthetized adults. The segmentations produced by our algorithm provide a basis for accurate tracking of suppression depth. PMID:23891828

Real-time segmentation of burst suppression patterns in critical care EEG monitoring.

PubMed

Brandon Westover, M; Shafi, Mouhsin M; Ching, Shinung; Chemali, Jessica J; Purdon, Patrick L; Cash, Sydney S; Brown, Emery N

2013-09-30

Develop a real-time algorithm to automatically discriminate suppressions from non-suppressions (bursts) in electroencephalograms of critically ill adult patients. A real-time method for segmenting adult ICU EEG data into bursts and suppressions is presented based on thresholding local voltage variance. Results are validated against manual segmentations by two experienced human electroencephalographers. We compare inter-rater agreement between manual EEG segmentations by experts with inter-rater agreement between human vs automatic segmentations, and investigate the robustness of segmentation quality to variations in algorithm parameter settings. We further compare the results of using these segmentations as input for calculating the burst suppression probability (BSP), a continuous measure of depth-of-suppression. Automated segmentation was comparable to manual segmentation, i.e. algorithm-vs-human agreement was comparable to human-vs-human agreement, as judged by comparing raw EEG segmentations or the derived BSP signals. Results were robust to modest variations in algorithm parameter settings. Our automated method satisfactorily segments burst suppression data across a wide range adult ICU EEG patterns. Performance is comparable to or exceeds that of manual segmentation by human electroencephalographers. Automated segmentation of burst suppression EEG patterns is an essential component of quantitative brain activity monitoring in critically ill and anesthetized adults. The segmentations produced by our algorithm provide a basis for accurate tracking of suppression depth. Copyright © 2013 Elsevier B.V. All rights reserved.

Effects of sarcoptic mange and its control with oil of Cedrus deodara, Pongamia glabra, Jatropha curcas and benzyl benzoate, both with and without ascorbic acid on growing sheep: assessment of weight gain, liver function, nutrient digestibility, wool production and meat quality.

PubMed

Dimri, U; Sharma, M C

2004-03-01

The aim of this study was to evaluate the therapeutic efficacy of commonly used acaricidal drugs in India and also to assess the effect of ascorbic acid as adjunct therapy in 72 growing sheep with sarcoptic mange, aged 5-6 months and weighing 20.4-31.7 kg. Eight replicates of nine animals were formed based on sex, and day 0 body weight. Drugs were applied locally on the affected parts daily and recovery changes in skin lesions were observed at the time of every application. L-ascorbic acid was administered intramuscularly. Skin scrapings were collected daily from each group and examined for the presence of mites. Body weights were measured every 10th day from day 0 to 60. Nutrient digestiblity was evaluated by studying digestibility coefficients for dry matter, crude protein, ether extract, crude fibre, nitrogen free extract, total carbohydrates and nutrient balance (nitrogen, calcium and phosphorus) for a 30-day period. The liver function was evaluated by bromosulphophthalein (BSP) dye retention time. The animals were shorn on day 60 post-treatment (PT). Meat quality assesment was carried out by killing sheep at 60 days PT and estimating pH, water-holding capacity (WHC), tenderness, muscle colour, rib eye area and fat thickness. The lambs treated with oil of Jatropha curcas ascorbic acid had significantly (P < 0.05) greater mean daily body weight gains (63.29 g) than the infected untreated control (41.10 g). This was also higher than the mean daily weight gain in other treated groups. Infected untreated sheep showed significantly (P < 0.01) reduced digestibility coefficients for dry matter, crude protein, crude fibre, ether extract and total carbohydrate, but no significant differences for nitrogen-free extract. Treated sheep had significantly higher positive nitrogen, calcium and phosphorus balances compared with infested untreated sheep. Oil of J. curcas plus ascorbic acid (OJC-AA) treated group was better over all other treated groups with respect to nutrient digestibility. The BSP test revealed significant (P < 0.05) increase in BSP retention time in sheep with sarcoptic mange. Post -treatment, the BSP retention time decreased in all treated groups and the decrease was maximum in OJC-AA treated group. The carcasses of sheep treated with OJC-AA had significantly (P < 0.01) higher water holding capacity, rib eye area and back fat thickness than the untreated infected control group. The muscle pH and tenderness values were significantly lower in OJC-AA treated group post-slaughter than infested untreated control group. Muscle colour of OJC-AA treated group was maximum bright red. The lambs treated with OJC-AA had significantly (P < 0.05) greater clean fleece weight and fleece yield than the untreated infected group. It is concluded that OJC was the better therapy for sarcoptic mange of sheep and ascorbic acid as adjunct therapy is advisable. OJC-AA therapy may be better from the point of view of improving two most important production parameters in sheep, that is, wool yield and meat production.

Parallelization and automatic data distribution for nuclear reactor simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liebrock, L.M.

1997-07-01

Detailed attempts at realistic nuclear reactor simulations currently take many times real time to execute on high performance workstations. Even the fastest sequential machine can not run these simulations fast enough to ensure that the best corrective measure is used during a nuclear accident to prevent a minor malfunction from becoming a major catastrophe. Since sequential computers have nearly reached the speed of light barrier, these simulations will have to be run in parallel to make significant improvements in speed. In physical reactor plants, parallelism abounds. Fluids flow, controls change, and reactions occur in parallel with only adjacent components directlymore » affecting each other. These do not occur in the sequentialized manner, with global instantaneous effects, that is often used in simulators. Development of parallel algorithms that more closely approximate the real-world operation of a reactor may, in addition to speeding up the simulations, actually improve the accuracy and reliability of the predictions generated. Three types of parallel architecture (shared memory machines, distributed memory multicomputers, and distributed networks) are briefly reviewed as targets for parallelization of nuclear reactor simulation. Various parallelization models (loop-based model, shared memory model, functional model, data parallel model, and a combined functional and data parallel model) are discussed along with their advantages and disadvantages for nuclear reactor simulation. A variety of tools are introduced for each of the models. Emphasis is placed on the data parallel model as the primary focus for two-phase flow simulation. Tools to support data parallel programming for multiple component applications and special parallelization considerations are also discussed.« less

High-Performance Psychometrics: The Parallel-E Parallel-M Algorithm for Generalized Latent Variable Models. Research Report. ETS RR-16-34

ERIC Educational Resources Information Center

von Davier, Matthias

2016-01-01

This report presents results on a parallel implementation of the expectation-maximization (EM) algorithm for multidimensional latent variable models. The developments presented here are based on code that parallelizes both the E step and the M step of the parallel-E parallel-M algorithm. Examples presented in this report include item response…

Scalable Amplification of Strand Subsets from Chip-Synthesized Oligonucleotide Libraries (Open Access)

DTIC Science & Technology

2015-11-16

detailed discussion of barcode designs in Supplementary Note 1, Supplementary Fig. 1 and sequences in Supplementary Note 2). Whereas the nicking and...eight subpools, each as a one- or as a two-barcode version ( design details in Supplementary Note 1). All subpools amplified strands with the expected...for the c2ca designs . We used the same restriction enzymes (Nb.BsrDI and Nt.BspQI) that were encoded between the primers and the target sequences to

Effect of sustained gene delivery of platelet-derived growth factor or its antagonist (PDGF-1308) on tissue-engineered cementum.

PubMed

Anusaksathien, Orasa; Jin, Qiming; Zhao, Ming; Somerman, Martha J; Giannobile, William V

2004-03-01

Cementum, a mineralized tissue lining the tooth root surface, is destroyed during the inflammatory process of periodontitis. Restoration of functional cementum is considered a criterion for successful regeneration of periodontal tissues, including formation of periodontal ligament, cementum, and alveolar bone. Short-term administration of platelet-derived growth factor (PDGF) has been shown to partially regenerate periodontal structures. Nonetheless, the role of PDGF in cementogenesis is not well understood. The aim of the present study was to determine the effect of sustained PDGF gene transfer on cementum formation in an ex vivo ectopic biomineralization model. Osteocalcin (OC) promoter-driven SV40 transgenic mice were used to obtain immortalized cementoblasts (OCCM). The OCCM cells were transduced with adenoviruses (Ad) encoding either PDGF-A, an antagonist of PDGF signaling (PDGF-1308), a control virus (green fluorescent protein, GFP), or no treatment (NT). The transduced cells were incorporated into polymer scaffolds and implanted subcutaneously into severe combined immunodeficient (SCID) mice. The implants were harvested at 3 and 6 weeks for histomorphometric analysis of the newly formed mineralized tissues. Northern blot analysis was performed to determine the expression levels of mineral-associated genes including bone sialoprotein (BSP), OC, and osteopontin (OPN) in the cell-implant specimens at 3 and 6 weeks. The results indicated mineralization was significantly reduced in both the Ad/PDGF-A and Ad/PDGF-1308 treated specimens when compared to the NT or Ad/GFP groups at 3 and 6 weeks (P<0.01). In addition, the size of the implants treated with Ad/PDGF-A and Ad/PDGF-1308 was significantly reduced compared to implants from Ad/GFP and NT groups at 3 weeks (P<0.05). At 6 weeks, the size of implants and mineral formation increased in NT, Ad/GFP, and Ad/PDGF-A groups, while the Ad/PDGF-1308 treated implants continued to decrease in size and mineral formation (P<0.01). Northern blot analysis revealed that in the Ad/PDGF-A treated implants OPN was increased, whereas OC gene expression was downregulated at 3 weeks. In the Ad/PDGF-1308 treated implants, BSP, OC, and OPN were all downregulated at 3 weeks. At 3 weeks, the Ad/PDGF-A treated implants contained significantly higher multinucleated giant cell (MNGC) density compared to NT, Ad/GFP, and Ad/PDGF-1308 specimens. The MNGC density in NT, Ad/GFP, and Ad/PDGF-A treated groups reduced over time, while the Ad/PDGF-1308 transduced implants continued to exhibit significantly higher MNGC density compared with the other treatment groups at 6 weeks. The results showed that continuous exposure to PDGF-A had an inhibitory effect on cementogenesis, possibly via the upregulation of OPN and subsequent enhancement of MNGCs at 3 weeks. On the other hand, Ad/PDGF-1308 inhibited mineralization of tissue-engineered cementum possibly due to the observed downregulation of BSP and OC and a persistence of stimulation of MNGCs. These findings suggest that continuous exogenous delivery of PDGF-A may delay mineral formation induced by cementoblasts, while PDGF is clearly required for mineral neogenesis.

Causes and correlations in cambium phenology: towards an integrated framework of xylogenesis.

PubMed

Rossi, Sergio; Morin, Hubert; Deslauriers, Annie

2012-03-01

Although habitually considered as a whole, xylogenesis is a complex process of division and maturation of a pool of cells where the relationship between the phenological phases generating such a growth pattern remains essentially unknown. This study investigated the causal relationships in cambium phenology of black spruce [Picea mariana (Mill.) BSP] monitored for 8 years on four sites of the boreal forest of Quebec, Canada. The dependency links connecting the timing of xylem cell differentiation and cell production were defined and the resulting causal model was analysed with d-sep tests and generalized mixed models with repeated measurements, and tested with Fisher's C statistics to determine whether and how causality propagates through the measured variables. The higher correlations were observed between the dates of emergence of the first developing cells and between the ending of the differentiation phases, while the number of cells was significantly correlated with all phenological phases. The model with eight dependency links was statistically valid for explaining the causes and correlations between the dynamics of cambium phenology. Causal modelling suggested that the phenological phases involved in xylogenesis are closely interconnected by complex relationships of cause and effect, with the onset of cell differentiation being the main factor directly or indirectly triggering all successive phases of xylem maturation.

Causes and correlations in cambium phenology: towards an integrated framework of xylogenesis

PubMed Central

Rossi, Sergio; Morin, Hubert; Deslauriers, Annie

2012-01-01

Although habitually considered as a whole, xylogenesis is a complex process of division and maturation of a pool of cells where the relationship between the phenological phases generating such a growth pattern remains essentially unknown. This study investigated the causal relationships in cambium phenology of black spruce [Picea mariana (Mill.) BSP] monitored for 8 years on four sites of the boreal forest of Quebec, Canada. The dependency links connecting the timing of xylem cell differentiation and cell production were defined and the resulting causal model was analysed with d-sep tests and generalized mixed models with repeated measurements, and tested with Fisher’s C statistics to determine whether and how causality propagates through the measured variables. The higher correlations were observed between the dates of emergence of the first developing cells and between the ending of the differentiation phases, while the number of cells was significantly correlated with all phenological phases. The model with eight dependency links was statistically valid for explaining the causes and correlations between the dynamics of cambium phenology. Causal modelling suggested that the phenological phases involved in xylogenesis are closely interconnected by complex relationships of cause and effect, with the onset of cell differentiation being the main factor directly or indirectly triggering all successive phases of xylem maturation. PMID:22174441

Characterizing the Late Pleistocene MSA Lithic Technology of Sibudu, KwaZulu-Natal, South Africa

PubMed Central

Will, Manuel; Bader, Gregor D.; Conard, Nicholas J.

2014-01-01

Studies of the African Middle Stone Age (MSA) have become central for defining the cultural adaptations that accompanied the evolution of modern humans. While much of recent research in South Africa has focused on the Still Bay and Howiesons Poort (HP), periods following these technocomplexes were often neglected. Here we examine lithic assemblages from Sibudu that post-date the HP to further the understanding of MSA cultural variability during the Late Pleistocene. Sibudu preserves an exceptionally thick, rich, and high-resolution archaeological sequence that dates to ∼58 ka, which has recently been proposed as type assemblage for the “Sibudan”. This study presents a detailed analysis of the six uppermost lithic assemblages from these deposits (BM-BSP) that we excavated from 2011–2013. We define the key elements of the lithic technology and compare our findings to other assemblages post-dating the HP. The six lithic assemblages provide a distinct and robust cultural signal, closely resembling each other in various technological, techno-functional, techno-economic, and typological characteristics. These results refute assertions that modern humans living after the HP possessed an unstructured and unsophisticated MSA lithic technology. While we observed several parallels with other contemporaneous MSA sites, particularly in the eastern part of southern Africa, the lithic assemblages at Sibudu demonstrate a distinct and so far unique combination of techno-typological traits. Our findings support the use of the Sibudan to help structuring this part of the southern African MSA and emphasize the need for further research to identify the spatial and temporal extent of this proposed cultural unit. PMID:24878544

ErbB2 and bone sialoprotein as markers for metastatic osteosarcoma cells

PubMed Central

Valabrega, G; Fagioli, F; Corso, S; Madon, E; Brach del Prever, A; Biasin, E; Linari, A; Aglietta, M; Giordano, S

2003-01-01

Osteosarcoma is the most common malignant bone neoplasia occurring in young patients in the first two decades of life, and represents 20% of all primitive malignant bone tumours. At present, treatment of metastatic osteosarcoma is unsatisfactory. High-dose chemotherapy followed by CD34+ leukapheresis rescue may improve these poor results. Neoplastic cells contaminating the apheresis may, however, contribute to relapse. To identify markers suitable for detecting osteosarcoma cells in aphereses we analysed the expression of bone-specific genes (Bone Sialoprotein (BSP) and Osteocalcin) and oncogenes (Met and ErbB2) in 22 patients with metastatic osteosarcoma and six healthy stem cell donors. The expression of these genes in aphereses of patients affected by metastatic osteosarcoma was assessed by RT–PCR and Southern blot analysis. Met and Osteocalcin proved to be not useful markers since they are positive in aphereses of both patients with metastatic osteosarcoma and healthy stem cell donors. On the contrary, BSP was expressed at significant levels in 85% of patients. Moreover, 18% of patients showed a strong and significantly positive (seven to 16 times higher than healthy stem cell donors) ErbB2 expression. In all positive cases, neoplastic tissue also expressed ErbB2. Our data show that ErbB2 can be a useful marker for tumour contamination in aphereses of patients affected by ErbB2-expressing osteosarcomas and that analysis of Bone Sialoprotein expression can be an alternative useful marker. PMID:12569382

The National Football League Combine: performance differences between drafted and nondrafted players entering the 2004 and 2005 drafts.

PubMed

Sierer, S Patrick; Battaglini, Claudio L; Mihalik, Jason P; Shields, Edgar W; Tomasini, Nathan T

2008-01-01

The purpose of this study was to examine performance differences between drafted and nondrafted athletes (N = 321) during the 2004 and 2005 National Football League (NFL) Combines. We categorized players into one of 3 groups: Skill, Big skill, and Linemen. Skill players (SP) consisted of wide receivers, cornerbacks, free safeties, strong safeties, and running backs. Big skill players (BSP) included fullbacks, linebackers, tight ends, and defensive ends. Linemen (LM) consisted of centers, offensive guards, offensive tackles, and defensive tackles. We analyzed player height and mass, as well as performance on the following combine drills: 40-yard dash, 225-lb bench press test, vertical jump, broad jump, pro-agility shuttle, and the 3-cone drill. Student t-tests compared performance on each of these measures between drafted and nondrafted players. Statistical significance was found between drafted and nondrafted SP for the 40-yard dash (P < 0.001), vertical jump (P = 0.003), pro-agility shuttle (P < 0.001), and 3-cone drill (P < 0.001). Drafted and nondrafted BSP performed differently on the 40-yard dash (P = 0.002) and 3-cone drill (P = 0.005). Finally, drafted LM performed significantly better than nondrafted LM on the 40-yard dash (P = 0.016), 225-lb bench press (P = 0.003), and 3-cone drill (P = 0.005). Certified strength and conditioning specialists will be able to utilize the significant findings to help better prepare athletes as they ready themselves for the NFL Combine.

Root cementum may modulate gene expression during periodontal regeneration: a preliminary study in humans.

PubMed

Gonçalves, Patricia F; Lima, Liana L; Sallum, Enilson A; Casati, Márcio Z; Nociti, Francisco H

2008-02-01

Previous data demonstrated that root cementum may affect periodontal regeneration. As such, this study aimed to explore further possible mechanisms involved in this process by investigating in humans whether root cementum modulates gene expression in the regenerating tissue formed under membrane-protected intrabony defects. Thirty subjects with deep intrabony defects (> or =5 mm; 2- or 3-wall) were selected and assigned to the control or test group. The control group received scaling and root planing with the removal of granulation tissue and root cementum; the test group underwent removal of granulation tissue and soft microbial deposits by cleaning the root surface with a microbrush and saline solution, aiming at cementum preservation. Guided tissue regeneration (GTR) was applied to both groups. Twenty-one days later, the newly formed tissue under the membrane was assessed for the expression of the following genes: alkaline phosphatase (ALP), osteopontin (OPN), osteocalcin (OCN), platelet-derived growth factor-alpha (PDGFA), bone sialoprotein (BSP), and basic fibroblast growth factor (bFGF). Data analysis demonstrated that mRNA levels for PDGFA, BSP, and bFGF were higher in the sites where root cementum was kept in place compared to the sites where root cementum was removed completely as part of the periodontal therapy (P <0.05); in contrast, OCN levels were lower (P <0.05). No difference for ALP or OPN was observed between the control and test groups (P >0.05). Root cementum may modulate the expression of growth and mineral-associated factors during periodontal regeneration.

Effects of canonical NF-κB signaling pathway on the proliferation and odonto/osteogenic differentiation of human stem cells from apical papilla.

PubMed

Li, Junjun; Yan, Ming; Wang, Zilu; Jing, Shuanglin; Li, Yao; Liu, Genxia; Yu, Jinhua; Fan, Zhipeng

2014-01-01

NF-κB signaling pathway plays a complicated role in the biological functions of mesenchymal stem cells. However, the effects of NF-κB pathway on the odonto/osteogenic differentiation of stem cells from apical papilla (SCAPs) remain unclear. The present study was designed to evaluate the effects of canonical NF-κB pathway on the osteo/odontogenic capacity of SCAPs in vitro. Western blot results demonstrated that NF-κB pathway in SCAPs was successfully activated by TNF-α or blocked by BMS-345541. NF-κB pathway-activated SCAPs presented a higher proliferation activity compared with control groups, as indicated by dimethyl-thiazol-diphenyl tetrazolium bromide assay (MTT) and flow cytometry assay (FCM). Wound scratch assay revealed that NF-κB pathway-activated SCAPs presented an improved migration capacity, enhanced alkaline phosphatase (ALP) activity, and upregulated mineralization capacity of SCAPs, as compared with control groups. Meanwhile, the odonto/osteogenic markers (ALP/ALP, RUNX2/RUNX2, OSX/OSX, OCN/OCN, OPN/OPN, BSP/BSP, DSPP/DSP, and DMP-1/DMP-1) in NF-κB pathway-activated SCAPs were also significantly upregulated as compared with control groups at both protein and mRNA levels. However, NF-κB pathway-inhibited SCAPs exhibited a lower proliferation/migration capacity, and decreased odonto/osteogenic ability in comparison with control groups. Our findings suggest that classical NF-κB pathway plays a paramount role in the proliferation and committed differentiation of SCAPs.

Identification and localization of the bilitranslocase homologue in white grape berries (Vitis vinifera L.) during ripening

PubMed Central

Bertolini, Alberto; Peresson, Carlo; Petrussa, Elisa; Braidot, Enrico; Passamonti, Sabina; Macrì, Francesco; Vianello, Angelo

2009-01-01

A homologue of the mammalian bilirubin transporter bilitranslocase (BTL) (TCDB 2.A.65.1.1), able to perform an apparent secondary active transport of flavonoids, has previously been found in carnation petals and red grape berries. In the present work, a BTL homologue was also shown in white berries from Vitis vinifera L. cv. Tocai/Friulano, using anti-sequence antibodies specific for rat liver BTL. This transporter, similarly to what found in red grape, was localized in the first layers of the epidermal tissue and in the vascular bundle cells of the mesocarp. In addition, a strong immunochemical reaction was detected in the placental tissue and particularly in peripheral integuments of the seed. The protein was expressed during the last maturation stages in both skin and pulp tissues and exhibited an apparent molecular mass of c. 31 kDa. Furthermore, the transport activity of such a carrier, measured as bromosulphophthalein (BSP) uptake, was detected in berry pulp microsomes, where it was inhibited by specific anti-BTL antibodies. The BTL homologue activity exhibited higher values, for both Km and Vmax, than those found in the red cultivar. Moreover, two non-pigmented flavonoids, such as quercetin (a flavonol) and eriodictyol (a flavanone), inhibited the uptake of BSP in an uncompetitive manner. Such results strengthen the hypothesis that this BTL homologue acts as a carrier involved also in the membrane transport of colourless flavonoids and demonstrate the presence of such a carrier in different organs and tissues. PMID:19596699

Physical properties and biological effects of mineral trioxide aggregate mixed with methylcellulose and calcium chloride.

PubMed

Lee, Bin-Na; Chun, Soo-Ji; Chang, Hoon-Sang; Hwang, Yun-Chan; Hwang, In-Nam; Oh, Won-Mann

2017-01-01

Methylcellulose (MC) is a chemical compound derived from cellulose. MTA mixed with MC reduces setting time and increases plasticity. This study assessed the influence of MC as an anti-washout ingredient and CaCl2 as a setting time accelerator on the physical and biological properties of MTA. Test materials were divided into 3 groups; Group 1(control): distilled water; Group 2: 1% MC/CaCl2; Group 3: 2% MC/CaCl2. Compressive strength, pH, flowability and cell viability were tested. The gene expression of bone sialoprotein (BSP) was detected by RT-PCR and real- time PCR. The expression of alkaline phosphatase (ALP) and mineralization behavior were evaluated using an ALP staining and an alizarin red staining. Compressive strength, pH, and cell viability of MTA mixed with MC/CaCl2 were not significantly different compared to the control group. The flowability of MTA with MC/CaCI2 has decreased significantly when compared to the control (p<.05). The mRNA level of BSP has increased significantly in MTA with MC/CaCl2 compared to the control (p<.05). This study revealed higher expression of ALP and mineralization in cells exposed to MTA mixed with water and MTA mixed with MC/CaCl2 compared to the control (p<.05). MC decreased the flowability of MTA and did not interrupt the physical and biological effect of MTA. It suggests that these cements may be useful as a root-end filling material.

Collaborative study for the calibration of replacement batches for the heparin low-molecular-mass for assay biological reference preparation.

PubMed

Terao, E; Daas, A

2016-01-01

The European Pharmacopoeia (Ph. Eur.) prescribes the control of the activity of low molecular mass heparins by assays for anti-Xa and anti-IIa activities (monograph 0828), using a reference standard calibrated in International Units (IU). An international collaborative study coded BSP133 was launched in the framework of the Biological Standardisation Programme (BSP) run under the aegis of the Council of Europe and the European Commission to calibrate replacement batches for the dwindling stocks of the Heparin low-molecular-mass for assay Biological Reference Preparation (BRP) batch 8. Thirteen official medicines control and manufacturers laboratories from European and non-European countries took part in this study to calibrate two freeze-dried candidate batches against the 3rd International Standard (IS) for heparin, low molecular weight (11/176; 3rd IS). The Heparin low-molecular-mass for assay BRP (batch 8) was also included in the test panel to check the continuity between subsequent BRP batches. Taking into account the stability data, the results of this collaborative study and on the basis of the central statistical analysis performed at the European Directorate for the Quality of Medicines & HealthCare (EDQM), the 2 candidate batches were officially adopted by the Commission of the European Pharmacopoeia as Heparin low-molecular-mass for assay BRP batches 9 and 10 with assigned anti-Xa activities of 102 and 100 IU/vial and anti-IIa activities of 34 and 33 IU/vial respectively.

Parallelization of fine-scale computation in Agile Multiscale Modelling Methodology

NASA Astrophysics Data System (ADS)

Macioł, Piotr; Michalik, Kazimierz

2016-10-01

Nowadays, multiscale modelling of material behavior is an extensively developed area. An important obstacle against its wide application is high computational demands. Among others, the parallelization of multiscale computations is a promising solution. Heterogeneous multiscale models are good candidates for parallelization, since communication between sub-models is limited. In this paper, the possibility of parallelization of multiscale models based on Agile Multiscale Methodology framework is discussed. A sequential, FEM based macroscopic model has been combined with concurrently computed fine-scale models, employing a MatCalc thermodynamic simulator. The main issues, being investigated in this work are: (i) the speed-up of multiscale models with special focus on fine-scale computations and (ii) on decreasing the quality of computations enforced by parallel execution. Speed-up has been evaluated on the basis of Amdahl's law equations. The problem of `delay error', rising from the parallel execution of fine scale sub-models, controlled by the sequential macroscopic sub-model is discussed. Some technical aspects of combining third-party commercial modelling software with an in-house multiscale framework and a MPI library are also discussed.

Performance Modeling and Measurement of Parallelized Code for Distributed Shared Memory Multiprocessors

NASA Technical Reports Server (NTRS)

Waheed, Abdul; Yan, Jerry

1998-01-01

This paper presents a model to evaluate the performance and overhead of parallelizing sequential code using compiler directives for multiprocessing on distributed shared memory (DSM) systems. With increasing popularity of shared address space architectures, it is essential to understand their performance impact on programs that benefit from shared memory multiprocessing. We present a simple model to characterize the performance of programs that are parallelized using compiler directives for shared memory multiprocessing. We parallelized the sequential implementation of NAS benchmarks using native Fortran77 compiler directives for an Origin2000, which is a DSM system based on a cache-coherent Non Uniform Memory Access (ccNUMA) architecture. We report measurement based performance of these parallelized benchmarks from four perspectives: efficacy of parallelization process; scalability; parallelization overhead; and comparison with hand-parallelized and -optimized version of the same benchmarks. Our results indicate that sequential programs can conveniently be parallelized for DSM systems using compiler directives but realizing performance gains as predicted by the performance model depends primarily on minimizing architecture-specific data locality overhead.

Parallel computation for biological sequence comparison: comparing a portable model to the native model for the Intel Hypercube.

PubMed

Nadkarni, P M; Miller, P L

1991-01-01

A parallel program for inter-database sequence comparison was developed on the Intel Hypercube using two models of parallel programming. One version was built using machine-specific Hypercube parallel programming commands. The other version was built using Linda, a machine-independent parallel programming language. The two versions of the program provide a case study comparing these two approaches to parallelization in an important biological application area. Benchmark tests with both programs gave comparable results with a small number of processors. As the number of processors was increased, the Linda version was somewhat less efficient. The Linda version was also run without change on Network Linda, a virtual parallel machine running on a network of desktop workstations.

Anatomically constrained neural network models for the categorization of facial expression

NASA Astrophysics Data System (ADS)

McMenamin, Brenton W.; Assadi, Amir H.

2004-12-01

The ability to recognize facial expression in humans is performed with the amygdala which uses parallel processing streams to identify the expressions quickly and accurately. Additionally, it is possible that a feedback mechanism may play a role in this process as well. Implementing a model with similar parallel structure and feedback mechanisms could be used to improve current facial recognition algorithms for which varied expressions are a source for error. An anatomically constrained artificial neural-network model was created that uses this parallel processing architecture and feedback to categorize facial expressions. The presence of a feedback mechanism was not found to significantly improve performance for models with parallel architecture. However the use of parallel processing streams significantly improved accuracy over a similar network that did not have parallel architecture. Further investigation is necessary to determine the benefits of using parallel streams and feedback mechanisms in more advanced object recognition tasks.

Anatomically constrained neural network models for the categorization of facial expression

NASA Astrophysics Data System (ADS)

McMenamin, Brenton W.; Assadi, Amir H.

2005-01-01

The ability to recognize facial expression in humans is performed with the amygdala which uses parallel processing streams to identify the expressions quickly and accurately. Additionally, it is possible that a feedback mechanism may play a role in this process as well. Implementing a model with similar parallel structure and feedback mechanisms could be used to improve current facial recognition algorithms for which varied expressions are a source for error. An anatomically constrained artificial neural-network model was created that uses this parallel processing architecture and feedback to categorize facial expressions. The presence of a feedback mechanism was not found to significantly improve performance for models with parallel architecture. However the use of parallel processing streams significantly improved accuracy over a similar network that did not have parallel architecture. Further investigation is necessary to determine the benefits of using parallel streams and feedback mechanisms in more advanced object recognition tasks.

Parallel and Preemptable Dynamically Dimensioned Search Algorithms for Single and Multi-objective Optimization in Water Resources

NASA Astrophysics Data System (ADS)

Tolson, B.; Matott, L. S.; Gaffoor, T. A.; Asadzadeh, M.; Shafii, M.; Pomorski, P.; Xu, X.; Jahanpour, M.; Razavi, S.; Haghnegahdar, A.; Craig, J. R.

2015-12-01

We introduce asynchronous parallel implementations of the Dynamically Dimensioned Search (DDS) family of algorithms including DDS, discrete DDS, PA-DDS and DDS-AU. These parallel algorithms are unique from most existing parallel optimization algorithms in the water resources field in that parallel DDS is asynchronous and does not require an entire population (set of candidate solutions) to be evaluated before generating and then sending a new candidate solution for evaluation. One key advance in this study is developing the first parallel PA-DDS multi-objective optimization algorithm. The other key advance is enhancing the computational efficiency of solving optimization problems (such as model calibration) by combining a parallel optimization algorithm with the deterministic model pre-emption concept. These two efficiency techniques can only be combined because of the asynchronous nature of parallel DDS. Model pre-emption functions to terminate simulation model runs early, prior to completely simulating the model calibration period for example, when intermediate results indicate the candidate solution is so poor that it will definitely have no influence on the generation of further candidate solutions. The computational savings of deterministic model preemption available in serial implementations of population-based algorithms (e.g., PSO) disappear in synchronous parallel implementations as these algorithms. In addition to the key advances above, we implement the algorithms across a range of computation platforms (Windows and Unix-based operating systems from multi-core desktops to a supercomputer system) and package these for future modellers within a model-independent calibration software package called Ostrich as well as MATLAB versions. Results across multiple platforms and multiple case studies (from 4 to 64 processors) demonstrate the vast improvement over serial DDS-based algorithms and highlight the important role model pre-emption plays in the performance of parallel, pre-emptable DDS algorithms. Case studies include single- and multiple-objective optimization problems in water resources model calibration and in many cases linear or near linear speedups are observed.

Serial vs. parallel models of attention in visual search: accounting for benchmark RT-distributions.

PubMed

Moran, Rani; Zehetleitner, Michael; Liesefeld, Heinrich René; Müller, Hermann J; Usher, Marius

2016-10-01

Visual search is central to the investigation of selective visual attention. Classical theories propose that items are identified by serially deploying focal attention to their locations. While this accounts for set-size effects over a continuum of task difficulties, it has been suggested that parallel models can account for such effects equally well. We compared the serial Competitive Guided Search model with a parallel model in their ability to account for RT distributions and error rates from a large visual search data-set featuring three classical search tasks: 1) a spatial configuration search (2 vs. 5); 2) a feature-conjunction search; and 3) a unique feature search (Wolfe, Palmer & Horowitz Vision Research, 50(14), 1304-1311, 2010). In the parallel model, each item is represented by a diffusion to two boundaries (target-present/absent); the search corresponds to a parallel race between these diffusors. The parallel model was highly flexible in that it allowed both for a parametric range of capacity-limitation and for set-size adjustments of identification boundaries. Furthermore, a quit unit allowed for a continuum of search-quitting policies when the target is not found, with "single-item inspection" and exhaustive searches comprising its extremes. The serial model was found to be superior to the parallel model, even before penalizing the parallel model for its increased complexity. We discuss the implications of the results and the need for future studies to resolve the debate.

Parallelized CCHE2D flow model with CUDA Fortran on Graphics Process Units

USDA-ARS?s Scientific Manuscript database

This paper presents the CCHE2D implicit flow model parallelized using CUDA Fortran programming technique on Graphics Processing Units (GPUs). A parallelized implicit Alternating Direction Implicit (ADI) solver using Parallel Cyclic Reduction (PCR) algorithm on GPU is developed and tested. This solve...

Examining Parallelism of Sets of Psychometric Measures Using Latent Variable Modeling

ERIC Educational Resources Information Center

Raykov, Tenko; Patelis, Thanos; Marcoulides, George A.

2011-01-01

A latent variable modeling approach that can be used to examine whether several psychometric tests are parallel is discussed. The method consists of sequentially testing the properties of parallel measures via a corresponding relaxation of parameter constraints in a saturated model or an appropriately constructed latent variable model. The…

Osterix Controls Cementoblast Differentiation through Downregulation of Wnt-signaling via Enhancing DKK1 Expression

PubMed Central

Cao, Zhengguo; Liu, Rubing; Zhang, Hua; Liao, Haiqing; Zhang, Yufeng; Hinton, Robert J.; Feng, Jian Q.

2015-01-01

Osterix (Osx), a transcriptional factor essential for osteogenesis, is also critical for in vivo cellular cementum formation. However, the molecular mechanism by which Osx regulates cementoblasts is largely unknown. In this study, we initially demonstrated that overexpression of Osx in a cementoblast cell line upregulated the expression of markers vital to cementogenesis such as osteopontin (OPN), osteocalcin (OCN), and bone sialoprotein (BSP) at both mRNA and protein levels, and enhanced alkaline phosphatase (ALP) activity. Unexpectedly, we demonstrated a sharp increase in the expression of DKK1 (a potent canonical Wnt antagonist), and a great reduction in protein levels of β-catenin and its nuclear translocation by overexpression of Osx. Further, transient transfection of Osx reduced protein levels of TCF1 (a target transcription factor of β-catenin), which were partially reversed by an addition of DKK1. We also demonstrated that activation of canonical Wnt signaling by LiCl or Wnt3a significantly enhanced levels of TCF1 and suppressed the expression of OPN, OCN, and BSP, as well as ALP activity and formation of extracellular mineralized nodules. Importantly, we confirmed that there were a sharp reduction in DKK1 and a concurrent increase in β-catenin in Osx cKO mice (crossing between the Osx loxP and 2.3 Col 1-Cre lines), in agreement with the in vitro data. Thus, we conclude that the key role of Osx in control of cementoblast proliferation and differentiation is to maintain a low level of Wnt-β-catenin via direct up-regulation of DKK1. PMID:25678852

Isolation and characterization of multipotent human periodontal ligament stem cells.

PubMed

Gay, I C; Chen, S; MacDougall, M

2007-08-01

Periodontal ligament (PDL) repair is thought to involve mesenchymal progenitor cells capable of forming fibroblasts, osteoblasts and cementoblasts. However, full characterization of PDL stem cell (SC) populations has not been achieved. To isolate and characterize PDLSC and assess their capability to differentiate into bone, cartilage and adipose tissue. Human PDL cells were stained for STRO-1, FACS sorted and expanded in culture. Human bone marrow SC (BMSC) served as a positive control. PDLSC and BMSC were cultured using standard conditions conducive for osteogenic, chondrogenic and adipogenic differentiation. Osteogenic induction was assayed using alizarine red S staining and expression of alkaline phosphatase (ALP) and bone sialoprotein (BSP). Adipogenic induction was assayed using Oil Red O staining and the expression of PPAR gamma 2 (early) and LPL (late) adipogenic markers. Chondrogenic induction was assayed by collagen type II expression and toluidine blue staining. Human PDL tissue contains about 27% STRO-1 positive cells with 3% strongly positive. In osteogenic cultures ALP was observed by day-7 in BMSC and day-14 in PDLSC. BSP expression was detectable by day-7; with more intense staining in PDLSC cultures. In adipogenic cultures both cell populations showed positive Oil Red O staining by day-25 with PPAR gamma 2 and LPL expression. By day-21, both BMSC and PDLSC chondrogenic induced cultures expressed collagen type II and glycosaminoglycans. The PDL contains SC that have the potential to differentiate into osteoblasts, chondrocytes and adipocytes, comparable with previously characterized BMSC. This adult PDLSC population can be utilized for potential therapeutic procedures related to PDL regeneration.

Naringin promotes osteogenic differentiation of bone marrow stromal cells by up-regulating Foxc2 expression via the IHH signaling pathway

PubMed Central

Lin, Fei-xiang; Du, Shi-xin; Liu, De-zhong; Hu, Qin-xiao; Yu, Guo-yong; Wu, Chu-cheng; Zheng, Gui-zhou; Xie, Da; Li, Xue-dong; Chang, Bo

2016-01-01

Naringin is an active compound extracted from Rhizoma Drynariae, and studies have revealed that naringin can promote proliferation and osteogenic differentiation of bone marrow stromal cells (BMSCs). In this study, we explored whether naringin could promote osteogenic differentiation of BMSCs by upregulating Foxc2 expression via the Indian hedgehog (IHH) signaling pathway. BMSCs were cultured in basal medium, basal medium with naringin, osteogenic induction medium, osteogenic induction medium with naringin and osteogenic induction medium with naringin in the presence of the IHH inhibitor cyclopamine (CPE). We examined cell proliferation by using a WST-8 assay, and differentiation by Alizarin Red S staining (for mineralization) and alkaline phosphatase (ALP) activity. In addition, we detected core-binding factor α1 (Cbfα1), osteocalcin (OCN), bone sialoprotein (BSP), peroxisome proliferation-activated receptor gamma 2 (PPARγ2) and Foxc2 expression by using RT-PCR. We also determined Foxc2 and IHH protein levels by western blotting. Naringin increased the mineralization of BMSCs, as shown by Alizarin red S assays, and induced ALP activity. In addition, naringin significantly increased the mRNA levels of Foxc2, Cbfα1, OCN, and BSP, while decreasing PPARγ2 mRNA levels. Furthermore, the IHH inhibitor CPE inhibited the osteogenesis-potentiating effects of naringin. Naringin increased Foxc2 and stimulated the activation of IHH, as evidenced by increased expression of proteins that were inhibited by CPE. Our findings indicate that naringin promotes osteogenic differentiation of BMSCs by up-regulating Foxc2 expression via the IHH signaling pathway. PMID:27904711

Effects of Canonical NF-κB Signaling Pathway on the Proliferation and Odonto/Osteogenic Differentiation of Human Stem Cells from Apical Papilla

PubMed Central

Li, Junjun; Yan, Ming; Wang, Zilu; Jing, Shuanglin; Li, Yao; Liu, Genxia; Yu, Jinhua; Fan, Zhipeng

2014-01-01

Background Information. NF-κB signaling pathway plays a complicated role in the biological functions of mesenchymal stem cells. However, the effects of NF-κB pathway on the odonto/osteogenic differentiation of stem cells from apical papilla (SCAPs) remain unclear. The present study was designed to evaluate the effects of canonical NF-κB pathway on the osteo/odontogenic capacity of SCAPs in vitro. Results. Western blot results demonstrated that NF-κB pathway in SCAPs was successfully activated by TNF-α or blocked by BMS-345541. NF-κB pathway-activated SCAPs presented a higher proliferation activity compared with control groups, as indicated by dimethyl-thiazol-diphenyl tetrazolium bromide assay (MTT) and flow cytometry assay (FCM). Wound scratch assay revealed that NF-κB pathway-activated SCAPs presented an improved migration capacity, enhanced alkaline phosphatase (ALP) activity, and upregulated mineralization capacity of SCAPs, as compared with control groups. Meanwhile, the odonto/osteogenic markers (ALP/ALP, RUNX2/RUNX2, OSX/OSX, OCN/OCN, OPN/OPN, BSP/BSP, DSPP/DSP, and DMP-1/DMP-1) in NF-κB pathway-activated SCAPs were also significantly upregulated as compared with control groups at both protein and mRNA levels. However, NF-κB pathway-inhibited SCAPs exhibited a lower proliferation/migration capacity, and decreased odonto/osteogenic ability in comparison with control groups. Conclusion. Our findings suggest that classical NF-κB pathway plays a paramount role in the proliferation and committed differentiation of SCAPs. PMID:24864235

Naringin promotes osteogenic differentiation of bone marrow stromal cells by up-regulating Foxc2 expression via the IHH signaling pathway.

PubMed

Lin, Fei-Xiang; Du, Shi-Xin; Liu, De-Zhong; Hu, Qin-Xiao; Yu, Guo-Yong; Wu, Chu-Cheng; Zheng, Gui-Zhou; Xie, Da; Li, Xue-Dong; Chang, Bo

2016-01-01

Naringin is an active compound extracted from Rhizoma Drynariae, and studies have revealed that naringin can promote proliferation and osteogenic differentiation of bone marrow stromal cells (BMSCs). In this study, we explored whether naringin could promote osteogenic differentiation of BMSCs by upregulating Foxc2 expression via the Indian hedgehog (IHH) signaling pathway. BMSCs were cultured in basal medium, basal medium with naringin, osteogenic induction medium, osteogenic induction medium with naringin and osteogenic induction medium with naringin in the presence of the IHH inhibitor cyclopamine (CPE). We examined cell proliferation by using a WST-8 assay, and differentiation by Alizarin Red S staining (for mineralization) and alkaline phosphatase (ALP) activity. In addition, we detected core-binding factor α1 (Cbfα1), osteocalcin (OCN), bone sialoprotein (BSP), peroxisome proliferation-activated receptor gamma 2 (PPARγ2) and Foxc2 expression by using RT-PCR. We also determined Foxc2 and IHH protein levels by western blotting. Naringin increased the mineralization of BMSCs, as shown by Alizarin red S assays, and induced ALP activity. In addition, naringin significantly increased the mRNA levels of Foxc2, Cbfα1, OCN, and BSP, while decreasing PPARγ2 mRNA levels. Furthermore, the IHH inhibitor CPE inhibited the osteogenesis-potentiating effects of naringin. Naringin increased Foxc2 and stimulated the activation of IHH, as evidenced by increased expression of proteins that were inhibited by CPE. Our findings indicate that naringin promotes osteogenic differentiation of BMSCs by up-regulating Foxc2 expression via the IHH signaling pathway.

Fibrin gel improves tissue ingrowth and cell differentiation in human immature premolars implanted in rats.

PubMed

Ruangsawasdi, Nisarat; Zehnder, Matthias; Weber, Franz E

2014-02-01

In pulpless immature human premolars implanted in rodents, this study investigated whether fibrin gel offered advantages over leaving the root canal empty regarding soft tissue ingrowth and cell differentiation. Root canals of extracted human immature premolars (n = 12) were accessed and then irrigated with 5% sodium hypochlorite followed by 17% ethylenediaminetetraacetic acid. Root canals were then either left empty or filled with a fibrin gel (n = 6 each) before being placed subcutaneously on top of the calvarial bone of rats (1 tooth per rat) for 12 weeks. After sacrifice, teeth were histologically assessed. Tissue ingrowth was quantified and compared between groups using the Mann-Whitney U test (P < .05). Cells adhering to the pulp canal wall were immunohistochemically screened for the presence of bone sialoprotein (BSP) and dentin sialoprotein (DSP). More tissue grew into the pulp space when teeth were filled with fibrin gel (P < .05). The presence of fibrin gel affected not only the extent of tissue ingrowth but also tissue morphology and differentiation of cells contacting the dentinal wall. In the fibrin gel group, newly formed tissue was similar to normal pulp, constituted of inner pulp, cell-rich zone, cell-free zone, and an apparent odontoblast layer, which stained positive for BSP and DSP. Newly formed blood vessels were also more abundant compared with the initially empty root canals. Under the conditions of this study, fibrin gel improved cell infiltration and cell-dentin interaction. Both are necessary for pulp tissue regeneration. Copyright © 2014 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Parallel computation for biological sequence comparison: comparing a portable model to the native model for the Intel Hypercube.

PubMed Central

Nadkarni, P. M.; Miller, P. L.

1991-01-01

A parallel program for inter-database sequence comparison was developed on the Intel Hypercube using two models of parallel programming. One version was built using machine-specific Hypercube parallel programming commands. The other version was built using Linda, a machine-independent parallel programming language. The two versions of the program provide a case study comparing these two approaches to parallelization in an important biological application area. Benchmark tests with both programs gave comparable results with a small number of processors. As the number of processors was increased, the Linda version was somewhat less efficient. The Linda version was also run without change on Network Linda, a virtual parallel machine running on a network of desktop workstations. PMID:1807632

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chrisochoides, N.; Sukup, F.

In this paper we present a parallel implementation of the Bowyer-Watson (BW) algorithm using the task-parallel programming model. The BW algorithm constitutes an ideal mesh refinement strategy for implementing a large class of unstructured mesh generation techniques on both sequential and parallel computers, by preventing the need for global mesh refinement. Its implementation on distributed memory multicomputes using the traditional data-parallel model has been proven very inefficient due to excessive synchronization needed among processors. In this paper we demonstrate that with the task-parallel model we can tolerate synchronization costs inherent to data-parallel methods by exploring concurrency in the processor level.more » Our preliminary performance data indicate that the task- parallel approach: (i) is almost four times faster than the existing data-parallel methods, (ii) scales linearly, and (iii) introduces minimum overheads compared to the {open_quotes}best{close_quotes} sequential implementation of the BW algorithm.« less

Modelling parallel programs and multiprocessor architectures with AXE

NASA Technical Reports Server (NTRS)

Yan, Jerry C.; Fineman, Charles E.

1991-01-01

AXE, An Experimental Environment for Parallel Systems, was designed to model and simulate for parallel systems at the process level. It provides an integrated environment for specifying computation models, multiprocessor architectures, data collection, and performance visualization. AXE is being used at NASA-Ames for developing resource management strategies, parallel problem formulation, multiprocessor architectures, and operating system issues related to the High Performance Computing and Communications Program. AXE's simple, structured user-interface enables the user to model parallel programs and machines precisely and efficiently. Its quick turn-around time keeps the user interested and productive. AXE models multicomputers. The user may easily modify various architectural parameters including the number of sites, connection topologies, and overhead for operating system activities. Parallel computations in AXE are represented as collections of autonomous computing objects known as players. Their use and behavior is described. Performance data of the multiprocessor model can be observed on a color screen. These include CPU and message routing bottlenecks, and the dynamic status of the software.

Ecophysiological modeling of photosynthesis and carbon allocation to the tree stem in the boreal forest

NASA Astrophysics Data System (ADS)

Gennaretti, Fabio; Gea-Izquierdo, Guillermo; Boucher, Etienne; Berninger, Frank; Arseneault, Dominique; Guiot, Joel

2017-11-01

A better understanding of the coupling between photosynthesis and carbon allocation in the boreal forest, together with its associated environmental factors and mechanistic rules, is crucial to accurately predict boreal forest carbon stocks and fluxes, which are significant components of the global carbon budget. Here, we adapted the MAIDEN ecophysiological forest model to consider important processes for boreal tree species, such as nonlinear acclimation of photosynthesis to temperature changes, canopy development as a function of previous-year climate variables influencing bud formation and the temperature dependence of carbon partition in summer. We tested these modifications in the eastern Canadian taiga using black spruce (Picea mariana (Mill.) B.S.P.) gross primary production and ring width data. MAIDEN explains 90 % of the observed daily gross primary production variability, 73 % of the annual ring width variability and 20-30 % of its high-frequency component (i.e., when decadal trends are removed). The positive effect on stem growth due to climate warming over the last several decades is well captured by the model. In addition, we illustrate how we improve the model with each introduced model adaptation and compare the model results with those of linear response functions. Our results demonstrate that MAIDEN simulates robust relationships with the most important climate variables (those detected by classical response-function analysis) and is a powerful tool for understanding how environmental factors interact with black spruce ecophysiology to influence present-day and future boreal forest carbon fluxes.

Parallel computing of a climate model on the dawn 1000 by domain decomposition method

NASA Astrophysics Data System (ADS)

Bi, Xunqiang

1997-12-01

In this paper the parallel computing of a grid-point nine-level atmospheric general circulation model on the Dawn 1000 is introduced. The model was developed by the Institute of Atmospheric Physics (IAP), Chinese Academy of Sciences (CAS). The Dawn 1000 is a MIMD massive parallel computer made by National Research Center for Intelligent Computer (NCIC), CAS. A two-dimensional domain decomposition method is adopted to perform the parallel computing. The potential ways to increase the speed-up ratio and exploit more resources of future massively parallel supercomputation are also discussed.

Using Hadoop MapReduce for Parallel Genetic Algorithms: A Comparison of the Global, Grid and Island Models.

PubMed

Ferrucci, Filomena; Salza, Pasquale; Sarro, Federica

2017-06-29

The need to improve the scalability of Genetic Algorithms (GAs) has motivated the research on Parallel Genetic Algorithms (PGAs), and different technologies and approaches have been used. Hadoop MapReduce represents one of the most mature technologies to develop parallel algorithms. Based on the fact that parallel algorithms introduce communication overhead, the aim of the present work is to understand if, and possibly when, the parallel GAs solutions using Hadoop MapReduce show better performance than sequential versions in terms of execution time. Moreover, we are interested in understanding which PGA model can be most effective among the global, grid, and island models. We empirically assessed the performance of these three parallel models with respect to a sequential GA on a software engineering problem, evaluating the execution time and the achieved speedup. We also analysed the behaviour of the parallel models in relation to the overhead produced by the use of Hadoop MapReduce and the GAs' computational effort, which gives a more machine-independent measure of these algorithms. We exploited three problem instances to differentiate the computation load and three cluster configurations based on 2, 4, and 8 parallel nodes. Moreover, we estimated the costs of the execution of the experimentation on a potential cloud infrastructure, based on the pricing of the major commercial cloud providers. The empirical study revealed that the use of PGA based on the island model outperforms the other parallel models and the sequential GA for all the considered instances and clusters. Using 2, 4, and 8 nodes, the island model achieves an average speedup over the three datasets of 1.8, 3.4, and 7.0 times, respectively. Hadoop MapReduce has a set of different constraints that need to be considered during the design and the implementation of parallel algorithms. The overhead of data store (i.e., HDFS) accesses, communication, and latency requires solutions that reduce data store operations. For this reason, the island model is more suitable for PGAs than the global and grid model, also in terms of costs when executed on a commercial cloud provider.

System and method for representing and manipulating three-dimensional objects on massively parallel architectures

DOEpatents

Karasick, Michael S.; Strip, David R.

1996-01-01

A parallel computing system is described that comprises a plurality of uniquely labeled, parallel processors, each processor capable of modelling a three-dimensional object that includes a plurality of vertices, faces and edges. The system comprises a front-end processor for issuing a modelling command to the parallel processors, relating to a three-dimensional object. Each parallel processor, in response to the command and through the use of its own unique label, creates a directed-edge (d-edge) data structure that uniquely relates an edge of the three-dimensional object to one face of the object. Each d-edge data structure at least includes vertex descriptions of the edge and a description of the one face. As a result, each processor, in response to the modelling command, operates upon a small component of the model and generates results, in parallel with all other processors, without the need for processor-to-processor intercommunication.

Fast hydrological model calibration based on the heterogeneous parallel computing accelerated shuffled complex evolution method

NASA Astrophysics Data System (ADS)

Kan, Guangyuan; He, Xiaoyan; Ding, Liuqian; Li, Jiren; Hong, Yang; Zuo, Depeng; Ren, Minglei; Lei, Tianjie; Liang, Ke

2018-01-01

Hydrological model calibration has been a hot issue for decades. The shuffled complex evolution method developed at the University of Arizona (SCE-UA) has been proved to be an effective and robust optimization approach. However, its computational efficiency deteriorates significantly when the amount of hydrometeorological data increases. In recent years, the rise of heterogeneous parallel computing has brought hope for the acceleration of hydrological model calibration. This study proposed a parallel SCE-UA method and applied it to the calibration of a watershed rainfall-runoff model, the Xinanjiang model. The parallel method was implemented on heterogeneous computing systems using OpenMP and CUDA. Performance testing and sensitivity analysis were carried out to verify its correctness and efficiency. Comparison results indicated that heterogeneous parallel computing-accelerated SCE-UA converged much more quickly than the original serial version and possessed satisfactory accuracy and stability for the task of fast hydrological model calibration.

Molecular Genetic Studies of Bone Mechanical Strain and of Pedigrees with Very High Bone Density

DTIC Science & Technology

2007-11-01

regulating the expression of BSP. 17 0-25 Map3k4 Clcn7 Thbs2 Traf7 Tnf Notch3 Vegfa Runx2 Involved in normal skeletal patterning. Critical for...Chrs cM Genes 8 38–69 Ptger1 Junb Mt1, 2 Cdh11 Hsd11b2 Cdh1 Cbfb Hsd17b2 Il17c 16 30–46 Col8a1 EphA3 Pit1 17 0–25 Map3k4 Clcn7 Thbs2 Traf7 Tnf Notch3

Iterative algorithms for large sparse linear systems on parallel computers

NASA Technical Reports Server (NTRS)

Adams, L. M.

1982-01-01

Algorithms for assembling in parallel the sparse system of linear equations that result from finite difference or finite element discretizations of elliptic partial differential equations, such as those that arise in structural engineering are developed. Parallel linear stationary iterative algorithms and parallel preconditioned conjugate gradient algorithms are developed for solving these systems. In addition, a model for comparing parallel algorithms on array architectures is developed and results of this model for the algorithms are given.

Parallel Markov chain Monte Carlo - bridging the gap to high-performance Bayesian computation in animal breeding and genetics.

PubMed

Wu, Xiao-Lin; Sun, Chuanyu; Beissinger, Timothy M; Rosa, Guilherme Jm; Weigel, Kent A; Gatti, Natalia de Leon; Gianola, Daniel

2012-09-25

Most Bayesian models for the analysis of complex traits are not analytically tractable and inferences are based on computationally intensive techniques. This is true of Bayesian models for genome-enabled selection, which uses whole-genome molecular data to predict the genetic merit of candidate animals for breeding purposes. In this regard, parallel computing can overcome the bottlenecks that can arise from series computing. Hence, a major goal of the present study is to bridge the gap to high-performance Bayesian computation in the context of animal breeding and genetics. Parallel Monte Carlo Markov chain algorithms and strategies are described in the context of animal breeding and genetics. Parallel Monte Carlo algorithms are introduced as a starting point including their applications to computing single-parameter and certain multiple-parameter models. Then, two basic approaches for parallel Markov chain Monte Carlo are described: one aims at parallelization within a single chain; the other is based on running multiple chains, yet some variants are discussed as well. Features and strategies of the parallel Markov chain Monte Carlo are illustrated using real data, including a large beef cattle dataset with 50K SNP genotypes. Parallel Markov chain Monte Carlo algorithms are useful for computing complex Bayesian models, which does not only lead to a dramatic speedup in computing but can also be used to optimize model parameters in complex Bayesian models. Hence, we anticipate that use of parallel Markov chain Monte Carlo will have a profound impact on revolutionizing the computational tools for genomic selection programs.

Parallel Markov chain Monte Carlo - bridging the gap to high-performance Bayesian computation in animal breeding and genetics

PubMed Central

2012-01-01

Background Most Bayesian models for the analysis of complex traits are not analytically tractable and inferences are based on computationally intensive techniques. This is true of Bayesian models for genome-enabled selection, which uses whole-genome molecular data to predict the genetic merit of candidate animals for breeding purposes. In this regard, parallel computing can overcome the bottlenecks that can arise from series computing. Hence, a major goal of the present study is to bridge the gap to high-performance Bayesian computation in the context of animal breeding and genetics. Results Parallel Monte Carlo Markov chain algorithms and strategies are described in the context of animal breeding and genetics. Parallel Monte Carlo algorithms are introduced as a starting point including their applications to computing single-parameter and certain multiple-parameter models. Then, two basic approaches for parallel Markov chain Monte Carlo are described: one aims at parallelization within a single chain; the other is based on running multiple chains, yet some variants are discussed as well. Features and strategies of the parallel Markov chain Monte Carlo are illustrated using real data, including a large beef cattle dataset with 50K SNP genotypes. Conclusions Parallel Markov chain Monte Carlo algorithms are useful for computing complex Bayesian models, which does not only lead to a dramatic speedup in computing but can also be used to optimize model parameters in complex Bayesian models. Hence, we anticipate that use of parallel Markov chain Monte Carlo will have a profound impact on revolutionizing the computational tools for genomic selection programs. PMID:23009363

A model for optimizing file access patterns using spatio-temporal parallelism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boonthanome, Nouanesengsy; Patchett, John; Geveci, Berk

2013-01-01

For many years now, I/O read time has been recognized as the primary bottleneck for parallel visualization and analysis of large-scale data. In this paper, we introduce a model that can estimate the read time for a file stored in a parallel filesystem when given the file access pattern. Read times ultimately depend on how the file is stored and the access pattern used to read the file. The file access pattern will be dictated by the type of parallel decomposition used. We employ spatio-temporal parallelism, which combines both spatial and temporal parallelism, to provide greater flexibility to possible filemore » access patterns. Using our model, we were able to configure the spatio-temporal parallelism to design optimized read access patterns that resulted in a speedup factor of approximately 400 over traditional file access patterns.« less

Optimisation of a parallel ocean general circulation model

NASA Astrophysics Data System (ADS)

Beare, M. I.; Stevens, D. P.

1997-10-01

This paper presents the development of a general-purpose parallel ocean circulation model, for use on a wide range of computer platforms, from traditional scalar machines to workstation clusters and massively parallel processors. Parallelism is provided, as a modular option, via high-level message-passing routines, thus hiding the technical intricacies from the user. An initial implementation highlights that the parallel efficiency of the model is adversely affected by a number of factors, for which optimisations are discussed and implemented. The resulting ocean code is portable and, in particular, allows science to be achieved on local workstations that could otherwise only be undertaken on state-of-the-art supercomputers.

National Centers for Environmental Prediction

Science.gov Websites

Products Operational Forecast Graphics Experimental Forecast Graphics Verification and Diagnostics Model PARALLEL/EXPERIMENTAL MODEL FORECAST GRAPHICS OPERATIONAL VERIFICATION / DIAGNOSTICS PARALLEL VERIFICATION Developmental Air Quality Forecasts and Verification Back to Table of Contents 2. PARALLEL/EXPERIMENTAL GRAPHICS

Performance Analysis and Optimization on the UCLA Parallel Atmospheric General Circulation Model Code

NASA Technical Reports Server (NTRS)

Lou, John; Ferraro, Robert; Farrara, John; Mechoso, Carlos

1996-01-01

An analysis is presented of several factors influencing the performance of a parallel implementation of the UCLA atmospheric general circulation model (AGCM) on massively parallel computer systems. Several modificaitons to the original parallel AGCM code aimed at improving its numerical efficiency, interprocessor communication cost, load-balance and issues affecting single-node code performance are discussed.

Studying an Eulerian Computer Model on Different High-performance Computer Platforms and Some Applications

NASA Astrophysics Data System (ADS)

Georgiev, K.; Zlatev, Z.

2010-11-01

The Danish Eulerian Model (DEM) is an Eulerian model for studying the transport of air pollutants on large scale. Originally, the model was developed at the National Environmental Research Institute of Denmark. The model computational domain covers Europe and some neighbour parts belong to the Atlantic Ocean, Asia and Africa. If DEM model is to be applied by using fine grids, then its discretization leads to a huge computational problem. This implies that such a model as DEM must be run only on high-performance computer architectures. The implementation and tuning of such a complex large-scale model on each different computer is a non-trivial task. Here, some comparison results of running of this model on different kind of vector (CRAY C92A, Fujitsu, etc.), parallel computers with distributed memory (IBM SP, CRAY T3E, Beowulf clusters, Macintosh G4 clusters, etc.), parallel computers with shared memory (SGI Origin, SUN, etc.) and parallel computers with two levels of parallelism (IBM SMP, IBM BlueGene/P, clusters of multiprocessor nodes, etc.) will be presented. The main idea in the parallel version of DEM is domain partitioning approach. Discussions according to the effective use of the cache and hierarchical memories of the modern computers as well as the performance, speed-ups and efficiency achieved will be done. The parallel code of DEM, created by using MPI standard library, appears to be highly portable and shows good efficiency and scalability on different kind of vector and parallel computers. Some important applications of the computer model output are presented in short.

An OpenACC-Based Unified Programming Model for Multi-accelerator Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Jungwon; Lee, Seyong; Vetter, Jeffrey S

2015-01-01

This paper proposes a novel SPMD programming model of OpenACC. Our model integrates the different granularities of parallelism from vector-level parallelism to node-level parallelism into a single, unified model based on OpenACC. It allows programmers to write programs for multiple accelerators using a uniform programming model whether they are in shared or distributed memory systems. We implement a prototype of our model and evaluate its performance with a GPU-based supercomputer using three benchmark applications.

Boundedness and exponential convergence in a chemotaxis model for tumor invasion

NASA Astrophysics Data System (ADS)

Jin, Hai-Yang; Xiang, Tian

2016-12-01

We revisit the following chemotaxis system modeling tumor invasion {ut=Δu-∇ṡ(u∇v),x∈Ω,t>0,vt=Δv+wz,x∈Ω,t>0,wt=-wz,x∈Ω,t>0,zt=Δz-z+u,x∈Ω,t>0, in a smooth bounded domain Ω \\subset {{{R}}n}(n≥slant 1) with homogeneous Neumann boundary and initial conditions. This model was recently proposed by Fujie et al (2014 Adv. Math. Sci. Appl. 24 67-84) as a model for tumor invasion with the role of extracellular matrix incorporated, and was analyzed later by Fujie et al (2016 Discrete Contin. Dyn. Syst. 36 151-69), showing the uniform boundedness and convergence for n≤slant 3 . In this work, we first show that the {{L}∞} -boundedness of the system can be reduced to the boundedness of \\parallel u(\\centerdot,t){{\\parallel}{{L\\frac{n{4}+ɛ}}(Ω )}} for some ɛ >0 alone, and then, for n≥slant 4 , if the initial data \\parallel {{u}0}{{\\parallel}{{L\\frac{n{4}}}}} , \\parallel {{z}0}{{\\parallel}{{L\\frac{n{2}}}}} and \\parallel \

An embedded multi-core parallel model for real-time stereo imaging

NASA Astrophysics Data System (ADS)

He, Wenjing; Hu, Jian; Niu, Jingyu; Li, Chuanrong; Liu, Guangyu

2018-04-01

The real-time processing based on embedded system will enhance the application capability of stereo imaging for LiDAR and hyperspectral sensor. The task partitioning and scheduling strategies for embedded multiprocessor system starts relatively late, compared with that for PC computer. In this paper, aimed at embedded multi-core processing platform, a parallel model for stereo imaging is studied and verified. After analyzing the computing amount, throughout capacity and buffering requirements, a two-stage pipeline parallel model based on message transmission is established. This model can be applied to fast stereo imaging for airborne sensors with various characteristics. To demonstrate the feasibility and effectiveness of the parallel model, a parallel software was designed using test flight data, based on the 8-core DSP processor TMS320C6678. The results indicate that the design performed well in workload distribution and had a speed-up ratio up to 6.4.

A phase II, multicentre trial evaluating the efficacy of de-escalated bisphosphonate therapy in metastatic breast cancer patients at low-risk of skeletal-related events.

PubMed

Addison, Christina L; Bouganim, Nathaniel; Hilton, John; Vandermeer, Lisa; Dent, Susan; Amir, Eitan; Hopkins, Sean; Kuchuk, Iryna; Segal, Roanne; Song, Xinni; Gertler, Stan; Mazzarello, Sasha; Dranitsaris, George; Ooi, Daylily; Pond, Gregory; Clemons, Mark

2014-04-01

The optimal frequency of intravenous (IV) bisphosphonate administration is unclear. We thus performed a study evaluating the effects of switching from 3-4 to 12 weekly therapy in patients with biochemically defined low-risk bone metastases. Patients with serum C-telopeptide (CTx) levels ≤600 ng/L after ≥3 months of 3-4 weekly IV pamidronate were switched to 12 weekly therapy for 48 weeks. Primary endpoint was the proportion of patients maintaining CTx levels in the lower-risk range. All endpoints (serum CTx and bone-specific alkaline phosphatase (BSAP), skeletal-related events (SREs) and self-reported pain) were measured at baseline, 6, 12, 24, 36 and 48 weeks. Treatment failure was defined as biochemical failure (CTx > 600 ng/L) or a SRE. Exploratory biomarkers including; serum TGF-β, activin-A, bone sialoprotein (BSP), procollagen type 1 N-terminal propeptide and urinary N-telopeptide (NTx) were assessed at baseline as predictors for failure to complete treatment. Seventy-one patients accrued and 43 (61 %) completed 48 weeks of de-escalated therapy. Reasons for failure to complete treatment included; biochemical failure (CTx > 600 ng/L) (n = 10, 14.1 %), on-study SRE (n = 9, 12.7 %), disease progression (n = 7, 9.9 % including death from disease [n = 1, 1.4 %]) or patient choice (n = 2, 2.8 %). Elevated baseline levels of CTx, BSAP, NTx and BSP were associated with treatment failure. The majority of patients in this biochemically defined low-risk population could switch from 3-4 weekly to 12 weekly bisphosphonate therapy with no effect on CTx levels or SREs during the 48 week study. Larger trials are required to assess the roles of biomarkers as predictors of adequacy of de-escalated therapy.

Phylogeny and population dynamics of respiratory syncytial virus (Rsv) A and B.

PubMed

Martinelli, Marianna; Frati, Elena Rosanna; Zappa, Alessandra; Ebranati, Erika; Bianchi, Silvia; Pariani, Elena; Amendola, Antonella; Zehender, Gianguglielmo; Tanzi, Elisabetta

2014-08-30

Respiratory syncytial virus (RSV) is a major cause of lower respiratory tract infections in infants and young children. RSV is characterised by high variability, especially in the G glycoprotein, which may play a significant role in RSV pathogenicity by allowing immune evasion. To reconstruct the origin and phylodynamic history of RSV, we evaluated the genetic diversity and evolutionary dynamics of RSV A and RSV B isolated from children under 3 years old infected in Italy from 2006 to 2012. Phylogenetic analysis revealed that most of the RSV A sequences clustered with the NA1 genotype, and RSV B sequences were included in the Buenos Aires genotype. The mean evolutionary rates for RSV A and RSV B were estimated to be 2.1 × 10(-3) substitutions (subs)/site/year and 3.03 × 10(-3) subs/site/year, respectively. The time of most recent common ancestor for the tree root went back to the 1940s (95% highest posterior density-HPD: 1927-1951) for RSV A and the 1950s (95%HPD: 1951-1960) for RSV B. The RSV A Bayesian skyline plot (BSP) showed a decrease in transmission events ending in about 2005, when a sharp growth restored the original viral population size. RSV B BSP showed a similar trend. Site-specific selection analysis identified 10 codons under positive selection in RSV A sequences and only one site in RSV B sequences. Although RSV remains difficult to control due to its antigenic diversity, it is important to monitor changes in its coding sequences, to permit the identification of future epidemic strains and to implement vaccine and therapy strategies. Copyright © 2014 Elsevier B.V. All rights reserved.

Aerosol and ozone distributions over the western North Atlantic during WATOX-86

NASA Astrophysics Data System (ADS)

Bridgman, H. A.; Schnell, Russell C.; Bodhaine, B. A.; Oltmans, S. J.

1988-03-01

On January 4, 6, 8, and 9, 1986, a series of National Oceanic and Atmospheric Administration WP-3D research flights was conducted over the western Atlantic Ocean 200-300 km off the coast of North America from Nova Scotia to Georgia as part of the Western Atlantic Ocean Experiment (WATOX). Rights were made perpendicular to NW airflow to establish the flux of gas and aerosol emissions off the North American continent to the ocean. Representative condensation nucleus (CN) concentrations averaged 150-250 cm-3 in the free troposphere in clean conditions, but in atmospheric layers containing anthropogenic air pollution transported from long distances, CN concentrations reached 6500 cm-3. In the marine boundary layer, CN concentrations averaged 500 to 750 cm-3 under relatively clean conditions, and 1500 to 3000 cm-3 in polluted air. Aerosol scattering extinction (bsp) ranged from 70 × 10-6 m-1 in the marine boundary layer to 20 × 10-6 m-1 in the free troposphere. Aerosol bsp was not as responsive to changes in atmospheric structure as CN although factor-of-2 changes across the marine boundary layer were observed. Aerosol size spectra in the marine boundary layer were an order of magnitude greater than those in the free troposphere. Consistent peaks in the volume spectra between 8 and 10 μm diameter established the importance of sea salt as a major aerosol component. Ozone profiles in the free troposphere, normally in the 30-40 ppb range, exhibited laminae of enhanced concentrations (up to 70 ppb) at moisture boundaries, suggesting that active ozone production was occurring at these levels. Ozone concentrations within the marine boundary layer were generally lower than in the free troposphere.

High-level expression and characterization of the Bacillus subtilis subsp. subtilis str. BSP1 YwaD aminopeptidase in Pichia pastoris.

PubMed

Tang, Wei; Li, Zhezhe; Li, Chunhua; Yu, Xianhong; Wang, Fei; Wan, Xin; Wang, Yaping; Ma, Lixin

2016-06-01

Aminopeptidases are widely used for creating protein hydrolysates and peptide sequencing. The ywaD gene from a new Bacillus isolate, named Bacillus subtilis subsp. subtilis str. BSP1, was cloned into the yeast expression vector pHBM905A and expressed and secreted by Pichia pastoris strain GS115. The deduced amino acid sequence of the aminopeptidase encoded by the ywaD gene shared up to 98% identity with aminopeptidases from B. subtilis strains 168 and zj016. The yield (3.81 g/l) and specific activity (788 U/mg) of recombinant YwaD in high-density fermentation were extremely high. And 829.83 mg of the purified enzyme (4089.72 U/mg) were harvested. YwaD was glycosylated, and its activity decreased after deglycosylation, which was similar to that of the aminopeptidase from B. subtilis strain zj016. YwaD was most active toward l-arginine-4-nitroanilide. Moreover, it exhibited high resistance to carbamide, which was not true for aminopeptidases from B. subtilis strains 168 and zj016, which could simplify the purification of YwaD. Moreover, the expression and parts of characterization of the aminopeptidase from B. subtilis strain 168 in Pichia pastoris were added as supplementary material. The sequence and other characteristics of YwaD were compared with those of aminopeptidases from B. subtilis strains 168 and zj016, and they will provide a solid foundation for further research on the influence of amino acid mutations on the function of aminopeptidases. Copyright © 2016 Elsevier Inc. All rights reserved.

Aerosol optical properties along the northeast coast of North America during the New England Air Quality Study-Intercontinental Transport and Chemical Transformation 2004 campaign and the influence of aerosol composition

NASA Astrophysics Data System (ADS)

Wang, Wei; Rood, Mark J.; Carrico, Christian M.; Covert, David S.; Quinn, Patricia K.; Bates, Timothy S.

2007-05-01

Optical and hygroscopic properties of submicrometer diameter aerosol particles were measured on board the NOAA R/V Ronald H. Brown as part of the NEAQS-ITCT field campaign. The campaign occurred along the northeast coast of North America during the summer of 2004. A scanning relative humidity (RH) nephelometry system (humidograph) measured total light scattering and backscattering coefficients (σsp and σbsp, respectively) at three wavelengths (λs) and RH = 26% and while RH was scanned between 40% and 85%. These measurements were combined with aerosol light absorption and composition measurements to describe σsp, σbsp, single scattering albedo (ω), Ångström exponent (å), and hemispheric backscatter fraction (b) at a low reference RH of 26 ± 4% and the aerosol's hygroscopic properties based on its optical response up to 85% RH. Humidogram curve structure was dominated by hygroscopic growth without hysteresis (76% frequency). Dependence of the aerosol's σsp values with changes in RH, fσsp(RH, 26), was observed to decrease with increasing mass fraction of particulate organic matter (POM, FO). Statistical analyses indicated that increasing FO resulted in a less hygroscopic aerosol, while increasing molar equivalence ratio (ER) resulted in lower hysteresis factors based on the aerosols' optical responses at a 0.95 confidence level. ω showed little RH dependence while å and b decreased with increasing RH values. Values for å(λ1, λ2), b, and fσsp(82, 26) increased with increasing λ values. Sensitivities of top of the atmosphere aerosol radiative forcing to changes in ω, b, and σsp with RH were also estimated.

Information needs assessment of medical equipment offices based on Critical Success Factors (CSF) and Business System Planning (BSP) methods.

PubMed

Khorrami, F; Ahmadi, M; Alizadeh, A; Roozbeh, N; Mohseni, S

2015-01-01

Introduction: Given the ever-increasing importance and value of information, providing the management with a reliable information system, which can facilitate decision-making regarding planning, organization and control, is vitally important. This study aimed to analyze and evaluate the information needs of medical equipment offices. Methods: This descriptive applied cross-sectional study was carried out in 2010. The population of the study included the managers of statistic and medical records at the offices of vice-chancellor for treatment in 39 medical universities in Iran. Data were collected by using structured questioners. With regard to different kinds of designing information systems, sampling was done by two methods, BSP (based on processes of job description) and CSF method (based on critical success factors). The data were analyzed by SPSS-16. Results: Our study showed that 41% of information needs were found to be critical success factors of managers of office. The first priority of managers was "the number of bed and bed occupancy in hospitals". Of 29 identified information needs, 62% were initial information needs of managers (from the viewpoints of managers). Of all, 4% of the information needs were obtained through the form, 14% through both the form and database, 11% through the web site, and 71% had no sources (forms, databases, web site). Conclusion: Since 71% of the information needs of medical equipment offices managers had no information sources, the development of information system in these offices seems to be necessary. Despite the important role of users in designing the information systems (identifying 62% of information needs), other scientific methods is also needed to be utilized in designing the information systems.

Optical properties of size-resolved particles at a Hong Kong urban site during winter

NASA Astrophysics Data System (ADS)

Gao, Yuan; Lai, Senchao; Lee, Shun-Cheng; Yau, Pui Shan; Huang, Yu; Cheng, Yan; Wang, Tao; Xu, Zheng; Yuan, Chao; Zhang, Yingyi

2015-03-01

Visibility degradation in Hong Kong is related to the city's serious air pollution problems. To investigate the aerosols' optical properties and their relationship with the chemical composition and size distribution of the particles, a monitoring campaign was conducted at an urban site in the early winter period (from October to December, 2010). The particle light scattering coefficient (Bsp) and absorption coefficient (Bap) were measured. Two collocated Micro-Orifice Uniform Deposit Impactor samplers (MOUDI110, MSP, USA) with nominal 50% cut-off aerodynamic diameters of 18, 10, 5.6, 3.2, 1.8, 1, 0.56, 0.32, 0.18, 0.1, and 0.056 μm were used to collect size-resolved particle samples. The average Bsp and Bap were 201.96 ± 105.82 Mm- 1 and 39.91 ± 19.16 Mm- 1, with an average single scattering albedo (ωo) of 0.82 ± 0.07. The theoretical method of light extinction calculation was used to determine the extinction of the size-resolved particulate matters (PM). The reconstructed light scattering coefficient correlated well with the measured scattering value in the Hong Kong urban area. Droplet mode (0.56-1.8 μm) particles contributed most to the particle light extinction (~ 69%). Organic matter, ammonium sulphate and elemental carbon were the key components causing visibility degradation in the droplet (0.56-1.8 μm) and condensation (0.1-0.56 μm) size ranges. Five sources contributing to particle light extinction have been identified using positive matrix factorisation (PMF). Traffic/engine exhausts and secondary aerosols accounted for ~ 36% and ~ 32% of particle light extinction, respectively, followed by sea salt (15%). The remaining sources, soil/fugitive dust and tire dust, contributed by ~ 10% and 7%, respectively, to particle light extinction.

Information needs assessment of medical equipment offices based on Critical Success Factors (CSF) and Business System Planning (BSP) methods

PubMed Central

Khorrami, F; Ahmadi, M; Alizadeh, A; Roozbeh, N; Mohseni, S

2015-01-01

Introduction: Given the ever-increasing importance and value of information, providing the management with a reliable information system, which can facilitate decision-making regarding planning, organization and control, is vitally important. This study aimed to analyze and evaluate the information needs of medical equipment offices. Methods: This descriptive applied cross-sectional study was carried out in 2010. The population of the study included the managers of statistic and medical records at the offices of vice-chancellor for treatment in 39 medical universities in Iran. Data were collected by using structured questioners. With regard to different kinds of designing information systems, sampling was done by two methods, BSP (based on processes of job description) and CSF method (based on critical success factors). The data were analyzed by SPSS-16. Results: Our study showed that 41% of information needs were found to be critical success factors of managers of office. The first priority of managers was “the number of bed and bed occupancy in hospitals”. Of 29 identified information needs, 62% were initial information needs of managers (from the viewpoints of managers). Of all, 4% of the information needs were obtained through the form, 14% through both the form and database, 11% through the web site, and 71% had no sources (forms, databases, web site). Conclusion: Since 71% of the information needs of medical equipment offices managers had no information sources, the development of information system in these offices seems to be necessary. Despite the important role of users in designing the information systems (identifying 62% of information needs), other scientific methods is also needed to be utilized in designing the information systems. PMID:28255389

A parallelized three-dimensional cellular automaton model for grain growth during additive manufacturing

NASA Astrophysics Data System (ADS)

Lian, Yanping; Lin, Stephen; Yan, Wentao; Liu, Wing Kam; Wagner, Gregory J.

2018-05-01

In this paper, a parallelized 3D cellular automaton computational model is developed to predict grain morphology for solidification of metal during the additive manufacturing process. Solidification phenomena are characterized by highly localized events, such as the nucleation and growth of multiple grains. As a result, parallelization requires careful treatment of load balancing between processors as well as interprocess communication in order to maintain a high parallel efficiency. We give a detailed summary of the formulation of the model, as well as a description of the communication strategies implemented to ensure parallel efficiency. Scaling tests on a representative problem with about half a billion cells demonstrate parallel efficiency of more than 80% on 8 processors and around 50% on 64; loss of efficiency is attributable to load imbalance due to near-surface grain nucleation in this test problem. The model is further demonstrated through an additive manufacturing simulation with resulting grain structures showing reasonable agreement with those observed in experiments.

A parallelized three-dimensional cellular automaton model for grain growth during additive manufacturing

NASA Astrophysics Data System (ADS)

Lian, Yanping; Lin, Stephen; Yan, Wentao; Liu, Wing Kam; Wagner, Gregory J.

2018-01-01

In this paper, a parallelized 3D cellular automaton computational model is developed to predict grain morphology for solidification of metal during the additive manufacturing process. Solidification phenomena are characterized by highly localized events, such as the nucleation and growth of multiple grains. As a result, parallelization requires careful treatment of load balancing between processors as well as interprocess communication in order to maintain a high parallel efficiency. We give a detailed summary of the formulation of the model, as well as a description of the communication strategies implemented to ensure parallel efficiency. Scaling tests on a representative problem with about half a billion cells demonstrate parallel efficiency of more than 80% on 8 processors and around 50% on 64; loss of efficiency is attributable to load imbalance due to near-surface grain nucleation in this test problem. The model is further demonstrated through an additive manufacturing simulation with resulting grain structures showing reasonable agreement with those observed in experiments.

System and method for representing and manipulating three-dimensional objects on massively parallel architectures

DOEpatents

Karasick, M.S.; Strip, D.R.

1996-01-30

A parallel computing system is described that comprises a plurality of uniquely labeled, parallel processors, each processor capable of modeling a three-dimensional object that includes a plurality of vertices, faces and edges. The system comprises a front-end processor for issuing a modeling command to the parallel processors, relating to a three-dimensional object. Each parallel processor, in response to the command and through the use of its own unique label, creates a directed-edge (d-edge) data structure that uniquely relates an edge of the three-dimensional object to one face of the object. Each d-edge data structure at least includes vertex descriptions of the edge and a description of the one face. As a result, each processor, in response to the modeling command, operates upon a small component of the model and generates results, in parallel with all other processors, without the need for processor-to-processor intercommunication. 8 figs.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yusa, Kazuyuki; Yamamoto, Osamu; Fukuda, Masayuki

Highlights: {yields} We isolated the Zn{sup 2+} ions (eluted Zn{sup 2+} ion; EZ) from zinc-incorporated titanium implant. {yields} The EZ promoted the cell viability in hBMCs. {yields} The EZ stimulated preosteoblast and osteoblast marker gene expression in hBMCs. {yields} The hBMCs supplemented with EZ showed typically cell morphology when osteoblast maturing. {yields} It is revealed that the EZ also stimulates the calcium deposition of hBMCs. -- Abstract: Zinc is one of the trace elements which induce the proliferation and the differentiation of the osteoblast. In the previous study, we found that zinc ions (Zn{sup 2+} ion)-releasing titanium implants had excellentmore » bone fixation using a rabbit femurs model. In this study, we isolated the Zn{sup 2+} ions (eluted Zn{sup 2+} ion; EZ) released from the implant surface, and evaluated the effect of EZ on the osteogenesis of human bone marrow-derived mesenchymal cells (hBMCs). In the result, it was found that the EZ stimulated cell viability, osteoblast marker gene (type I collagen, osteocalcin (OC), alkaline phosphatase (ALP) and bone sialoprotein (BSP)) expressions and calcium deposition in hBMCs.« less

Parallel Monte Carlo transport modeling in the context of a time-dependent, three-dimensional multi-physics code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Procassini, R.J.

1997-12-31

The fine-scale, multi-space resolution that is envisioned for accurate simulations of complex weapons systems in three spatial dimensions implies flop-rate and memory-storage requirements that will only be obtained in the near future through the use of parallel computational techniques. Since the Monte Carlo transport models in these simulations usually stress both of these computational resources, they are prime candidates for parallelization. The MONACO Monte Carlo transport package, which is currently under development at LLNL, will utilize two types of parallelism within the context of a multi-physics design code: decomposition of the spatial domain across processors (spatial parallelism) and distribution ofmore » particles in a given spatial subdomain across additional processors (particle parallelism). This implementation of the package will utilize explicit data communication between domains (message passing). Such a parallel implementation of a Monte Carlo transport model will result in non-deterministic communication patterns. The communication of particles between subdomains during a Monte Carlo time step may require a significant level of effort to achieve a high parallel efficiency.« less

Real-time implementations of image segmentation algorithms on shared memory multicore architecture: a survey (Conference Presentation)

NASA Astrophysics Data System (ADS)

Akil, Mohamed

2017-05-01

The real-time processing is getting more and more important in many image processing applications. Image segmentation is one of the most fundamental tasks image analysis. As a consequence, many different approaches for image segmentation have been proposed. The watershed transform is a well-known image segmentation tool. The watershed transform is a very data intensive task. To achieve acceleration and obtain real-time processing of watershed algorithms, parallel architectures and programming models for multicore computing have been developed. This paper focuses on the survey of the approaches for parallel implementation of sequential watershed algorithms on multicore general purpose CPUs: homogeneous multicore processor with shared memory. To achieve an efficient parallel implementation, it's necessary to explore different strategies (parallelization/distribution/distributed scheduling) combined with different acceleration and optimization techniques to enhance parallelism. In this paper, we give a comparison of various parallelization of sequential watershed algorithms on shared memory multicore architecture. We analyze the performance measurements of each parallel implementation and the impact of the different sources of overhead on the performance of the parallel implementations. In this comparison study, we also discuss the advantages and disadvantages of the parallel programming models. Thus, we compare the OpenMP (an application programming interface for multi-Processing) with Ptheads (POSIX Threads) to illustrate the impact of each parallel programming model on the performance of the parallel implementations.

Hierarchical Parallelism in Finite Difference Analysis of Heat Conduction

NASA Technical Reports Server (NTRS)

Padovan, Joseph; Krishna, Lala; Gute, Douglas

1997-01-01

Based on the concept of hierarchical parallelism, this research effort resulted in highly efficient parallel solution strategies for very large scale heat conduction problems. Overall, the method of hierarchical parallelism involves the partitioning of thermal models into several substructured levels wherein an optimal balance into various associated bandwidths is achieved. The details are described in this report. Overall, the report is organized into two parts. Part 1 describes the parallel modelling methodology and associated multilevel direct, iterative and mixed solution schemes. Part 2 establishes both the formal and computational properties of the scheme.

An Overview of Kinematic and Calibration Models Using Internal/External Sensors or Constraints to Improve the Behavior of Spatial Parallel Mechanisms

PubMed Central

Majarena, Ana C.; Santolaria, Jorge; Samper, David; Aguilar, Juan J.

2010-01-01

This paper presents an overview of the literature on kinematic and calibration models of parallel mechanisms, the influence of sensors in the mechanism accuracy and parallel mechanisms used as sensors. The most relevant classifications to obtain and solve kinematic models and to identify geometric and non-geometric parameters in the calibration of parallel robots are discussed, examining the advantages and disadvantages of each method, presenting new trends and identifying unsolved problems. This overview tries to answer and show the solutions developed by the most up-to-date research to some of the most frequent questions that appear in the modelling of a parallel mechanism, such as how to measure, the number of sensors and necessary configurations, the type and influence of errors or the number of necessary parameters. PMID:22163469

Retargeting of existing FORTRAN program and development of parallel compilers

NASA Technical Reports Server (NTRS)

Agrawal, Dharma P.

1988-01-01

The software models used in implementing the parallelizing compiler for the B-HIVE multiprocessor system are described. The various models and strategies used in the compiler development are: flexible granularity model, which allows a compromise between two extreme granularity models; communication model, which is capable of precisely describing the interprocessor communication timings and patterns; loop type detection strategy, which identifies different types of loops; critical path with coloring scheme, which is a versatile scheduling strategy for any multicomputer with some associated communication costs; and loop allocation strategy, which realizes optimum overlapped operations between computation and communication of the system. Using these models, several sample routines of the AIR3D package are examined and tested. It may be noted that automatically generated codes are highly parallelized to provide the maximized degree of parallelism, obtaining the speedup up to a 28 to 32-processor system. A comparison of parallel codes for both the existing and proposed communication model, is performed and the corresponding expected speedup factors are obtained. The experimentation shows that the B-HIVE compiler produces more efficient codes than existing techniques. Work is progressing well in completing the final phase of the compiler. Numerous enhancements are needed to improve the capabilities of the parallelizing compiler.

Research on Multi - Person Parallel Modeling Method Based on Integrated Model Persistent Storage

NASA Astrophysics Data System (ADS)

Qu, MingCheng; Wu, XiangHu; Tao, YongChao; Liu, Ying

2018-03-01

This paper mainly studies the multi-person parallel modeling method based on the integrated model persistence storage. The integrated model refers to a set of MDDT modeling graphics system, which can carry out multi-angle, multi-level and multi-stage description of aerospace general embedded software. Persistent storage refers to converting the data model in memory into a storage model and converting the storage model into a data model in memory, where the data model refers to the object model and the storage model is a binary stream. And multi-person parallel modeling refers to the need for multi-person collaboration, the role of separation, and even real-time remote synchronization modeling.

Fully Parallel MHD Stability Analysis Tool

NASA Astrophysics Data System (ADS)

Svidzinski, Vladimir; Galkin, Sergei; Kim, Jin-Soo; Liu, Yueqiang

2014-10-01

Progress on full parallelization of the plasma stability code MARS will be reported. MARS calculates eigenmodes in 2D axisymmetric toroidal equilibria in MHD-kinetic plasma models. It is a powerful tool for studying MHD and MHD-kinetic instabilities and it is widely used by fusion community. Parallel version of MARS is intended for simulations on local parallel clusters. It will be an efficient tool for simulation of MHD instabilities with low, intermediate and high toroidal mode numbers within both fluid and kinetic plasma models, already implemented in MARS. Parallelization of the code includes parallelization of the construction of the matrix for the eigenvalue problem and parallelization of the inverse iterations algorithm, implemented in MARS for the solution of the formulated eigenvalue problem. Construction of the matrix is parallelized by distributing the load among processors assigned to different magnetic surfaces. Parallelization of the solution of the eigenvalue problem is made by repeating steps of the present MARS algorithm using parallel libraries and procedures. Initial results of the code parallelization will be reported. Work is supported by the U.S. DOE SBIR program.

Partitioning and packing mathematical simulation models for calculation on parallel computers

NASA Technical Reports Server (NTRS)

Arpasi, D. J.; Milner, E. J.

1986-01-01

The development of multiprocessor simulations from a serial set of ordinary differential equations describing a physical system is described. Degrees of parallelism (i.e., coupling between the equations) and their impact on parallel processing are discussed. The problem of identifying computational parallelism within sets of closely coupled equations that require the exchange of current values of variables is described. A technique is presented for identifying this parallelism and for partitioning the equations for parallel solution on a multiprocessor. An algorithm which packs the equations into a minimum number of processors is also described. The results of the packing algorithm when applied to a turbojet engine model are presented in terms of processor utilization.

OpenMP parallelization of a gridded SWAT (SWATG)

NASA Astrophysics Data System (ADS)

Zhang, Ying; Hou, Jinliang; Cao, Yongpan; Gu, Juan; Huang, Chunlin

2017-12-01

Large-scale, long-term and high spatial resolution simulation is a common issue in environmental modeling. A Gridded Hydrologic Response Unit (HRU)-based Soil and Water Assessment Tool (SWATG) that integrates grid modeling scheme with different spatial representations also presents such problems. The time-consuming problem affects applications of very high resolution large-scale watershed modeling. The OpenMP (Open Multi-Processing) parallel application interface is integrated with SWATG (called SWATGP) to accelerate grid modeling based on the HRU level. Such parallel implementation takes better advantage of the computational power of a shared memory computer system. We conducted two experiments at multiple temporal and spatial scales of hydrological modeling using SWATG and SWATGP on a high-end server. At 500-m resolution, SWATGP was found to be up to nine times faster than SWATG in modeling over a roughly 2000 km2 watershed with 1 CPU and a 15 thread configuration. The study results demonstrate that parallel models save considerable time relative to traditional sequential simulation runs. Parallel computations of environmental models are beneficial for model applications, especially at large spatial and temporal scales and at high resolutions. The proposed SWATGP model is thus a promising tool for large-scale and high-resolution water resources research and management in addition to offering data fusion and model coupling ability.

The TCAR Report: Translational Cell and Animal Research Space (1965-2011) Sponsored by NASA Ames Research Center

NASA Technical Reports Server (NTRS)

Ronca, A. E.; Mains, Richard; Alwood, J. S.; French, A. J.; Smith, J. D.; Miller, Virginia; Tash, Joseph; Jenkins, Marjorie

2015-01-01

Five decades ago, NASA Ames Research Center (ARC) began a vigorous program of space biology research utilizing animal cells, tissues and whole organisms. Since its inception, this program has yielded exciting new insights into how spaceflight influences fundamental processes of living systems. These are findings with important translational implications for human health in space and on Earth. The TCAR Report is a compilation of 394 flight experiments conducted across the period spanning 1965 - 2011 with individual chapters devoted to: (1) Bone Physiology, (2) Cardiovascular/Cardiopulmonary Physiology, (3) Developmental Biology, (4) Immunology, (5) Microbial Growth and Virulence, (6) Muscle Physiology, (7) Neurophysiology and (8) Regulatory Physiology. Specialists in those disciplines reviewed the research and each prepared an overview including the translational relevance of the findings for human health in space and on Earth. The Report will be made available in early 2015 through standard NASA publication resources and on the NASA Life Sciences Data Archive (http://lsda.jsc.nasa.gov/lsda_home1.aspx). The LSDA can be mined for detailed information, including Experiment, Mission, Available Biospecimens, Document, Hardware, Dataset, Personnel, and includes a searchable Photo Gallery. Space biology translational topic highlights include: Inflight centrifugation protection of bone strength losses; Assessment of evidence related to visual impairment in astronauts; Mammalian development including vestibular system plasticity and vestibular-visual integration; Verification of limb unloading ground-based studies as a model for spaceflight unloading; Immune system impairment and increased microbiological virulence aligned with immune dysfunction; and Rapid bone and muscle tissue and functional losses associated with unloading. In addition to astronauts, these results may help humans on Earth, by providing insight into the definition of fundamental mechanisms and potential treatments for debilitating changes that result from human aging and disease. The TCAR effort has resulted in significant new insights. Modern tools now widely available for "Omics" research with model organisms and humans provide new opportunities for translational research. Omics research at various levels is greatly complemented by studies at the tissue and organismal levels. Key discoveries can occur at either the basic research or the health surveillance level such as vision problems observed in astronauts stimulating studies of eye tissues in rodents that identified relevant changes. The Ames Biospecimen Sharing Program (BSP), serving the NASA Space Biology and HRP programs, was created to maximize utilization and scientific return from unique animal specimens derived from rare, complex and costly NASA spaceflight and ground-based analog experiments. The BSP is a valuable tool for advancing translational science at NASA. Dynamic methods for tracking translational linkages across NASA space life sciences and medicine are strongly encouraged for translational science.

Integrated Task and Data Parallel Programming

NASA Technical Reports Server (NTRS)

Grimshaw, A. S.

1998-01-01

This research investigates the combination of task and data parallel language constructs within a single programming language. There are an number of applications that exhibit properties which would be well served by such an integrated language. Examples include global climate models, aircraft design problems, and multidisciplinary design optimization problems. Our approach incorporates data parallel language constructs into an existing, object oriented, task parallel language. The language will support creation and manipulation of parallel classes and objects of both types (task parallel and data parallel). Ultimately, the language will allow data parallel and task parallel classes to be used either as building blocks or managers of parallel objects of either type, thus allowing the development of single and multi-paradigm parallel applications. 1995 Research Accomplishments In February I presented a paper at Frontiers 1995 describing the design of the data parallel language subset. During the spring I wrote and defended my dissertation proposal. Since that time I have developed a runtime model for the language subset. I have begun implementing the model and hand-coding simple examples which demonstrate the language subset. I have identified an astrophysical fluid flow application which will validate the data parallel language subset. 1996 Research Agenda Milestones for the coming year include implementing a significant portion of the data parallel language subset over the Legion system. Using simple hand-coded methods, I plan to demonstrate (1) concurrent task and data parallel objects and (2) task parallel objects managing both task and data parallel objects. My next steps will focus on constructing a compiler and implementing the fluid flow application with the language. Concurrently, I will conduct a search for a real-world application exhibiting both task and data parallelism within the same program. Additional 1995 Activities During the fall I collaborated with Andrew Grimshaw and Adam Ferrari to write a book chapter which will be included in Parallel Processing in C++ edited by Gregory Wilson. I also finished two courses, Compilers and Advanced Compilers, in 1995. These courses complete my class requirements at the University of Virginia. I have only my dissertation research and defense to complete.

Integrated Task And Data Parallel Programming: Language Design

NASA Technical Reports Server (NTRS)

Grimshaw, Andrew S.; West, Emily A.

1998-01-01

his research investigates the combination of task and data parallel language constructs within a single programming language. There are an number of applications that exhibit properties which would be well served by such an integrated language. Examples include global climate models, aircraft design problems, and multidisciplinary design optimization problems. Our approach incorporates data parallel language constructs into an existing, object oriented, task parallel language. The language will support creation and manipulation of parallel classes and objects of both types (task parallel and data parallel). Ultimately, the language will allow data parallel and task parallel classes to be used either as building blocks or managers of parallel objects of either type, thus allowing the development of single and multi-paradigm parallel applications. 1995 Research Accomplishments In February I presented a paper at Frontiers '95 describing the design of the data parallel language subset. During the spring I wrote and defended my dissertation proposal. Since that time I have developed a runtime model for the language subset. I have begun implementing the model and hand-coding simple examples which demonstrate the language subset. I have identified an astrophysical fluid flow application which will validate the data parallel language subset. 1996 Research Agenda Milestones for the coming year include implementing a significant portion of the data parallel language subset over the Legion system. Using simple hand-coded methods, I plan to demonstrate (1) concurrent task and data parallel objects and (2) task parallel objects managing both task and data parallel objects. My next steps will focus on constructing a compiler and implementing the fluid flow application with the language. Concurrently, I will conduct a search for a real-world application exhibiting both task and data parallelism within the same program m. Additional 1995 Activities During the fall I collaborated with Andrew Grimshaw and Adam Ferrari to write a book chapter which will be included in Parallel Processing in C++ edited by Gregory Wilson. I also finished two courses, Compilers and Advanced Compilers, in 1995. These courses complete my class requirements at the University of Virginia. I have only my dissertation research and defense to complete.

The Research of the Parallel Computing Development from the Angle of Cloud Computing

NASA Astrophysics Data System (ADS)

Peng, Zhensheng; Gong, Qingge; Duan, Yanyu; Wang, Yun

2017-10-01

Cloud computing is the development of parallel computing, distributed computing and grid computing. The development of cloud computing makes parallel computing come into people’s lives. Firstly, this paper expounds the concept of cloud computing and introduces two several traditional parallel programming model. Secondly, it analyzes and studies the principles, advantages and disadvantages of OpenMP, MPI and Map Reduce respectively. Finally, it takes MPI, OpenMP models compared to Map Reduce from the angle of cloud computing. The results of this paper are intended to provide a reference for the development of parallel computing.

Describing, using 'recognition cones'. [parallel-series model with English-like computer program

NASA Technical Reports Server (NTRS)

Uhr, L.

1973-01-01

A parallel-serial 'recognition cone' model is examined, taking into account the model's ability to describe scenes of objects. An actual program is presented in an English-like language. The concept of a 'description' is discussed together with possible types of descriptive information. Questions regarding the level and the variety of detail are considered along with approaches for improving the serial representations of parallel systems.

Parallel distributed, reciprocal Monte Carlo radiation in coupled, large eddy combustion simulations

NASA Astrophysics Data System (ADS)

Hunsaker, Isaac L.

Radiation is the dominant mode of heat transfer in high temperature combustion environments. Radiative heat transfer affects the gas and particle phases, including all the associated combustion chemistry. The radiative properties are in turn affected by the turbulent flow field. This bi-directional coupling of radiation turbulence interactions poses a major challenge in creating parallel-capable, high-fidelity combustion simulations. In this work, a new model was developed in which reciprocal monte carlo radiation was coupled with a turbulent, large-eddy simulation combustion model. A technique wherein domain patches are stitched together was implemented to allow for scalable parallelism. The combustion model runs in parallel on a decomposed domain. The radiation model runs in parallel on a recomposed domain. The recomposed domain is stored on each processor after information sharing of the decomposed domain is handled via the message passing interface. Verification and validation testing of the new radiation model were favorable. Strong scaling analyses were performed on the Ember cluster and the Titan cluster for the CPU-radiation model and GPU-radiation model, respectively. The model demonstrated strong scaling to over 1,700 and 16,000 processing cores on Ember and Titan, respectively.

Real-world hydrologic assessment of a fully-distributed hydrological model in a parallel computing environment

NASA Astrophysics Data System (ADS)

Vivoni, Enrique R.; Mascaro, Giuseppe; Mniszewski, Susan; Fasel, Patricia; Springer, Everett P.; Ivanov, Valeriy Y.; Bras, Rafael L.

2011-10-01

SummaryA major challenge in the use of fully-distributed hydrologic models has been the lack of computational capabilities for high-resolution, long-term simulations in large river basins. In this study, we present the parallel model implementation and real-world hydrologic assessment of the Triangulated Irregular Network (TIN)-based Real-time Integrated Basin Simulator (tRIBS). Our parallelization approach is based on the decomposition of a complex watershed using the channel network as a directed graph. The resulting sub-basin partitioning divides effort among processors and handles hydrologic exchanges across boundaries. Through numerical experiments in a set of nested basins, we quantify parallel performance relative to serial runs for a range of processors, simulation complexities and lengths, and sub-basin partitioning methods, while accounting for inter-run variability on a parallel computing system. In contrast to serial simulations, the parallel model speed-up depends on the variability of hydrologic processes. Load balancing significantly improves parallel speed-up with proportionally faster runs as simulation complexity (domain resolution and channel network extent) increases. The best strategy for large river basins is to combine a balanced partitioning with an extended channel network, with potential savings through a lower TIN resolution. Based on these advances, a wider range of applications for fully-distributed hydrologic models are now possible. This is illustrated through a set of ensemble forecasts that account for precipitation uncertainty derived from a statistical downscaling model.

Modelling and simulation of parallel triangular triple quantum dots (TTQD) by using SIMON 2.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fathany, Maulana Yusuf, E-mail: myfathany@gmail.com; Fuada, Syifaul, E-mail: fsyifaul@gmail.com; Lawu, Braham Lawas, E-mail: bram-labs@rocketmail.com

2016-04-19

This research presents analysis of modeling on Parallel Triple Quantum Dots (TQD) by using SIMON (SIMulation Of Nano-structures). Single Electron Transistor (SET) is used as the basic concept of modeling. We design the structure of Parallel TQD by metal material with triangular geometry model, it is called by Triangular Triple Quantum Dots (TTQD). We simulate it with several scenarios using different parameters; such as different value of capacitance, various gate voltage, and different thermal condition.

Development of a Distributed Parallel Computing Framework to Facilitate Regional/Global Gridded Crop Modeling with Various Scenarios

NASA Astrophysics Data System (ADS)

Jang, W.; Engda, T. A.; Neff, J. C.; Herrick, J.

2017-12-01

Many crop models are increasingly used to evaluate crop yields at regional and global scales. However, implementation of these models across large areas using fine-scale grids is limited by computational time requirements. In order to facilitate global gridded crop modeling with various scenarios (i.e., different crop, management schedule, fertilizer, and irrigation) using the Environmental Policy Integrated Climate (EPIC) model, we developed a distributed parallel computing framework in Python. Our local desktop with 14 cores (28 threads) was used to test the distributed parallel computing framework in Iringa, Tanzania which has 406,839 grid cells. High-resolution soil data, SoilGrids (250 x 250 m), and climate data, AgMERRA (0.25 x 0.25 deg) were also used as input data for the gridded EPIC model. The framework includes a master file for parallel computing, input database, input data formatters, EPIC model execution, and output analyzers. Through the master file for parallel computing, the user-defined number of threads of CPU divides the EPIC simulation into jobs. Then, Using EPIC input data formatters, the raw database is formatted for EPIC input data and the formatted data moves into EPIC simulation jobs. Then, 28 EPIC jobs run simultaneously and only interesting results files are parsed and moved into output analyzers. We applied various scenarios with seven different slopes and twenty-four fertilizer ranges. Parallelized input generators create different scenarios as a list for distributed parallel computing. After all simulations are completed, parallelized output analyzers are used to analyze all outputs according to the different scenarios. This saves significant computing time and resources, making it possible to conduct gridded modeling at regional to global scales with high-resolution data. For example, serial processing for the Iringa test case would require 113 hours, while using the framework developed in this study requires only approximately 6 hours, a nearly 95% reduction in computing time.

Parallelization of elliptic solver for solving 1D Boussinesq model

NASA Astrophysics Data System (ADS)

Tarwidi, D.; Adytia, D.

2018-03-01

In this paper, a parallel implementation of an elliptic solver in solving 1D Boussinesq model is presented. Numerical solution of Boussinesq model is obtained by implementing a staggered grid scheme to continuity, momentum, and elliptic equation of Boussinesq model. Tridiagonal system emerging from numerical scheme of elliptic equation is solved by cyclic reduction algorithm. The parallel implementation of cyclic reduction is executed on multicore processors with shared memory architectures using OpenMP. To measure the performance of parallel program, large number of grids is varied from 28 to 214. Two test cases of numerical experiment, i.e. propagation of solitary and standing wave, are proposed to evaluate the parallel program. The numerical results are verified with analytical solution of solitary and standing wave. The best speedup of solitary and standing wave test cases is about 2.07 with 214 of grids and 1.86 with 213 of grids, respectively, which are executed by using 8 threads. Moreover, the best efficiency of parallel program is 76.2% and 73.5% for solitary and standing wave test cases, respectively.

A hybrid parallel framework for the cellular Potts model simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Yi; He, Kejing; Dong, Shoubin

2009-01-01

The Cellular Potts Model (CPM) has been widely used for biological simulations. However, most current implementations are either sequential or approximated, which can't be used for large scale complex 3D simulation. In this paper we present a hybrid parallel framework for CPM simulations. The time-consuming POE solving, cell division, and cell reaction operation are distributed to clusters using the Message Passing Interface (MPI). The Monte Carlo lattice update is parallelized on shared-memory SMP system using OpenMP. Because the Monte Carlo lattice update is much faster than the POE solving and SMP systems are more and more common, this hybrid approachmore » achieves good performance and high accuracy at the same time. Based on the parallel Cellular Potts Model, we studied the avascular tumor growth using a multiscale model. The application and performance analysis show that the hybrid parallel framework is quite efficient. The hybrid parallel CPM can be used for the large scale simulation ({approx}10{sup 8} sites) of complex collective behavior of numerous cells ({approx}10{sup 6}).« less

A Parallel Saturation Algorithm on Shared Memory Architectures

NASA Technical Reports Server (NTRS)

Ezekiel, Jonathan; Siminiceanu

2007-01-01

Symbolic state-space generators are notoriously hard to parallelize. However, the Saturation algorithm implemented in the SMART verification tool differs from other sequential symbolic state-space generators in that it exploits the locality of ring events in asynchronous system models. This paper explores whether event locality can be utilized to efficiently parallelize Saturation on shared-memory architectures. Conceptually, we propose to parallelize the ring of events within a decision diagram node, which is technically realized via a thread pool. We discuss the challenges involved in our parallel design and conduct experimental studies on its prototypical implementation. On a dual-processor dual core PC, our studies show speed-ups for several example models, e.g., of up to 50% for a Kanban model, when compared to running our algorithm only on a single core.

Research on Parallel Three Phase PWM Converters base on RTDS

NASA Astrophysics Data System (ADS)

Xia, Yan; Zou, Jianxiao; Li, Kai; Liu, Jingbo; Tian, Jun

2018-01-01

Converters parallel operation can increase capacity of the system, but it may lead to potential zero-sequence circulating current, so the control of circulating current was an important goal in the design of parallel inverters. In this paper, the Real Time Digital Simulator (RTDS) is used to model the converters parallel system in real time and study the circulating current restraining. The equivalent model of two parallel converters and zero-sequence circulating current(ZSCC) were established and analyzed, then a strategy using variable zero vector control was proposed to suppress the circulating current. For two parallel modular converters, hardware-in-the-loop(HIL) study based on RTDS and practical experiment were implemented, results prove that the proposed control strategy is feasible and effective.

Capabilities of Fully Parallelized MHD Stability Code MARS

NASA Astrophysics Data System (ADS)

Svidzinski, Vladimir; Galkin, Sergei; Kim, Jin-Soo; Liu, Yueqiang

2016-10-01

Results of full parallelization of the plasma stability code MARS will be reported. MARS calculates eigenmodes in 2D axisymmetric toroidal equilibria in MHD-kinetic plasma models. Parallel version of MARS, named PMARS, has been recently developed at FAR-TECH. Parallelized MARS is an efficient tool for simulation of MHD instabilities with low, intermediate and high toroidal mode numbers within both fluid and kinetic plasma models, implemented in MARS. Parallelization of the code included parallelization of the construction of the matrix for the eigenvalue problem and parallelization of the inverse vector iterations algorithm, implemented in MARS for the solution of the formulated eigenvalue problem. Construction of the matrix is parallelized by distributing the load among processors assigned to different magnetic surfaces. Parallelization of the solution of the eigenvalue problem is made by repeating steps of the MARS algorithm using parallel libraries and procedures. Parallelized MARS is capable of calculating eigenmodes with significantly increased spatial resolution: up to 5,000 adapted radial grid points with up to 500 poloidal harmonics. Such resolution is sufficient for simulation of kink, tearing and peeling-ballooning instabilities with physically relevant parameters. Work is supported by the U.S. DOE SBIR program.

Fully Parallel MHD Stability Analysis Tool

NASA Astrophysics Data System (ADS)

Svidzinski, Vladimir; Galkin, Sergei; Kim, Jin-Soo; Liu, Yueqiang

2015-11-01

Progress on full parallelization of the plasma stability code MARS will be reported. MARS calculates eigenmodes in 2D axisymmetric toroidal equilibria in MHD-kinetic plasma models. It is a powerful tool for studying MHD and MHD-kinetic instabilities and it is widely used by fusion community. Parallel version of MARS is intended for simulations on local parallel clusters. It will be an efficient tool for simulation of MHD instabilities with low, intermediate and high toroidal mode numbers within both fluid and kinetic plasma models, already implemented in MARS. Parallelization of the code includes parallelization of the construction of the matrix for the eigenvalue problem and parallelization of the inverse iterations algorithm, implemented in MARS for the solution of the formulated eigenvalue problem. Construction of the matrix is parallelized by distributing the load among processors assigned to different magnetic surfaces. Parallelization of the solution of the eigenvalue problem is made by repeating steps of the present MARS algorithm using parallel libraries and procedures. Results of MARS parallelization and of the development of a new fix boundary equilibrium code adapted for MARS input will be reported. Work is supported by the U.S. DOE SBIR program.

Flood predictions using the parallel version of distributed numerical physical rainfall-runoff model TOPKAPI

NASA Astrophysics Data System (ADS)

Boyko, Oleksiy; Zheleznyak, Mark

2015-04-01

The original numerical code TOPKAPI-IMMS of the distributed rainfall-runoff model TOPKAPI ( Todini et al, 1996-2014) is developed and implemented in Ukraine. The parallel version of the code has been developed recently to be used on multiprocessors systems - multicore/processors PC and clusters. Algorithm is based on binary-tree decomposition of the watershed for the balancing of the amount of computation for all processors/cores. Message passing interface (MPI) protocol is used as a parallel computing framework. The numerical efficiency of the parallelization algorithms is demonstrated for the case studies for the flood predictions of the mountain watersheds of the Ukrainian Carpathian regions. The modeling results is compared with the predictions based on the lumped parameters models.

Dynamic modeling of parallel robots for computed-torque control implementation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Codourey, A.

1998-12-01

In recent years, increased interest in parallel robots has been observed. Their control with modern theory, such as the computed-torque method, has, however, been restrained, essentially due to the difficulty in establishing a simple dynamic model that can be calculated in real time. In this paper, a simple method based on the virtual work principle is proposed for modeling parallel robots. The mass matrix of the robot, needed for decoupling control strategies, does not explicitly appear in the formulation; however, it can be computed separately, based on kinetic energy considerations. The method is applied to the DELTA parallel robot, leadingmore » to a very efficient model that has been implemented in a real-time computed-torque control algorithm.« less

A communication library for the parallelization of air quality models on structured grids

NASA Astrophysics Data System (ADS)

Miehe, Philipp; Sandu, Adrian; Carmichael, Gregory R.; Tang, Youhua; Dăescu, Dacian

PAQMSG is an MPI-based, Fortran 90 communication library for the parallelization of air quality models (AQMs) on structured grids. It consists of distribution, gathering and repartitioning routines for different domain decompositions implementing a master-worker strategy. The library is architecture and application independent and includes optimization strategies for different architectures. This paper presents the library from a user perspective. Results are shown from the parallelization of STEM-III on Beowulf clusters. The PAQMSG library is available on the web. The communication routines are easy to use, and should allow for an immediate parallelization of existing AQMs. PAQMSG can also be used for constructing new models.

Toward a Model Framework of Generalized Parallel Componential Processing of Multi-Symbol Numbers

ERIC Educational Resources Information Center

Huber, Stefan; Cornelsen, Sonja; Moeller, Korbinian; Nuerk, Hans-Christoph

2015-01-01

In this article, we propose and evaluate a new model framework of parallel componential multi-symbol number processing, generalizing the idea of parallel componential processing of multi-digit numbers to the case of negative numbers by considering the polarity signs similar to single digits. In a first step, we evaluated this account by defining…

Xyce Parallel Electronic Simulator : users' guide, version 2.0.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hoekstra, Robert John; Waters, Lon J.; Rankin, Eric Lamont

2004-06-01

This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator capable of simulating electrical circuits at a variety of abstraction levels. Primarily, Xyce has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability the current state-of-the-art in the following areas: {sm_bullet} Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). Note that this includes support for most popular parallel and serial computers. {sm_bullet} Improved performance for allmore » numerical kernels (e.g., time integrator, nonlinear and linear solvers) through state-of-the-art algorithms and novel techniques. {sm_bullet} Device models which are specifically tailored to meet Sandia's needs, including many radiation-aware devices. {sm_bullet} A client-server or multi-tiered operating model wherein the numerical kernel can operate independently of the graphical user interface (GUI). {sm_bullet} Object-oriented code design and implementation using modern coding practices that ensure that the Xyce Parallel Electronic Simulator will be maintainable and extensible far into the future. Xyce is a parallel code in the most general sense of the phrase - a message passing of computing platforms. These include serial, shared-memory and distributed-memory parallel implementation - which allows it to run efficiently on the widest possible number parallel as well as heterogeneous platforms. Careful attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. One feature required by designers is the ability to add device models, many specific to the needs of Sandia, to the code. To this end, the device package in the Xyce These input formats include standard analytical models, behavioral models look-up Parallel Electronic Simulator is designed to support a variety of device model inputs. tables, and mesh-level PDE device models. Combined with this flexible interface is an architectural design that greatly simplifies the addition of circuit models. One of the most important feature of Xyce is in providing a platform for computational research and development aimed specifically at the needs of the Laboratory. With Xyce, Sandia now has an 'in-house' capability with which both new electrical (e.g., device model development) and algorithmic (e.g., faster time-integration methods) research and development can be performed. Ultimately, these capabilities are migrated to end users.« less

Search asymmetries: parallel processing of uncertain sensory information.

PubMed

Vincent, Benjamin T

2011-08-01

What is the mechanism underlying search phenomena such as search asymmetry? Two-stage models such as Feature Integration Theory and Guided Search propose parallel pre-attentive processing followed by serial post-attentive processing. They claim search asymmetry effects are indicative of finding pairs of features, one processed in parallel, the other in serial. An alternative proposal is that a 1-stage parallel process is responsible, and search asymmetries occur when one stimulus has greater internal uncertainty associated with it than another. While the latter account is simpler, only a few studies have set out to empirically test its quantitative predictions, and many researchers still subscribe to the 2-stage account. This paper examines three separate parallel models (Bayesian optimal observer, max rule, and a heuristic decision rule). All three parallel models can account for search asymmetry effects and I conclude that either people can optimally utilise the uncertain sensory data available to them, or are able to select heuristic decision rules which approximate optimal performance. Copyright © 2011 Elsevier Ltd. All rights reserved.

F-Nets and Software Cabling: Deriving a Formal Model and Language for Portable Parallel Programming

NASA Technical Reports Server (NTRS)

DiNucci, David C.; Saini, Subhash (Technical Monitor)

1998-01-01

Parallel programming is still being based upon antiquated sequence-based definitions of the terms "algorithm" and "computation", resulting in programs which are architecture dependent and difficult to design and analyze. By focusing on obstacles inherent in existing practice, a more portable model is derived here, which is then formalized into a model called Soviets which utilizes a combination of imperative and functional styles. This formalization suggests more general notions of algorithm and computation, as well as insights into the meaning of structured programming in a parallel setting. To illustrate how these principles can be applied, a very-high-level graphical architecture-independent parallel language, called Software Cabling, is described, with many of the features normally expected from today's computer languages (e.g. data abstraction, data parallelism, and object-based programming constructs).

War and peace: morphemes and full forms in a noninteractive activation parallel dual-route model.

PubMed

Baayen, H; Schreuder, R

This article introduces a computational tool for modeling the process of morphological segmentation in visual and auditory word recognition in the framework of a parallel dual-route model. Copyright 1999 Academic Press.

Efficient Parallel Levenberg-Marquardt Model Fitting towards Real-Time Automated Parametric Imaging Microscopy

PubMed Central

Zhu, Xiang; Zhang, Dianwen

2013-01-01

We present a fast, accurate and robust parallel Levenberg-Marquardt minimization optimizer, GPU-LMFit, which is implemented on graphics processing unit for high performance scalable parallel model fitting processing. GPU-LMFit can provide a dramatic speed-up in massive model fitting analyses to enable real-time automated pixel-wise parametric imaging microscopy. We demonstrate the performance of GPU-LMFit for the applications in superresolution localization microscopy and fluorescence lifetime imaging microscopy. PMID:24130785

Distributed computing feasibility in a non-dedicated homogeneous distributed system

NASA Technical Reports Server (NTRS)

Leutenegger, Scott T.; Sun, Xian-He

1993-01-01

The low cost and availability of clusters of workstations have lead researchers to re-explore distributed computing using independent workstations. This approach may provide better cost/performance than tightly coupled multiprocessors. In practice, this approach often utilizes wasted cycles to run parallel jobs. The feasibility of such a non-dedicated parallel processing environment assuming workstation processes have preemptive priority over parallel tasks is addressed. An analytical model is developed to predict parallel job response times. Our model provides insight into how significantly workstation owner interference degrades parallel program performance. A new term task ratio, which relates the parallel task demand to the mean service demand of nonparallel workstation processes, is introduced. It was proposed that task ratio is a useful metric for determining how large the demand of a parallel applications must be in order to make efficient use of a non-dedicated distributed system.

Linearly exact parallel closures for slab geometry

NASA Astrophysics Data System (ADS)

Ji, Jeong-Young; Held, Eric D.; Jhang, Hogun

2013-08-01

Parallel closures are obtained by solving a linearized kinetic equation with a model collision operator using the Fourier transform method. The closures expressed in wave number space are exact for time-dependent linear problems to within the limits of the model collision operator. In the adiabatic, collisionless limit, an inverse Fourier transform is performed to obtain integral (nonlocal) parallel closures in real space; parallel heat flow and viscosity closures for density, temperature, and flow velocity equations replace Braginskii's parallel closure relations, and parallel flow velocity and heat flow closures for density and temperature equations replace Spitzer's parallel transport relations. It is verified that the closures reproduce the exact linear response function of Hammett and Perkins [Phys. Rev. Lett. 64, 3019 (1990)] for Landau damping given a temperature gradient. In contrast to their approximate closures where the vanishing viscosity coefficient numerically gives an exact response, our closures relate the heat flow and nonvanishing viscosity to temperature and flow velocity (gradients).

Verification of Electromagnetic Physics Models for Parallel Computing Architectures in the GeantV Project

DOE Office of Scientific and Technical Information (OSTI.GOV)

Amadio, G.; et al.

An intensive R&D and programming effort is required to accomplish new challenges posed by future experimental high-energy particle physics (HEP) programs. The GeantV project aims to narrow the gap between the performance of the existing HEP detector simulation software and the ideal performance achievable, exploiting latest advances in computing technology. The project has developed a particle detector simulation prototype capable of transporting in parallel particles in complex geometries exploiting instruction level microparallelism (SIMD and SIMT), task-level parallelism (multithreading) and high-level parallelism (MPI), leveraging both the multi-core and the many-core opportunities. We present preliminary verification results concerning the electromagnetic (EM) physicsmore » models developed for parallel computing architectures within the GeantV project. In order to exploit the potential of vectorization and accelerators and to make the physics model effectively parallelizable, advanced sampling techniques have been implemented and tested. In this paper we introduce a set of automated statistical tests in order to verify the vectorized models by checking their consistency with the corresponding Geant4 models and to validate them against experimental data.« less

Xyce parallel electronic simulator users guide, version 6.1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keiter, Eric R; Mei, Ting; Russo, Thomas V.

This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas; Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). This includes support for most popular parallel and serial computers; A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to developmore » new types of analysis without requiring the implementation of analysis-specific device models; Device models that are specifically tailored to meet Sandia's needs, including some radiationaware devices (for Sandia users only); and Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase-a message passing parallel implementation-which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows.« less

Xyce parallel electronic simulator users' guide, Version 6.0.1.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keiter, Eric R; Mei, Ting; Russo, Thomas V.

This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to developmore » new types of analysis without requiring the implementation of analysis-specific device models. Device models that are specifically tailored to meet Sandias needs, including some radiationaware devices (for Sandia users only). Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase a message passing parallel implementation which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows.« less

Xyce parallel electronic simulator users guide, version 6.0.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keiter, Eric R; Mei, Ting; Russo, Thomas V.

This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to developmore » new types of analysis without requiring the implementation of analysis-specific device models. Device models that are specifically tailored to meet Sandias needs, including some radiationaware devices (for Sandia users only). Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase a message passing parallel implementation which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows.« less

Multirate parallel distributed compensation of a cluster in wireless sensor and actor networks

NASA Astrophysics Data System (ADS)

Yang, Chun-xi; Huang, Ling-yun; Zhang, Hao; Hua, Wang

2016-01-01

The stabilisation problem for one of the clusters with bounded multiple random time delays and packet dropouts in wireless sensor and actor networks is investigated in this paper. A new multirate switching model is constructed to describe the feature of this single input multiple output linear system. According to the difficulty of controller design under multi-constraints in multirate switching model, this model can be converted to a Takagi-Sugeno fuzzy model. By designing a multirate parallel distributed compensation, a sufficient condition is established to ensure this closed-loop fuzzy control system to be globally exponentially stable. The solution of the multirate parallel distributed compensation gains can be obtained by solving an auxiliary convex optimisation problem. Finally, two numerical examples are given to show, compared with solving switching controller, multirate parallel distributed compensation can be obtained easily. Furthermore, it has stronger robust stability than arbitrary switching controller and single-rate parallel distributed compensation under the same conditions.

Development Of A Parallel Performance Model For The THOR Neutral Particle Transport Code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yessayan, Raffi; Azmy, Yousry; Schunert, Sebastian

The THOR neutral particle transport code enables simulation of complex geometries for various problems from reactor simulations to nuclear non-proliferation. It is undergoing a thorough V&V requiring computational efficiency. This has motivated various improvements including angular parallelization, outer iteration acceleration, and development of peripheral tools. For guiding future improvements to the code’s efficiency, better characterization of its parallel performance is useful. A parallel performance model (PPM) can be used to evaluate the benefits of modifications and to identify performance bottlenecks. Using INL’s Falcon HPC, the PPM development incorporates an evaluation of network communication behavior over heterogeneous links and a functionalmore » characterization of the per-cell/angle/group runtime of each major code component. After evaluating several possible sources of variability, this resulted in a communication model and a parallel portion model. The former’s accuracy is bounded by the variability of communication on Falcon while the latter has an error on the order of 1%.« less

Parallel imports and the pricing of pharmaceutical products: evidence from the European Union.

PubMed

Ganslandt, Mattias; Maskus, Keith E

2004-09-01

We consider policy issues regarding parallel imports (PIs) of brand-name pharmaceuticals in the European Union, where such trade is permitted. We develop a simple model in which an original manufacturer competes in its home market with PI firms. The model suggests that for small trade costs the original manufacturer will accommodate the import decisions of parallel traders and that the price in the home market falls as the volume of parallel imports rises. Using data from Sweden we find that the prices of drugs subject to competition from parallel imports fell relative to other drugs over the period 1994-1999. Econometric analysis finds that parallel imports significantly reduced manufacturing prices, by 12-19%. There is evidence that this effect increases with multiple PI entrants.

Efficient parallel implementation of active appearance model fitting algorithm on GPU.

PubMed

Wang, Jinwei; Ma, Xirong; Zhu, Yuanping; Sun, Jizhou

2014-01-01

The active appearance model (AAM) is one of the most powerful model-based object detecting and tracking methods which has been widely used in various situations. However, the high-dimensional texture representation causes very time-consuming computations, which makes the AAM difficult to apply to real-time systems. The emergence of modern graphics processing units (GPUs) that feature a many-core, fine-grained parallel architecture provides new and promising solutions to overcome the computational challenge. In this paper, we propose an efficient parallel implementation of the AAM fitting algorithm on GPUs. Our design idea is fine grain parallelism in which we distribute the texture data of the AAM, in pixels, to thousands of parallel GPU threads for processing, which makes the algorithm fit better into the GPU architecture. We implement our algorithm using the compute unified device architecture (CUDA) on the Nvidia's GTX 650 GPU, which has the latest Kepler architecture. To compare the performance of our algorithm with different data sizes, we built sixteen face AAM models of different dimensional textures. The experiment results show that our parallel AAM fitting algorithm can achieve real-time performance for videos even on very high-dimensional textures.

Efficient Parallel Implementation of Active Appearance Model Fitting Algorithm on GPU

PubMed Central

Wang, Jinwei; Ma, Xirong; Zhu, Yuanping; Sun, Jizhou

2014-01-01

The active appearance model (AAM) is one of the most powerful model-based object detecting and tracking methods which has been widely used in various situations. However, the high-dimensional texture representation causes very time-consuming computations, which makes the AAM difficult to apply to real-time systems. The emergence of modern graphics processing units (GPUs) that feature a many-core, fine-grained parallel architecture provides new and promising solutions to overcome the computational challenge. In this paper, we propose an efficient parallel implementation of the AAM fitting algorithm on GPUs. Our design idea is fine grain parallelism in which we distribute the texture data of the AAM, in pixels, to thousands of parallel GPU threads for processing, which makes the algorithm fit better into the GPU architecture. We implement our algorithm using the compute unified device architecture (CUDA) on the Nvidia's GTX 650 GPU, which has the latest Kepler architecture. To compare the performance of our algorithm with different data sizes, we built sixteen face AAM models of different dimensional textures. The experiment results show that our parallel AAM fitting algorithm can achieve real-time performance for videos even on very high-dimensional textures. PMID:24723812

Considering Horn's Parallel Analysis from a Random Matrix Theory Point of View.

PubMed

Saccenti, Edoardo; Timmerman, Marieke E

2017-03-01

Horn's parallel analysis is a widely used method for assessing the number of principal components and common factors. We discuss the theoretical foundations of parallel analysis for principal components based on a covariance matrix by making use of arguments from random matrix theory. In particular, we show that (i) for the first component, parallel analysis is an inferential method equivalent to the Tracy-Widom test, (ii) its use to test high-order eigenvalues is equivalent to the use of the joint distribution of the eigenvalues, and thus should be discouraged, and (iii) a formal test for higher-order components can be obtained based on a Tracy-Widom approximation. We illustrate the performance of the two testing procedures using simulated data generated under both a principal component model and a common factors model. For the principal component model, the Tracy-Widom test performs consistently in all conditions, while parallel analysis shows unpredictable behavior for higher-order components. For the common factor model, including major and minor factors, both procedures are heuristic approaches, with variable performance. We conclude that the Tracy-Widom procedure is preferred over parallel analysis for statistically testing the number of principal components based on a covariance matrix.

High Performance Programming Using Explicit Shared Memory Model on Cray T3D1

NASA Technical Reports Server (NTRS)

Simon, Horst D.; Saini, Subhash; Grassi, Charles

1994-01-01

The Cray T3D system is the first-phase system in Cray Research, Inc.'s (CRI) three-phase massively parallel processing (MPP) program. This system features a heterogeneous architecture that closely couples DEC's Alpha microprocessors and CRI's parallel-vector technology, i.e., the Cray Y-MP and Cray C90. An overview of the Cray T3D hardware and available programming models is presented. Under Cray Research adaptive Fortran (CRAFT) model four programming methods (data parallel, work sharing, message-passing using PVM, and explicit shared memory model) are available to the users. However, at this time data parallel and work sharing programming models are not available to the user community. The differences between standard PVM and CRI's PVM are highlighted with performance measurements such as latencies and communication bandwidths. We have found that the performance of neither standard PVM nor CRI s PVM exploits the hardware capabilities of the T3D. The reasons for the bad performance of PVM as a native message-passing library are presented. This is illustrated by the performance of NAS Parallel Benchmarks (NPB) programmed in explicit shared memory model on Cray T3D. In general, the performance of standard PVM is about 4 to 5 times less than obtained by using explicit shared memory model. This degradation in performance is also seen on CM-5 where the performance of applications using native message-passing library CMMD on CM-5 is also about 4 to 5 times less than using data parallel methods. The issues involved (such as barriers, synchronization, invalidating data cache, aligning data cache etc.) while programming in explicit shared memory model are discussed. Comparative performance of NPB using explicit shared memory programming model on the Cray T3D and other highly parallel systems such as the TMC CM-5, Intel Paragon, Cray C90, IBM-SP1, etc. is presented.

Parallel Computing Using Web Servers and "Servlets".

ERIC Educational Resources Information Center

Lo, Alfred; Bloor, Chris; Choi, Y. K.

2000-01-01

Describes parallel computing and presents inexpensive ways to implement a virtual parallel computer with multiple Web servers. Highlights include performance measurement of parallel systems; models for using Java and intranet technology including single server, multiple clients and multiple servers, single client; and a comparison of CGI (common…

Parallel Computation of the Regional Ocean Modeling System (ROMS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, P; Song, Y T; Chao, Y

2005-04-05

The Regional Ocean Modeling System (ROMS) is a regional ocean general circulation modeling system solving the free surface, hydrostatic, primitive equations over varying topography. It is free software distributed world-wide for studying both complex coastal ocean problems and the basin-to-global scale ocean circulation. The original ROMS code could only be run on shared-memory systems. With the increasing need to simulate larger model domains with finer resolutions and on a variety of computer platforms, there is a need in the ocean-modeling community to have a ROMS code that can be run on any parallel computer ranging from 10 to hundreds ofmore » processors. Recently, we have explored parallelization for ROMS using the MPI programming model. In this paper, an efficient parallelization strategy for such a large-scale scientific software package, based on an existing shared-memory computing model, is presented. In addition, scientific applications and data-performance issues on a couple of SGI systems, including Columbia, the world's third-fastest supercomputer, are discussed.« less

Performance of GeantV EM Physics Models

NASA Astrophysics Data System (ADS)

Amadio, G.; Ananya, A.; Apostolakis, J.; Aurora, A.; Bandieramonte, M.; Bhattacharyya, A.; Bianchini, C.; Brun, R.; Canal, P.; Carminati, F.; Cosmo, G.; Duhem, L.; Elvira, D.; Folger, G.; Gheata, A.; Gheata, M.; Goulas, I.; Iope, R.; Jun, S. Y.; Lima, G.; Mohanty, A.; Nikitina, T.; Novak, M.; Pokorski, W.; Ribon, A.; Seghal, R.; Shadura, O.; Vallecorsa, S.; Wenzel, S.; Zhang, Y.

2017-10-01

The recent progress in parallel hardware architectures with deeper vector pipelines or many-cores technologies brings opportunities for HEP experiments to take advantage of SIMD and SIMT computing models. Launched in 2013, the GeantV project studies performance gains in propagating multiple particles in parallel, improving instruction throughput and data locality in HEP event simulation on modern parallel hardware architecture. Due to the complexity of geometry description and physics algorithms of a typical HEP application, performance analysis is indispensable in identifying factors limiting parallel execution. In this report, we will present design considerations and preliminary computing performance of GeantV physics models on coprocessors (Intel Xeon Phi and NVidia GPUs) as well as on mainstream CPUs.

A Bold Step Forward: Juxtaposition of the Constructivist and Freeschooling Learning Model

ERIC Educational Resources Information Center

Chiatul, Victoria Oliaku

2015-01-01

This article discusses the juxtaposition of learning within the parallel structure of the constructivist and freeschooling models of education. To begin, characteristics describing the constructivist-learning model are provided, followed by a summary of the major components of the freeschooling-learning model. Finally, the parallel structure…

Validation of neoclassical bootstrap current models in the edge of an H-mode plasma.

PubMed

Wade, M R; Murakami, M; Politzer, P A

2004-06-11

Analysis of the parallel electric field E(parallel) evolution following an L-H transition in the DIII-D tokamak indicates the generation of a large negative pulse near the edge which propagates inward, indicative of the generation of a noninductive edge current. Modeling indicates that the observed E(parallel) evolution is consistent with a narrow current density peak generated in the plasma edge. Very good quantitative agreement is found between the measured E(parallel) evolution and that expected from neoclassical theory predictions of the bootstrap current.

Improving operating room productivity via parallel anesthesia processing.

PubMed

Brown, Michael J; Subramanian, Arun; Curry, Timothy B; Kor, Daryl J; Moran, Steven L; Rohleder, Thomas R

2014-01-01

Parallel processing of regional anesthesia may improve operating room (OR) efficiency in patients undergoes upper extremity surgical procedures. The purpose of this paper is to evaluate whether performing regional anesthesia outside the OR in parallel increases total cases per day, improve efficiency and productivity. Data from all adult patients who underwent regional anesthesia as their primary anesthetic for upper extremity surgery over a one-year period were used to develop a simulation model. The model evaluated pure operating modes of regional anesthesia performed within and outside the OR in a parallel manner. The scenarios were used to evaluate how many surgeries could be completed in a standard work day (555 minutes) and assuming a standard three cases per day, what was the predicted end-of-day time overtime. Modeling results show that parallel processing of regional anesthesia increases the average cases per day for all surgeons included in the study. The average increase was 0.42 surgeries per day. Where it was assumed that three cases per day would be performed by all surgeons, the days going to overtime was reduced by 43 percent with parallel block. The overtime with parallel anesthesia was also projected to be 40 minutes less per day per surgeon. Key limitations include the assumption that all cases used regional anesthesia in the comparisons. Many days may have both regional and general anesthesia. Also, as a case study, single-center research may limit generalizability. Perioperative care providers should consider parallel administration of regional anesthesia where there is a desire to increase daily upper extremity surgical case capacity. Where there are sufficient resources to do parallel anesthesia processing, efficiency and productivity can be significantly improved. Simulation modeling can be an effective tool to show practice change effects at a system-wide level.

Connectionism, parallel constraint satisfaction processes, and gestalt principles: (re) introducing cognitive dynamics to social psychology.

PubMed

Read, S J; Vanman, E J; Miller, L C

1997-01-01

We argue that recent work in connectionist modeling, in particular the parallel constraint satisfaction processes that are central to many of these models, has great importance for understanding issues of both historical and current concern for social psychologists. We first provide a brief description of connectionist modeling, with particular emphasis on parallel constraint satisfaction processes. Second, we examine the tremendous similarities between parallel constraint satisfaction processes and the Gestalt principles that were the foundation for much of modem social psychology. We propose that parallel constraint satisfaction processes provide a computational implementation of the principles of Gestalt psychology that were central to the work of such seminal social psychologists as Asch, Festinger, Heider, and Lewin. Third, we then describe how parallel constraint satisfaction processes have been applied to three areas that were key to the beginnings of modern social psychology and remain central today: impression formation and causal reasoning, cognitive consistency (balance and cognitive dissonance), and goal-directed behavior. We conclude by discussing implications of parallel constraint satisfaction principles for a number of broader issues in social psychology, such as the dynamics of social thought and the integration of social information within the narrow time frame of social interaction.

Reliability models for dataflow computer systems

NASA Technical Reports Server (NTRS)

Kavi, K. M.; Buckles, B. P.

1985-01-01

The demands for concurrent operation within a computer system and the representation of parallelism in programming languages have yielded a new form of program representation known as data flow (DENN 74, DENN 75, TREL 82a). A new model based on data flow principles for parallel computations and parallel computer systems is presented. Necessary conditions for liveness and deadlock freeness in data flow graphs are derived. The data flow graph is used as a model to represent asynchronous concurrent computer architectures including data flow computers.

Screening for (anti)androgenic properties using a standard operation protocol based on the human stably transfected androgen sensitive PALM cell line. First steps towards validation.

PubMed

Freyberger, A; Witters, H; Weimer, M; Lofink, W; Berckmans, P; Ahr, H-J

2010-08-01

Despite more than a decade of research in the field of endocrine active compounds targeting the androgen receptor (AR), and although suitable cell lines can be obtained, no validated human stably transfected androgen sensitive transactivation assay is available. Bayer Schering Pharma (BSP) and the Flemish Institute for Technological Research (VITO), partners within the EU-sponsored 6th framework project ReProTect, made first steps towards such a validation. A standard operation protocol (SOP) developed at BSP based on the androgen sensitive PALM cell line was transferred to VITO and its performance and transferability were thoroughly studied. The investigation followed a generic protocol prepared for all reporter gene assays evaluated within ReProTect, and in both laboratories at least three independent experiments were performed. The highest concentration to be tested was limited to 10 microM, if needed. A few compounds, 17alpha-methyltestosterone (17alpha-MT), vinclozolin and linuron, were studied using a real world scenario, i.e., assuming that their interaction with the AR was not known: A prescreening for agonism and true, competitive antagonism was used to select conditions such as the appropriate mode of action, and the working range excluding cytotoxicity for the final screening. All other compounds were tested according to the generic protocol: Compounds screened for agonism were the reference androgen 17alpha-methyldihydrotestosterone (MDHT), levonorgestrel, norethynodrel, progesterone, o,p'-DDT, and dibutylphthalate (DBP), while compounds screened for antagonism were the reference anti-androgen flutamide, prochloraz, o,p'-DDT, progesterone, norethynodrel, and DBP. Cytotoxicity was assessed in parallel as lactate dehydrogenase release. The prescreen classified 17alpha-MT as androgenic, vinclozolin and linuron as anti-androgenic and compounds were tested accordingly. In the absence of cytotoxicity, appropriate androgenic properties of reference and test compounds were detected by both laboratories, o,p'-DDT and DBP had no androgenic activity. Across the two laboratories EC(50)-values for MDHT, 17alpha-MT, and levonorgestrel varied by not more than a factor of 3.4, for norethynodrel by a factor of 9.7. Progesterone effects could not fully be evaluated, as frequently concentration response curves were incomplete. In the absence of cytotoxicity anti-androgenic properties of reference and test compounds were also detected in both laboratories. DBP, the putative negative reference compound, was inactive, norethynodrel rather showed agonistic properties. Progesterone was an antagonist at low concentrations, but agonistic properties were observed in one laboratory at high concentrations. Since the highest test concentration was limited to 10 microM, for some compounds no complete concentration response curves were obtained and estimation of EC(50)-values was less robust. Our data demonstrated that the SOP was transferable, and that the assay was able to rank compounds with strong, weak, and without affinity for the AR and to discriminate agonists and antagonists. The sensitivity of the assay could be improved further, if the limit of solubility or beginning cytotoxicity was chosen as the highest test concentration. The assay avoids the use of tissues from laboratory animals, and thus contributes to the 3R concept. Furthermore, it could be adjusted to an intermediate/high throughput format. On the whole, this PALM assay is a promising candidate for further validation. Copyright 2009 Elsevier Inc. All rights reserved.

Turbomachinery CFD on parallel computers

NASA Technical Reports Server (NTRS)

Blech, Richard A.; Milner, Edward J.; Quealy, Angela; Townsend, Scott E.

1992-01-01

The role of multistage turbomachinery simulation in the development of propulsion system models is discussed. Particularly, the need for simulations with higher fidelity and faster turnaround time is highlighted. It is shown how such fast simulations can be used in engineering-oriented environments. The use of parallel processing to achieve the required turnaround times is discussed. Current work by several researchers in this area is summarized. Parallel turbomachinery CFD research at the NASA Lewis Research Center is then highlighted. These efforts are focused on implementing the average-passage turbomachinery model on MIMD, distributed memory parallel computers. Performance results are given for inviscid, single blade row and viscous, multistage applications on several parallel computers, including networked workstations.

Parallel solution of sparse one-dimensional dynamic programming problems

NASA Technical Reports Server (NTRS)

Nicol, David M.

1989-01-01

Parallel computation offers the potential for quickly solving large computational problems. However, it is often a non-trivial task to effectively use parallel computers. Solution methods must sometimes be reformulated to exploit parallelism; the reformulations are often more complex than their slower serial counterparts. We illustrate these points by studying the parallelization of sparse one-dimensional dynamic programming problems, those which do not obviously admit substantial parallelization. We propose a new method for parallelizing such problems, develop analytic models which help us to identify problems which parallelize well, and compare the performance of our algorithm with existing algorithms on a multiprocessor.

Biocellion: accelerating computer simulation of multicellular biological system models

PubMed Central

Kang, Seunghwa; Kahan, Simon; McDermott, Jason; Flann, Nicholas; Shmulevich, Ilya

2014-01-01

Motivation: Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming. Results: We have developed Biocellion, a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion, modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies. Availability and implementation: Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information. Contact: seunghwa.kang@pnnl.gov PMID:25064572

Stage-by-Stage and Parallel Flow Path Compressor Modeling for a Variable Cycle Engine

NASA Technical Reports Server (NTRS)

Kopasakis, George; Connolly, Joseph W.; Cheng, Larry

2015-01-01

This paper covers the development of stage-by-stage and parallel flow path compressor modeling approaches for a Variable Cycle Engine. The stage-by-stage compressor modeling approach is an extension of a technique for lumped volume dynamics and performance characteristic modeling. It was developed to improve the accuracy of axial compressor dynamics over lumped volume dynamics modeling. The stage-by-stage compressor model presented here is formulated into a parallel flow path model that includes both axial and rotational dynamics. This is done to enable the study of compressor and propulsion system dynamic performance under flow distortion conditions. The approaches utilized here are generic and should be applicable for the modeling of any axial flow compressor design.

Development of a parallel FE simulator for modeling the whole trans-scale failure process of rock from meso- to engineering-scale

NASA Astrophysics Data System (ADS)

Li, Gen; Tang, Chun-An; Liang, Zheng-Zhao

2017-01-01

Multi-scale high-resolution modeling of rock failure process is a powerful means in modern rock mechanics studies to reveal the complex failure mechanism and to evaluate engineering risks. However, multi-scale continuous modeling of rock, from deformation, damage to failure, has raised high requirements on the design, implementation scheme and computation capacity of the numerical software system. This study is aimed at developing the parallel finite element procedure, a parallel rock failure process analysis (RFPA) simulator that is capable of modeling the whole trans-scale failure process of rock. Based on the statistical meso-damage mechanical method, the RFPA simulator is able to construct heterogeneous rock models with multiple mechanical properties, deal with and represent the trans-scale propagation of cracks, in which the stress and strain fields are solved for the damage evolution analysis of representative volume element by the parallel finite element method (FEM) solver. This paper describes the theoretical basis of the approach and provides the details of the parallel implementation on a Windows - Linux interactive platform. A numerical model is built to test the parallel performance of FEM solver. Numerical simulations are then carried out on a laboratory-scale uniaxial compression test, and field-scale net fracture spacing and engineering-scale rock slope examples, respectively. The simulation results indicate that relatively high speedup and computation efficiency can be achieved by the parallel FEM solver with a reasonable boot process. In laboratory-scale simulation, the well-known physical phenomena, such as the macroscopic fracture pattern and stress-strain responses, can be reproduced. In field-scale simulation, the formation process of net fracture spacing from initiation, propagation to saturation can be revealed completely. In engineering-scale simulation, the whole progressive failure process of the rock slope can be well modeled. It is shown that the parallel FE simulator developed in this study is an efficient tool for modeling the whole trans-scale failure process of rock from meso- to engineering-scale.

Applications of New Surrogate Global Optimization Algorithms including Efficient Synchronous and Asynchronous Parallelism for Calibration of Expensive Nonlinear Geophysical Simulation Models.

NASA Astrophysics Data System (ADS)

Shoemaker, C. A.; Pang, M.; Akhtar, T.; Bindel, D.

2016-12-01

New parallel surrogate global optimization algorithms are developed and applied to objective functions that are expensive simulations (possibly with multiple local minima). The algorithms can be applied to most geophysical simulations, including those with nonlinear partial differential equations. The optimization does not require simulations be parallelized. Asynchronous (and synchronous) parallel execution is available in the optimization toolbox "pySOT". The parallel algorithms are modified from serial to eliminate fine grained parallelism. The optimization is computed with open source software pySOT, a Surrogate Global Optimization Toolbox that allows user to pick the type of surrogate (or ensembles), the search procedure on surrogate, and the type of parallelism (synchronous or asynchronous). pySOT also allows the user to develop new algorithms by modifying parts of the code. In the applications here, the objective function takes up to 30 minutes for one simulation, and serial optimization can take over 200 hours. Results from Yellowstone (NSF) and NCSS (Singapore) supercomputers are given for groundwater contaminant hydrology simulations with applications to model parameter estimation and decontamination management. All results are compared with alternatives. The first results are for optimization of pumping at many wells to reduce cost for decontamination of groundwater at a superfund site. The optimization runs with up to 128 processors. Superlinear speed up is obtained for up to 16 processors, and efficiency with 64 processors is over 80%. Each evaluation of the objective function requires the solution of nonlinear partial differential equations to describe the impact of spatially distributed pumping and model parameters on model predictions for the spatial and temporal distribution of groundwater contaminants. The second application uses an asynchronous parallel global optimization for groundwater quality model calibration. The time for a single objective function evaluation varies unpredictably, so efficiency is improved with asynchronous parallel calculations to improve load balancing. The third application (done at NCSS) incorporates new global surrogate multi-objective parallel search algorithms into pySOT and applies it to a large watershed calibration problem.

Application of a hybrid MPI/OpenMP approach for parallel groundwater model calibration using multi-core computers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang, Guoping; D'Azevedo, Ed F; Zhang, Fan

2010-01-01

Calibration of groundwater models involves hundreds to thousands of forward solutions, each of which may solve many transient coupled nonlinear partial differential equations, resulting in a computationally intensive problem. We describe a hybrid MPI/OpenMP approach to exploit two levels of parallelisms in software and hardware to reduce calibration time on multi-core computers. HydroGeoChem 5.0 (HGC5) is parallelized using OpenMP for direct solutions for a reactive transport model application, and a field-scale coupled flow and transport model application. In the reactive transport model, a single parallelizable loop is identified to account for over 97% of the total computational time using GPROF.more » Addition of a few lines of OpenMP compiler directives to the loop yields a speedup of about 10 on a 16-core compute node. For the field-scale model, parallelizable loops in 14 of 174 HGC5 subroutines that require 99% of the execution time are identified. As these loops are parallelized incrementally, the scalability is found to be limited by a loop where Cray PAT detects over 90% cache missing rates. With this loop rewritten, similar speedup as the first application is achieved. The OpenMP-parallelized code can be run efficiently on multiple workstations in a network or multiple compute nodes on a cluster as slaves using parallel PEST to speedup model calibration. To run calibration on clusters as a single task, the Levenberg Marquardt algorithm is added to HGC5 with the Jacobian calculation and lambda search parallelized using MPI. With this hybrid approach, 100 200 compute cores are used to reduce the calibration time from weeks to a few hours for these two applications. This approach is applicable to most of the existing groundwater model codes for many applications.« less

On the impact of communication complexity in the design of parallel numerical algorithms

NASA Technical Reports Server (NTRS)

Gannon, D.; Vanrosendale, J.

1984-01-01

This paper describes two models of the cost of data movement in parallel numerical algorithms. One model is a generalization of an approach due to Hockney, and is suitable for shared memory multiprocessors where each processor has vector capabilities. The other model is applicable to highly parallel nonshared memory MIMD systems. In the second model, algorithm performance is characterized in terms of the communication network design. Techniques used in VLSI complexity theory are also brought in, and algorithm independent upper bounds on system performance are derived for several problems that are important to scientific computation.

On the impact of communication complexity on the design of parallel numerical algorithms

NASA Technical Reports Server (NTRS)

Gannon, D. B.; Van Rosendale, J.

1984-01-01

This paper describes two models of the cost of data movement in parallel numerical alorithms. One model is a generalization of an approach due to Hockney, and is suitable for shared memory multiprocessors where each processor has vector capabilities. The other model is applicable to highly parallel nonshared memory MIMD systems. In this second model, algorithm performance is characterized in terms of the communication network design. Techniques used in VLSI complexity theory are also brought in, and algorithm-independent upper bounds on system performance are derived for several problems that are important to scientific computation.

Designing a parallel evolutionary algorithm for inferring gene networks on the cloud computing environment.

PubMed

Lee, Wei-Po; Hsiao, Yu-Ting; Hwang, Wei-Che

2014-01-16

To improve the tedious task of reconstructing gene networks through testing experimentally the possible interactions between genes, it becomes a trend to adopt the automated reverse engineering procedure instead. Some evolutionary algorithms have been suggested for deriving network parameters. However, to infer large networks by the evolutionary algorithm, it is necessary to address two important issues: premature convergence and high computational cost. To tackle the former problem and to enhance the performance of traditional evolutionary algorithms, it is advisable to use parallel model evolutionary algorithms. To overcome the latter and to speed up the computation, it is advocated to adopt the mechanism of cloud computing as a promising solution: most popular is the method of MapReduce programming model, a fault-tolerant framework to implement parallel algorithms for inferring large gene networks. This work presents a practical framework to infer large gene networks, by developing and parallelizing a hybrid GA-PSO optimization method. Our parallel method is extended to work with the Hadoop MapReduce programming model and is executed in different cloud computing environments. To evaluate the proposed approach, we use a well-known open-source software GeneNetWeaver to create several yeast S. cerevisiae sub-networks and use them to produce gene profiles. Experiments have been conducted and the results have been analyzed. They show that our parallel approach can be successfully used to infer networks with desired behaviors and the computation time can be largely reduced. Parallel population-based algorithms can effectively determine network parameters and they perform better than the widely-used sequential algorithms in gene network inference. These parallel algorithms can be distributed to the cloud computing environment to speed up the computation. By coupling the parallel model population-based optimization method and the parallel computational framework, high quality solutions can be obtained within relatively short time. This integrated approach is a promising way for inferring large networks.

Designing a parallel evolutionary algorithm for inferring gene networks on the cloud computing environment

PubMed Central

2014-01-01

Background To improve the tedious task of reconstructing gene networks through testing experimentally the possible interactions between genes, it becomes a trend to adopt the automated reverse engineering procedure instead. Some evolutionary algorithms have been suggested for deriving network parameters. However, to infer large networks by the evolutionary algorithm, it is necessary to address two important issues: premature convergence and high computational cost. To tackle the former problem and to enhance the performance of traditional evolutionary algorithms, it is advisable to use parallel model evolutionary algorithms. To overcome the latter and to speed up the computation, it is advocated to adopt the mechanism of cloud computing as a promising solution: most popular is the method of MapReduce programming model, a fault-tolerant framework to implement parallel algorithms for inferring large gene networks. Results This work presents a practical framework to infer large gene networks, by developing and parallelizing a hybrid GA-PSO optimization method. Our parallel method is extended to work with the Hadoop MapReduce programming model and is executed in different cloud computing environments. To evaluate the proposed approach, we use a well-known open-source software GeneNetWeaver to create several yeast S. cerevisiae sub-networks and use them to produce gene profiles. Experiments have been conducted and the results have been analyzed. They show that our parallel approach can be successfully used to infer networks with desired behaviors and the computation time can be largely reduced. Conclusions Parallel population-based algorithms can effectively determine network parameters and they perform better than the widely-used sequential algorithms in gene network inference. These parallel algorithms can be distributed to the cloud computing environment to speed up the computation. By coupling the parallel model population-based optimization method and the parallel computational framework, high quality solutions can be obtained within relatively short time. This integrated approach is a promising way for inferring large networks. PMID:24428926

Parallelization of the TRIGRS model for rainfall-induced landslides using the message passing interface

USGS Publications Warehouse

Alvioli, M.; Baum, R.L.

2016-01-01

We describe a parallel implementation of TRIGRS, the Transient Rainfall Infiltration and Grid-Based Regional Slope-Stability Model for the timing and distribution of rainfall-induced shallow landslides. We have parallelized the four time-demanding execution modes of TRIGRS, namely both the saturated and unsaturated model with finite and infinite soil depth options, within the Message Passing Interface framework. In addition to new features of the code, we outline details of the parallel implementation and show the performance gain with respect to the serial code. Results are obtained both on commercial hardware and on a high-performance multi-node machine, showing the different limits of applicability of the new code. We also discuss the implications for the application of the model on large-scale areas and as a tool for real-time landslide hazard monitoring.

Analysis of multigrid methods on massively parallel computers: Architectural implications

NASA Technical Reports Server (NTRS)

Matheson, Lesley R.; Tarjan, Robert E.

1993-01-01

We study the potential performance of multigrid algorithms running on massively parallel computers with the intent of discovering whether presently envisioned machines will provide an efficient platform for such algorithms. We consider the domain parallel version of the standard V cycle algorithm on model problems, discretized using finite difference techniques in two and three dimensions on block structured grids of size 10(exp 6) and 10(exp 9), respectively. Our models of parallel computation were developed to reflect the computing characteristics of the current generation of massively parallel multicomputers. These models are based on an interconnection network of 256 to 16,384 message passing, 'workstation size' processors executing in an SPMD mode. The first model accomplishes interprocessor communications through a multistage permutation network. The communication cost is a logarithmic function which is similar to the costs in a variety of different topologies. The second model allows single stage communication costs only. Both models were designed with information provided by machine developers and utilize implementation derived parameters. With the medium grain parallelism of the current generation and the high fixed cost of an interprocessor communication, our analysis suggests an efficient implementation requires the machine to support the efficient transmission of long messages, (up to 1000 words) or the high initiation cost of a communication must be significantly reduced through an alternative optimization technique. Furthermore, with variable length message capability, our analysis suggests the low diameter multistage networks provide little or no advantage over a simple single stage communications network.

The Parallel System for Integrating Impact Models and Sectors (pSIMS)

NASA Technical Reports Server (NTRS)

Elliott, Joshua; Kelly, David; Chryssanthacopoulos, James; Glotter, Michael; Jhunjhnuwala, Kanika; Best, Neil; Wilde, Michael; Foster, Ian

2014-01-01

We present a framework for massively parallel climate impact simulations: the parallel System for Integrating Impact Models and Sectors (pSIMS). This framework comprises a) tools for ingesting and converting large amounts of data to a versatile datatype based on a common geospatial grid; b) tools for translating this datatype into custom formats for site-based models; c) a scalable parallel framework for performing large ensemble simulations, using any one of a number of different impacts models, on clusters, supercomputers, distributed grids, or clouds; d) tools and data standards for reformatting outputs to common datatypes for analysis and visualization; and e) methodologies for aggregating these datatypes to arbitrary spatial scales such as administrative and environmental demarcations. By automating many time-consuming and error-prone aspects of large-scale climate impacts studies, pSIMS accelerates computational research, encourages model intercomparison, and enhances reproducibility of simulation results. We present the pSIMS design and use example assessments to demonstrate its multi-model, multi-scale, and multi-sector versatility.

The interaction of turbulence with parallel and perpendicular shocks

NASA Astrophysics Data System (ADS)

Adhikari, L.; Zank, G. P.; Hunana, P.; Hu, Q.

2016-11-01

Interplanetary shocks exist in most astrophysical flows, and modify the properties of the background flow. We apply the Zank et al 2012 six coupled turbulence transport model equations to study the interaction of turbulence with parallel and perpendicular shock waves in the solar wind. We model the 1D structure of a stationary perpendicular or parallel shock wave using a hyperbolic tangent function and the Rankine-Hugoniot conditions. A reduced turbulence transport model (the 4-equation model) is applied to parallel and perpendicular shock waves, and solved using a 4th- order Runge Kutta method. We compare the model results with ACE spacecraft observations. We identify one quasi-parallel and one quasi-perpendicular event in the ACE spacecraft data sets, and compute various turbulent observed values such as the fluctuating magnetic and kinetic energy, the energy in forward and backward propagating modes, the total turbulent energy in the upstream and downstream of the shock. We also calculate the error associated with each turbulent observed value, and fit the observed values by a least square method and use a Fourier series fitting function. We find that the theoretical results are in reasonable agreement with observations. The energy in turbulent fluctuations is enhanced and the correlation length is approximately constant at the shock. Similarly, the normalized cross helicity increases across a perpendicular shock, and decreases across a parallel shock.

Xyce Parallel Electronic Simulator Users' Guide Version 6.8

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keiter, Eric R.; Aadithya, Karthik Venkatraman; Mei, Ting

This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been de- signed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: Capability to solve extremely large circuit problems by supporting large-scale parallel com- puting platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows onemore » to develop new types of analysis without requiring the implementation of analysis-specific device models. Device models that are specifically tailored to meet Sandia's needs, including some radiation- aware devices (for Sandia users only). Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase$-$ a message passing parallel implementation $-$ which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows.« less

Human umbilical vein endothelial cells synergize osteo/odontogenic differentiation of periodontal ligament stem cells in 3D cell sheets.

PubMed

Pandula, P K C Prgeeth; Samaranayake, L P; Jin, L J; Zhang, C F

2014-06-01

To investigate the expression of osteo/odontogenic differentiation markers and vascular network formation in a 3D cell sheet with varying cell ratios of periodontal ligament stem cells (PDLSCs) and human umbilical vein endothelial cells (HUVECs). Human PDLSCs were isolated and characterized by flow cytometry, and co-cultured with HUVECs for the construction of cell sheets. Both types of cells were seeded on temperature-responsive culture dishes with PDLSCs alone, HUVECs alone and various ratios of the latter cells (1 : 1, 2 : 1, 5 : 1 and 1 : 5) to obtain confluent cell sheets. The expressions of osteo/odontogenic pathway markers, including alkaline phosphatase (ALP), bone sialoprotein (BSP) and runt-related transcription factor 2 (RUNX2), were analyzed at 3 and 7 d using RT-PCR. Further ALP protein quantification was performed at 7 and 14 d using ALP assay. The calcium nodule formation was assessed qualitatively and quantitatively by alizarin red assay. Histological evaluations of three cell sheet constructs treated with different combinations (PDLSC-PDLSC-PDLSC/PDLSC-HUVEC-PDLSC/co-culture-co-culture-co-culture) were performed with hematoxylin and eosin and immunofluorescence staining. Statistical analysis was performed using t-test (p < 0.05). Significantly higher ALP gene expression was observed at 3 d in 1 : 1 (PDLSC-HUVEC) (2.52 ± 0.67) and 5 : 1 (4.05 ± 1.07) co-culture groups compared with other groups (p < 0.05); this was consistent with ALP protein quantification. However, the expression of BSP and RUNX2 genes was higher at 7 d compared to 3 d. Significant calcium mineralization was detected as quantified by alizarin red assay at 14 d in 1 : 1 (1323.55 ± 6.54 μm) and 5 : 1 (994.67 ± 4.15 μm) co-cultures as compared with monoculture cell sheets (p < 0.05). Hematoxylin and eosin and CD31 immunostaining clearly exemplified the development of a layered cell sheet structure with endothelial cell islands within the constructed PDLSC-HUVEC-PDLSC and co-culture groups. Furthermore, HUVECs invaded the layered cell sheet, suggestive of rudimentary vascular network initiation. This study suggests that the PDLSC-HUVEC co-culture, cell sheet, model exhibits significantly high levels of osteo/odontogenic markers with signs of initial vascular formation. This novel 3D cell sheet-based approach may be potentially beneficial for periodontal regenerative therapy. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

MPI, HPF or OpenMP: A Study with the NAS Benchmarks

NASA Technical Reports Server (NTRS)

Jin, Hao-Qiang; Frumkin, Michael; Hribar, Michelle; Waheed, Abdul; Yan, Jerry; Saini, Subhash (Technical Monitor)

1999-01-01

Porting applications to new high performance parallel and distributed platforms is a challenging task. Writing parallel code by hand is time consuming and costly, but the task can be simplified by high level languages and would even better be automated by parallelizing tools and compilers. The definition of HPF (High Performance Fortran, based on data parallel model) and OpenMP (based on shared memory parallel model) standards has offered great opportunity in this respect. Both provide simple and clear interfaces to language like FORTRAN and simplify many tedious tasks encountered in writing message passing programs. In our study we implemented the parallel versions of the NAS Benchmarks with HPF and OpenMP directives. Comparison of their performance with the MPI implementation and pros and cons of different approaches will be discussed along with experience of using computer-aided tools to help parallelize these benchmarks. Based on the study,potentials of applying some of the techniques to realistic aerospace applications will be presented

Second International Workshop on Software Engineering and Code Design in Parallel Meteorological and Oceanographic Applications

NASA Technical Reports Server (NTRS)

OKeefe, Matthew (Editor); Kerr, Christopher L. (Editor)

1998-01-01

This report contains the abstracts and technical papers from the Second International Workshop on Software Engineering and Code Design in Parallel Meteorological and Oceanographic Applications, held June 15-18, 1998, in Scottsdale, Arizona. The purpose of the workshop is to bring together software developers in meteorology and oceanography to discuss software engineering and code design issues for parallel architectures, including Massively Parallel Processors (MPP's), Parallel Vector Processors (PVP's), Symmetric Multi-Processors (SMP's), Distributed Shared Memory (DSM) multi-processors, and clusters. Issues to be discussed include: (1) code architectures for current parallel models, including basic data structures, storage allocation, variable naming conventions, coding rules and styles, i/o and pre/post-processing of data; (2) designing modular code; (3) load balancing and domain decomposition; (4) techniques that exploit parallelism efficiently yet hide the machine-related details from the programmer; (5) tools for making the programmer more productive; and (6) the proliferation of programming models (F--, OpenMP, MPI, and HPF).

MPI, HPF or OpenMP: A Study with the NAS Benchmarks

NASA Technical Reports Server (NTRS)

Jin, H.; Frumkin, M.; Hribar, M.; Waheed, A.; Yan, J.; Saini, Subhash (Technical Monitor)

1999-01-01

Porting applications to new high performance parallel and distributed platforms is a challenging task. Writing parallel code by hand is time consuming and costly, but this task can be simplified by high level languages and would even better be automated by parallelizing tools and compilers. The definition of HPF (High Performance Fortran, based on data parallel model) and OpenMP (based on shared memory parallel model) standards has offered great opportunity in this respect. Both provide simple and clear interfaces to language like FORTRAN and simplify many tedious tasks encountered in writing message passing programs. In our study, we implemented the parallel versions of the NAS Benchmarks with HPF and OpenMP directives. Comparison of their performance with the MPI implementation and pros and cons of different approaches will be discussed along with experience of using computer-aided tools to help parallelize these benchmarks. Based on the study, potentials of applying some of the techniques to realistic aerospace applications will be presented.

Effects of imbalanced currents on large-format LiFePO4/graphite batteries systems connected in parallel

NASA Astrophysics Data System (ADS)

Shi, Wei; Hu, Xiaosong; Jin, Chao; Jiang, Jiuchun; Zhang, Yanru; Yip, Tony

2016-05-01

With the development and popularization of electric vehicles, it is urgent and necessary to develop effective management and diagnosis technology for battery systems. In this work, we design a parallel battery model, according to equivalent circuits of parallel voltage and branch current, to study effects of imbalanced currents on parallel large-format LiFePO4/graphite battery systems. Taking a 60 Ah LiFePO4/graphite battery system manufactured by ATL (Amperex Technology Limited, China) as an example, causes of imbalanced currents in the parallel connection are analyzed using our model, and the associated effect mechanisms on long-term stability of each single battery are examined. Theoretical and experimental results show that continuously increasing imbalanced currents during cycling are mainly responsible for the capacity fade of LiFePO4/graphite parallel batteries. It is thus a good way to avoid fast performance fade of parallel battery systems by suppressing variations of branch currents.

Performance Characteristics of the Multi-Zone NAS Parallel Benchmarks

NASA Technical Reports Server (NTRS)

Jin, Haoqiang; VanderWijngaart, Rob F.

2003-01-01

We describe a new suite of computational benchmarks that models applications featuring multiple levels of parallelism. Such parallelism is often available in realistic flow computations on systems of grids, but had not previously been captured in bench-marks. The new suite, named NPB Multi-Zone, is extended from the NAS Parallel Benchmarks suite, and involves solving the application benchmarks LU, BT and SP on collections of loosely coupled discretization meshes. The solutions on the meshes are updated independently, but after each time step they exchange boundary value information. This strategy provides relatively easily exploitable coarse-grain parallelism between meshes. Three reference implementations are available: one serial, one hybrid using the Message Passing Interface (MPI) and OpenMP, and another hybrid using a shared memory multi-level programming model (SMP+OpenMP). We examine the effectiveness of hybrid parallelization paradigms in these implementations on three different parallel computers. We also use an empirical formula to investigate the performance characteristics of the multi-zone benchmarks.

A parallel implementation of an off-lattice individual-based model of multicellular populations

NASA Astrophysics Data System (ADS)

Harvey, Daniel G.; Fletcher, Alexander G.; Osborne, James M.; Pitt-Francis, Joe

2015-07-01

As computational models of multicellular populations include ever more detailed descriptions of biophysical and biochemical processes, the computational cost of simulating such models limits their ability to generate novel scientific hypotheses and testable predictions. While developments in microchip technology continue to increase the power of individual processors, parallel computing offers an immediate increase in available processing power. To make full use of parallel computing technology, it is necessary to develop specialised algorithms. To this end, we present a parallel algorithm for a class of off-lattice individual-based models of multicellular populations. The algorithm divides the spatial domain between computing processes and comprises communication routines that ensure the model is correctly simulated on multiple processors. The parallel algorithm is shown to accurately reproduce the results of a deterministic simulation performed using a pre-existing serial implementation. We test the scaling of computation time, memory use and load balancing as more processes are used to simulate a cell population of fixed size. We find approximate linear scaling of both speed-up and memory consumption on up to 32 processor cores. Dynamic load balancing is shown to provide speed-up for non-regular spatial distributions of cells in the case of a growing population.

Toward an automated parallel computing environment for geosciences

NASA Astrophysics Data System (ADS)

Zhang, Huai; Liu, Mian; Shi, Yaolin; Yuen, David A.; Yan, Zhenzhen; Liang, Guoping

2007-08-01

Software for geodynamic modeling has not kept up with the fast growing computing hardware and network resources. In the past decade supercomputing power has become available to most researchers in the form of affordable Beowulf clusters and other parallel computer platforms. However, to take full advantage of such computing power requires developing parallel algorithms and associated software, a task that is often too daunting for geoscience modelers whose main expertise is in geosciences. We introduce here an automated parallel computing environment built on open-source algorithms and libraries. Users interact with this computing environment by specifying the partial differential equations, solvers, and model-specific properties using an English-like modeling language in the input files. The system then automatically generates the finite element codes that can be run on distributed or shared memory parallel machines. This system is dynamic and flexible, allowing users to address different problems in geosciences. It is capable of providing web-based services, enabling users to generate source codes online. This unique feature will facilitate high-performance computing to be integrated with distributed data grids in the emerging cyber-infrastructures for geosciences. In this paper we discuss the principles of this automated modeling environment and provide examples to demonstrate its versatility.

Synchronization Of Parallel Discrete Event Simulations

NASA Technical Reports Server (NTRS)

Steinman, Jeffrey S.

1992-01-01

Adaptive, parallel, discrete-event-simulation-synchronization algorithm, Breathing Time Buckets, developed in Synchronous Parallel Environment for Emulation and Discrete Event Simulation (SPEEDES) operating system. Algorithm allows parallel simulations to process events optimistically in fluctuating time cycles that naturally adapt while simulation in progress. Combines best of optimistic and conservative synchronization strategies while avoiding major disadvantages. Algorithm processes events optimistically in time cycles adapting while simulation in progress. Well suited for modeling communication networks, for large-scale war games, for simulated flights of aircraft, for simulations of computer equipment, for mathematical modeling, for interactive engineering simulations, and for depictions of flows of information.

Parallel community climate model: Description and user`s guide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Drake, J.B.; Flanery, R.E.; Semeraro, B.D.

This report gives an overview of a parallel version of the NCAR Community Climate Model, CCM2, implemented for MIMD massively parallel computers using a message-passing programming paradigm. The parallel implementation was developed on an Intel iPSC/860 with 128 processors and on the Intel Delta with 512 processors, and the initial target platform for the production version of the code is the Intel Paragon with 2048 processors. Because the implementation uses a standard, portable message-passing libraries, the code has been easily ported to other multiprocessors supporting a message-passing programming paradigm. The parallelization strategy used is to decompose the problem domain intomore » geographical patches and assign each processor the computation associated with a distinct subset of the patches. With this decomposition, the physics calculations involve only grid points and data local to a processor and are performed in parallel. Using parallel algorithms developed for the semi-Lagrangian transport, the fast Fourier transform and the Legendre transform, both physics and dynamics are computed in parallel with minimal data movement and modest change to the original CCM2 source code. Sequential or parallel history tapes are written and input files (in history tape format) are read sequentially by the parallel code to promote compatibility with production use of the model on other computer systems. A validation exercise has been performed with the parallel code and is detailed along with some performance numbers on the Intel Paragon and the IBM SP2. A discussion of reproducibility of results is included. A user`s guide for the PCCM2 version 2.1 on the various parallel machines completes the report. Procedures for compilation, setup and execution are given. A discussion of code internals is included for those who may wish to modify and use the program in their own research.« less

Controlled delivery of icariin on small intestine submucosa for bone tissue engineering.

PubMed

Li, Mei; Gu, Qiaoqiao; Chen, Mengjie; Zhang, Chi; Chen, Songdi; Zhao, Jiyuan

2017-02-01

Small intestine submucosa (SIS) has been reported as an excellent biomaterial for tissue engineering because of its naturally occurring collagenous extracellular matrix property with growth factors. However, SIS from submucosal layer of intestine provides different microenvironment from bone tissue, which limits its application to bone regeneration. The object of this study was to improve osteoinductivity of SIS by controlled local delivery of icariin (Ic), a potent osteogenic compound. Sustained release of icariin from SIS scaffold was achieved for >30days and the loading of icariin on SIS scaffold was uniform as scanned by SEM. In vitro experiments revealed that expression of osteogenic differentiation markers (Alp, Bsp and Ocn) was increased after treatment of Ic-SIS scaffold, without significant cytotoxicity. In an in vivo mouse calvarial defect model, bone regeneration was enhanced by SIS implantation at 8weeks, compared to control defect. New bone formation was further improved by implantation with Ic-SIS (low and high) at both 4 and 8weeks. The results of this study suggest that SIS scaffold has the potential as an icariin delivery carrier for enhancement of bone regeneration. Copyright © 2016 Elsevier B.V. All rights reserved.

Parallel Ray Tracing Using the Message Passing Interface

DTIC Science & Technology

2007-09-01

software is available for lens design and for general optical systems modeling. It tends to be designed to run on a single processor and can be very...Cameron, Senior Member, IEEE Abstract—Ray-tracing software is available for lens design and for general optical systems modeling. It tends to be designed to...National Aeronautics and Space Administration (NASA), optical ray tracing, parallel computing, parallel pro- cessing, prime numbers, ray tracing

Efficient partitioning and assignment on programs for multiprocessor execution

NASA Technical Reports Server (NTRS)

Standley, Hilda M.

1993-01-01

The general problem studied is that of segmenting or partitioning programs for distribution across a multiprocessor system. Efficient partitioning and the assignment of program elements are of great importance since the time consumed in this overhead activity may easily dominate the computation, effectively eliminating any gains made by the use of the parallelism. In this study, the partitioning of sequentially structured programs (written in FORTRAN) is evaluated. Heuristics, developed for similar applications are examined. Finally, a model for queueing networks with finite queues is developed which may be used to analyze multiprocessor system architectures with a shared memory approach to the problem of partitioning. The properties of sequentially written programs form obstacles to large scale (at the procedure or subroutine level) parallelization. Data dependencies of even the minutest nature, reflecting the sequential development of the program, severely limit parallelism. The design of heuristic algorithms is tied to the experience gained in the parallel splitting. Parallelism obtained through the physical separation of data has seen some success, especially at the data element level. Data parallelism on a grander scale requires models that accurately reflect the effects of blocking caused by finite queues. A model for the approximation of the performance of finite queueing networks is developed. This model makes use of the decomposition approach combined with the efficiency of product form solutions.

Parallel 3-D numerical simulation of dielectric barrier discharge plasma actuators

NASA Astrophysics Data System (ADS)

Houba, Tomas

Dielectric barrier discharge plasma actuators have shown promise in a range of applications including flow control, sterilization and ozone generation. Developing numerical models of plasma actuators is of great importance, because a high-fidelity parallel numerical model allows new design configurations to be tested rapidly. Additionally, it provides a better understanding of the plasma actuator physics which is useful for further innovation. The physics of plasma actuators is studied numerically. A loosely coupled approach is utilized for the coupling of the plasma to the neutral fluid. The state of the art in numerical plasma modeling is advanced by the development of a parallel, three-dimensional, first-principles model with detailed air chemistry. The model incorporates 7 charged species and 18 reactions, along with a solution of the electron energy equation. To the author's knowledge, a parallel three-dimensional model of a gas discharge with a detailed air chemistry model and the solution of electron energy is unique. Three representative geometries are studied using the gas discharge model. The discharge of gas between two parallel electrodes is used to validate the air chemistry model developed for the gas discharge code. The gas discharge model is then applied to the discharge produced by placing a dc powered wire and grounded plate electrodes in a channel. Finally, a three-dimensional simulation of gas discharge produced by electrodes placed inside a riblet is carried out. The body force calculated with the gas discharge model is loosely coupled with a fluid model to predict the induced flow inside the riblet.

Massively Parallel Assimilation of TOGA/TAO and Topex/Poseidon Measurements into a Quasi Isopycnal Ocean General Circulation Model Using an Ensemble Kalman Filter

NASA Technical Reports Server (NTRS)

Keppenne, Christian L.; Rienecker, Michele; Borovikov, Anna Y.; Suarez, Max

1999-01-01

A massively parallel ensemble Kalman filter (EnKF)is used to assimilate temperature data from the TOGA/TAO array and altimetry from TOPEX/POSEIDON into a Pacific basin version of the NASA Seasonal to Interannual Prediction Project (NSIPP)ls quasi-isopycnal ocean general circulation model. The EnKF is an approximate Kalman filter in which the error-covariance propagation step is modeled by the integration of multiple instances of a numerical model. An estimate of the true error covariances is then inferred from the distribution of the ensemble of model state vectors. This inplementation of the filter takes advantage of the inherent parallelism in the EnKF algorithm by running all the model instances concurrently. The Kalman filter update step also occurs in parallel by having each processor process the observations that occur in the region of physical space for which it is responsible. The massively parallel data assimilation system is validated by withholding some of the data and then quantifying the extent to which the withheld information can be inferred from the assimilation of the remaining data. The distributions of the forecast and analysis error covariances predicted by the ENKF are also examined.

The source of dual-task limitations: Serial or parallel processing of multiple response selections?

PubMed Central

Marois, René

2014-01-01

Although it is generally recognized that the concurrent performance of two tasks incurs costs, the sources of these dual-task costs remain controversial. The serial bottleneck model suggests that serial postponement of task performance in dual-task conditions results from a central stage of response selection that can only process one task at a time. Cognitive-control models, by contrast, propose that multiple response selections can proceed in parallel, but that serial processing of task performance is predominantly adopted because its processing efficiency is higher than that of parallel processing. In the present study, we empirically tested this proposition by examining whether parallel processing would occur when it was more efficient and financially rewarded. The results indicated that even when parallel processing was more efficient and was incentivized by financial reward, participants still failed to process tasks in parallel. We conclude that central information processing is limited by a serial bottleneck. PMID:23864266

National Combustion Code: Parallel Implementation and Performance

NASA Technical Reports Server (NTRS)

Quealy, A.; Ryder, R.; Norris, A.; Liu, N.-S.

2000-01-01

The National Combustion Code (NCC) is being developed by an industry-government team for the design and analysis of combustion systems. CORSAIR-CCD is the current baseline reacting flow solver for NCC. This is a parallel, unstructured grid code which uses a distributed memory, message passing model for its parallel implementation. The focus of the present effort has been to improve the performance of the NCC flow solver to meet combustor designer requirements for model accuracy and analysis turnaround time. Improving the performance of this code contributes significantly to the overall reduction in time and cost of the combustor design cycle. This paper describes the parallel implementation of the NCC flow solver and summarizes its current parallel performance on an SGI Origin 2000. Earlier parallel performance results on an IBM SP-2 are also included. The performance improvements which have enabled a turnaround of less than 15 hours for a 1.3 million element fully reacting combustion simulation are described.

Decoupling Principle Analysis and Development of a Parallel Three-Dimensional Force Sensor

PubMed Central

Zhao, Yanzhi; Jiao, Leihao; Weng, Dacheng; Zhang, Dan; Zheng, Rencheng

2016-01-01

In the development of the multi-dimensional force sensor, dimension coupling is the ubiquitous factor restricting the improvement of the measurement accuracy. To effectively reduce the influence of dimension coupling on the parallel multi-dimensional force sensor, a novel parallel three-dimensional force sensor is proposed using a mechanical decoupling principle, and the influence of the friction on dimension coupling is effectively reduced by making the friction rolling instead of sliding friction. In this paper, the mathematical model is established by combining with the structure model of the parallel three-dimensional force sensor, and the modeling and analysis of mechanical decoupling are carried out. The coupling degree (ε) of the designed sensor is defined and calculated, and the calculation results show that the mechanical decoupling parallel structure of the sensor possesses good decoupling performance. A prototype of the parallel three-dimensional force sensor was developed, and FEM analysis was carried out. The load calibration and data acquisition experiment system are built, and then calibration experiments were done. According to the calibration experiments, the measurement accuracy is less than 2.86% and the coupling accuracy is less than 3.02%. The experimental results show that the sensor system possesses high measuring accuracy, which provides a basis for the applied research of the parallel multi-dimensional force sensor. PMID:27649194

Reduced-Order Structure-Preserving Model for Parallel-Connected Three-Phase Grid-Tied Inverters: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Brian B; Purba, Victor; Jafarpour, Saber

Given that next-generation infrastructures will contain large numbers of grid-connected inverters and these interfaces will be satisfying a growing fraction of system load, it is imperative to analyze the impacts of power electronics on such systems. However, since each inverter model has a relatively large number of dynamic states, it would be impractical to execute complex system models where the full dynamics of each inverter are retained. To address this challenge, we derive a reduced-order structure-preserving model for parallel-connected grid-tied three-phase inverters. Here, each inverter in the system is assumed to have a full-bridge topology, LCL filter at the pointmore » of common coupling, and the control architecture for each inverter includes a current controller, a power controller, and a phase-locked loop for grid synchronization. We outline a structure-preserving reduced-order inverter model for the setting where the parallel inverters are each designed such that the filter components and controller gains scale linearly with the power rating. By structure preserving, we mean that the reduced-order three-phase inverter model is also composed of an LCL filter, a power controller, current controller, and PLL. That is, we show that the system of parallel inverters can be modeled exactly as one aggregated inverter unit and this equivalent model has the same number of dynamical states as an individual inverter in the paralleled system. Numerical simulations validate the reduced-order models.« less

Biocellion: accelerating computer simulation of multicellular biological system models.

PubMed

Kang, Seunghwa; Kahan, Simon; McDermott, Jason; Flann, Nicholas; Shmulevich, Ilya

2014-11-01

Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming. We have developed Biocellion, a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion, modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies. Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

On extending parallelism to serial simulators

NASA Technical Reports Server (NTRS)

Nicol, David; Heidelberger, Philip

1994-01-01

This paper describes an approach to discrete event simulation modeling that appears to be effective for developing portable and efficient parallel execution of models of large distributed systems and communication networks. In this approach, the modeler develops submodels using an existing sequential simulation modeling tool, using the full expressive power of the tool. A set of modeling language extensions permit automatically synchronized communication between submodels; however, the automation requires that any such communication must take a nonzero amount off simulation time. Within this modeling paradigm, a variety of conservative synchronization protocols can transparently support conservative execution of submodels on potentially different processors. A specific implementation of this approach, U.P.S. (Utilitarian Parallel Simulator), is described, along with performance results on the Intel Paragon.

Implicit Regularization for Reconstructing 3D Building Rooftop Models Using Airborne LiDAR Data

PubMed Central

Jung, Jaewook; Jwa, Yoonseok; Sohn, Gunho

2017-01-01

With rapid urbanization, highly accurate and semantically rich virtualization of building assets in 3D become more critical for supporting various applications, including urban planning, emergency response and location-based services. Many research efforts have been conducted to automatically reconstruct building models at city-scale from remotely sensed data. However, developing a fully-automated photogrammetric computer vision system enabling the massive generation of highly accurate building models still remains a challenging task. One the most challenging task for 3D building model reconstruction is to regularize the noises introduced in the boundary of building object retrieved from a raw data with lack of knowledge on its true shape. This paper proposes a data-driven modeling approach to reconstruct 3D rooftop models at city-scale from airborne laser scanning (ALS) data. The focus of the proposed method is to implicitly derive the shape regularity of 3D building rooftops from given noisy information of building boundary in a progressive manner. This study covers a full chain of 3D building modeling from low level processing to realistic 3D building rooftop modeling. In the element clustering step, building-labeled point clouds are clustered into homogeneous groups by applying height similarity and plane similarity. Based on segmented clusters, linear modeling cues including outer boundaries, intersection lines, and step lines are extracted. Topology elements among the modeling cues are recovered by the Binary Space Partitioning (BSP) technique. The regularity of the building rooftop model is achieved by an implicit regularization process in the framework of Minimum Description Length (MDL) combined with Hypothesize and Test (HAT). The parameters governing the MDL optimization are automatically estimated based on Min-Max optimization and Entropy-based weighting method. The performance of the proposed method is tested over the International Society for Photogrammetry and Remote Sensing (ISPRS) benchmark datasets. The results show that the proposed method can robustly produce accurate regularized 3D building rooftop models. PMID:28335486

Implicit Regularization for Reconstructing 3D Building Rooftop Models Using Airborne LiDAR Data.

PubMed

Jung, Jaewook; Jwa, Yoonseok; Sohn, Gunho

2017-03-19

With rapid urbanization, highly accurate and semantically rich virtualization of building assets in 3D become more critical for supporting various applications, including urban planning, emergency response and location-based services. Many research efforts have been conducted to automatically reconstruct building models at city-scale from remotely sensed data. However, developing a fully-automated photogrammetric computer vision system enabling the massive generation of highly accurate building models still remains a challenging task. One the most challenging task for 3D building model reconstruction is to regularize the noises introduced in the boundary of building object retrieved from a raw data with lack of knowledge on its true shape. This paper proposes a data-driven modeling approach to reconstruct 3D rooftop models at city-scale from airborne laser scanning (ALS) data. The focus of the proposed method is to implicitly derive the shape regularity of 3D building rooftops from given noisy information of building boundary in a progressive manner. This study covers a full chain of 3D building modeling from low level processing to realistic 3D building rooftop modeling. In the element clustering step, building-labeled point clouds are clustered into homogeneous groups by applying height similarity and plane similarity. Based on segmented clusters, linear modeling cues including outer boundaries, intersection lines, and step lines are extracted. Topology elements among the modeling cues are recovered by the Binary Space Partitioning (BSP) technique. The regularity of the building rooftop model is achieved by an implicit regularization process in the framework of Minimum Description Length (MDL) combined with Hypothesize and Test (HAT). The parameters governing the MDL optimization are automatically estimated based on Min-Max optimization and Entropy-based weighting method. The performance of the proposed method is tested over the International Society for Photogrammetry and Remote Sensing (ISPRS) benchmark datasets. The results show that the proposed method can robustly produce accurate regularized 3D building rooftop models.

National Centers for Environmental Prediction

Science.gov Websites

/ VISION | About EMC EMC > NAM > EXPERIMENTAL DATA Home NAM Operational Products HIRESW Operational Products Operational Forecast Graphics Experimental Forecast Graphics Verification and Diagnostics Model PARALLEL/EXPERIMENTAL MODEL FORECAST GRAPHICS OPERATIONAL VERIFICATION / DIAGNOSTICS PARALLEL VERIFICATION

Coupled electromechanical model of the heart: Parallel finite element formulation.

PubMed

Lafortune, Pierre; Arís, Ruth; Vázquez, Mariano; Houzeaux, Guillaume

2012-01-01

In this paper, a highly parallel coupled electromechanical model of the heart is presented and assessed. The parallel-coupled model is thoroughly discussed, with scalability proven up to hundreds of cores. This work focuses on the mechanical part, including the constitutive model (proposing some modifications to pre-existent models), the numerical scheme and the coupling strategy. The model is next assessed through two examples. First, the simulation of a small piece of cardiac tissue is used to introduce the main features of the coupled model and calibrate its parameters against experimental evidence. Then, a more realistic problem is solved using those parameters, with a mesh of the Oxford ventricular rabbit model. The results of both examples demonstrate the capability of the model to run efficiently in hundreds of processors and to reproduce some basic characteristic of cardiac deformation.

A parallel computational model for GATE simulations.

PubMed

Rannou, F R; Vega-Acevedo, N; El Bitar, Z

2013-12-01

GATE/Geant4 Monte Carlo simulations are computationally demanding applications, requiring thousands of processor hours to produce realistic results. The classical strategy of distributing the simulation of individual events does not apply efficiently for Positron Emission Tomography (PET) experiments, because it requires a centralized coincidence processing and large communication overheads. We propose a parallel computational model for GATE that handles event generation and coincidence processing in a simple and efficient way by decentralizing event generation and processing but maintaining a centralized event and time coordinator. The model is implemented with the inclusion of a new set of factory classes that can run the same executable in sequential or parallel mode. A Mann-Whitney test shows that the output produced by this parallel model in terms of number of tallies is equivalent (but not equal) to its sequential counterpart. Computational performance evaluation shows that the software is scalable and well balanced. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Tutorial: Parallel Computing of Simulation Models for Risk Analysis.

PubMed

Reilly, Allison C; Staid, Andrea; Gao, Michael; Guikema, Seth D

2016-10-01

Simulation models are widely used in risk analysis to study the effects of uncertainties on outcomes of interest in complex problems. Often, these models are computationally complex and time consuming to run. This latter point may be at odds with time-sensitive evaluations or may limit the number of parameters that are considered. In this article, we give an introductory tutorial focused on parallelizing simulation code to better leverage modern computing hardware, enabling risk analysts to better utilize simulation-based methods for quantifying uncertainty in practice. This article is aimed primarily at risk analysts who use simulation methods but do not yet utilize parallelization to decrease the computational burden of these models. The discussion is focused on conceptual aspects of embarrassingly parallel computer code and software considerations. Two complementary examples are shown using the languages MATLAB and R. A brief discussion of hardware considerations is located in the Appendix. © 2016 Society for Risk Analysis.

Classification of hyperspectral imagery using MapReduce on a NVIDIA graphics processing unit (Conference Presentation)

NASA Astrophysics Data System (ADS)

Ramirez, Andres; Rahnemoonfar, Maryam

2017-04-01

A hyperspectral image provides multidimensional figure rich in data consisting of hundreds of spectral dimensions. Analyzing the spectral and spatial information of such image with linear and non-linear algorithms will result in high computational time. In order to overcome this problem, this research presents a system using a MapReduce-Graphics Processing Unit (GPU) model that can help analyzing a hyperspectral image through the usage of parallel hardware and a parallel programming model, which will be simpler to handle compared to other low-level parallel programming models. Additionally, Hadoop was used as an open-source version of the MapReduce parallel programming model. This research compared classification accuracy results and timing results between the Hadoop and GPU system and tested it against the following test cases: the CPU and GPU test case, a CPU test case and a test case where no dimensional reduction was applied.

Lengthening of the duration of xylogenesis engenders disproportionate increases in xylem production.

PubMed

Rossi, Sergio; Girard, Marie-Josée; Morin, Hubert

2014-07-01

In cold climates, the expected global warming will lead to earlier cambial resumptions in spring, with a resultant lengthening of the growing season but unknown consequences on forest productivity. The phenological traits of cambium activity and xylem formation were analyzed at a short time scale along a thermal gradient represented by an alti-latitudinal range from the 48th to 53rd parallels and covering the whole closed black-spruce [Picea mariana (Mill.) BSP] forest in Quebec, Canada. A hypothesis was tested that warmer temperatures influence cambium phenology, allowing longer duration and higher intensity of growth, and resulting in proportionally increased xylem production. From April to October 2012, cell division in cambium and post-cambial differentiation of xylem were observed on anatomical sections obtained from microcores collected weekly from the stem of fifty trees. The southern and warmer site was characterized by the highest radial growth, which corresponded to both the highest rates and longest durations of cell production. The differences in terms of xylem phenology and growth were marginal between the other sites. Xylem growth was positively correlated with rate and duration of cell production, with the latter explaining most variability in growth. Within the range analyzed, the relationship between temperature and most phenological phases of xylogenesis was linear. On the contrary, temperature was related with cell production according to an exponential pattern. Periods of xylogenesis of 14 days longer (+13.1%) corresponded to a massive increase in cell production (33 cells, +109%). This disproportionate change occurred at a May-September average temperature of ca. 14 °C and a snow-free period of 210-235 days. At the lower boundary of the distribution of black spruce, small environmental changes allowing marginal lengthening of the period of cell division could potentially lead to disproportionate increases in xylem cell production, with substantial consequences for the productivity of this boreal species. © 2013 John Wiley & Sons Ltd.

Parallel implementation of approximate atomistic models of the AMOEBA polarizable model

NASA Astrophysics Data System (ADS)

Demerdash, Omar; Head-Gordon, Teresa

2016-11-01

In this work we present a replicated data hybrid OpenMP/MPI implementation of a hierarchical progression of approximate classical polarizable models that yields speedups of up to ∼10 compared to the standard OpenMP implementation of the exact parent AMOEBA polarizable model. In addition, our parallel implementation exhibits reasonable weak and strong scaling. The resulting parallel software will prove useful for those who are interested in how molecular properties converge in the condensed phase with respect to the MBE, it provides a fruitful test bed for exploring different electrostatic embedding schemes, and offers an interesting possibility for future exascale computing paradigms.

Automating the selection of standard parallels for conic map projections

NASA Astrophysics Data System (ADS)

Šavriǒ, Bojan; Jenny, Bernhard

2016-05-01

Conic map projections are appropriate for mapping regions at medium and large scales with east-west extents at intermediate latitudes. Conic projections are appropriate for these cases because they show the mapped area with less distortion than other projections. In order to minimize the distortion of the mapped area, the two standard parallels of conic projections need to be selected carefully. Rules of thumb exist for placing the standard parallels based on the width-to-height ratio of the map. These rules of thumb are simple to apply, but do not result in maps with minimum distortion. There also exist more sophisticated methods that determine standard parallels such that distortion in the mapped area is minimized. These methods are computationally expensive and cannot be used for real-time web mapping and GIS applications where the projection is adjusted automatically to the displayed area. This article presents a polynomial model that quickly provides the standard parallels for the three most common conic map projections: the Albers equal-area, the Lambert conformal, and the equidistant conic projection. The model defines the standard parallels with polynomial expressions based on the spatial extent of the mapped area. The spatial extent is defined by the length of the mapped central meridian segment, the central latitude of the displayed area, and the width-to-height ratio of the map. The polynomial model was derived from 3825 maps-each with a different spatial extent and computationally determined standard parallels that minimize the mean scale distortion index. The resulting model is computationally simple and can be used for the automatic selection of the standard parallels of conic map projections in GIS software and web mapping applications.

Performance Models for the Spike Banded Linear System Solver

DOE PAGES

Manguoglu, Murat; Saied, Faisal; Sameh, Ahmed; ...

2011-01-01

With availability of large-scale parallel platforms comprised of tens-of-thousands of processors and beyond, there is significant impetus for the development of scalable parallel sparse linear system solvers and preconditioners. An integral part of this design process is the development of performance models capable of predicting performance and providing accurate cost models for the solvers and preconditioners. There has been some work in the past on characterizing performance of the iterative solvers themselves. In this paper, we investigate the problem of characterizing performance and scalability of banded preconditioners. Recent work has demonstrated the superior convergence properties and robustness of banded preconditioners,more » compared to state-of-the-art ILU family of preconditioners as well as algebraic multigrid preconditioners. Furthermore, when used in conjunction with efficient banded solvers, banded preconditioners are capable of significantly faster time-to-solution. Our banded solver, the Truncated Spike algorithm is specifically designed for parallel performance and tolerance to deep memory hierarchies. Its regular structure is also highly amenable to accurate performance characterization. Using these characteristics, we derive the following results in this paper: (i) we develop parallel formulations of the Truncated Spike solver, (ii) we develop a highly accurate pseudo-analytical parallel performance model for our solver, (iii) we show excellent predication capabilities of our model – based on which we argue the high scalability of our solver. Our pseudo-analytical performance model is based on analytical performance characterization of each phase of our solver. These analytical models are then parameterized using actual runtime information on target platforms. An important consequence of our performance models is that they reveal underlying performance bottlenecks in both serial and parallel formulations. All of our results are validated on diverse heterogeneous multiclusters – platforms for which performance prediction is particularly challenging. Finally, we provide predict the scalability of the Spike algorithm using up to 65,536 cores with our model. In this paper we extend the results presented in the Ninth International Symposium on Parallel and Distributed Computing.« less

The 2nd Symposium on the Frontiers of Massively Parallel Computations

NASA Technical Reports Server (NTRS)

Mills, Ronnie (Editor)

1988-01-01

Programming languages, computer graphics, neural networks, massively parallel computers, SIMD architecture, algorithms, digital terrain models, sort computation, simulation of charged particle transport on the massively parallel processor and image processing are among the topics discussed.

Wnt/β-catenin pathway regulates Bmp2-mediated differentiation of dental follicle cells

PubMed Central

Silvério, Karina G.; Davidson, Kathryn C.; James, Richard G.; Adams, Allison M.; Foster, Brian L.; Nociti, Francisco H.; Somermam, Martha J.; Moon, Randall T.

2013-01-01

Background and Objectives Bmp2-induced osteogenic differentiation has been shown to occur through the canonical Wnt/β-catenin pathway, whereas factors promoting canonical Wnt signaling in cementoblasts inhibited cell differentiation and promoted cell proliferation in vitro. The aim of this study was to investigate whether putative precursor cells of cementoblasts, dental follicle cells (murine SVF4 cells), when stimulated with Bmp2, would exhibit changes in genes/proteins associated with the Wnt/β-catenin pathway. Materials and Methods SVF4 cells were stimulated with Bmp2, and the following assays were carried out: 1) Wnt/β-catenin pathway activation assessed by western blot, β-catenin/TCF reporter assay, and gene expression of lymphoid enhancer-binding factor-1 (Lef1), transcription factor 7 (Tcf7), Wnt inhibitor factor 1 (Wif1) and Axin2, and 2) cementoblast/osteoblast differentiation assessed by mineralization in vitro, and mRNA levels of runt-related transcription factor 2 (Runx2), osterix (Osx), alkaline phosphatase (Alp), osteocalcin (Ocn) and bone sialoprotein (Bsp) by qPCR after Wnt3a treatment and knockdown of β-catenin. Results Wnt3a induced β-catenin nuclear translocation and upregulated the transcriptional activity of a canonical Wnt-responsive reporter, suggesting the Wnt/β-catenin pathway functions in SVF4 cells. Activation of Wnt signaling with Wnt3a suppressed Bmp2-mediated induction of cementoblast/osteoblast maturation of SVF4 cells. However, β-catenin knockdown showed that Bmp2-induced expression of cementoblast/osteoblast differentiation markers requires endogenous β-catenin. Wnt3a down-regulated transcripts for Runx2, Alp and Ocn in SVF4 cells compared to untreated cells. In contrast, Bmp2 induction of Bsp transcripts occurred independent of Wnt/β-catenin signaling. Conclusions These data suggest that stabilization of β-catenin by Wnt-3a treatment inhibits Bmp2-mediated induction of cementoblast/osteoblast differentiation in SVF4 cells, although Bmp2 requires endogenous Wnt/β-catenin signaling to promote cell maturation. PMID:22150562

Ram seminal plasma proteome and its impact on liquid preservation of spermatozoa.

PubMed

Soleilhavoup, C; Tsikis, G; Labas, V; Harichaux, G; Kohnke, P L; Dacheux, J L; Guérin, Y; Gatti, J L; de Graaf, S P; Druart, X

2014-09-23

Seminal plasma is composed of secretions from the epididymis and the accessory sex glands and plays a critical role in the fertilising ability of spermatozoa. In rams, analysis of seminal plasma by GeLC-MS/MS has allowed the identification of more than 700 proteins, including a high abundance of Binder of Sperm family proteins (BSP1, BSP5, SPADH1, SPADH2), the spermadhesin family (bodhesin2), lactoferrin and newly identified proteins like UPF0762 (C6orf58 gene). When spermatogenesis was stopped by scrotal insulation, changes in the proteome profile revealed the sperm origin of 40 seminal proteins, such as glycolysis pathway enzymes, the chaperonin containing TCP1 (CCT) complex and the 26S proteasome complex. Sperm mobility after liquid preservation (24h in milk at 15°C) is male dependent and can be correlated to differences in the seminal plasma proteome, detected by spectral counting. The negative association of zinc alpha-2 glycoprotein (ZAG) with semen preservation was confirmed by the use of recombinant human ZAG, which induced an increase in mobility of fresh sperm, but then decreased sperm mobility after 24h of incubation. Several sperm membrane proteins interacting with the cytoskeleton, glycolysis enzymes and sperm-associated proteins involved in capacitation correlated with better liquid storage and can be considered as seminal biomarkers of sperm preservation. Extensive analysis of the ram seminal plasma proteome reveals a complex and diverse protein composition. This composition varies between males with different sperm preservation abilities. Several proteins were shown to originate from the spermatozoa and positively correlate with sperm liquid preservation, indicating that these proteins can be traced as sperm biomarkers within the seminal plasma. The zinc alpha-2 glycoprotein (ZAG) was found to have a biphasic effect on sperm mobility, with a short-term stimulation followed by a long-term exhaustion of sperm mobility after a 24h preservation period. Copyright © 2014 Elsevier B.V. All rights reserved.

Biological and Mechanical Effects of Micro-Nanostructured Titanium Surface on an Osteoblastic Cell Line In vitro and Osteointegration In vivo.

PubMed

Hao, Jingzu; Li, Ying; Li, Baoe; Wang, Xiaolin; Li, Haipeng; Liu, Shimin; Liang, Chunyong; Wang, Hongshui

2017-09-01

Hybrid micro-nanostructure implant surface was produced on titanium (Ti) surface by acid etching and anodic oxidation to improve the biological and mechanical properties. The biological properties of the micro-nanostructure were investigated by simulated body fluid (SBF) soaking test and MC3T3-E1 cell co-culture experiment. The cell proliferation, spreading, and bone sialoprotein (BSP) gene expression were examined by MTT, SEM, and reverse transcription-polymerase chain reaction (RT-PCR), respectively. In addition, the mechanical properties were evaluated by instrumented nanoindentation test and friction-wear test. Furthermore, the effect of the micro-nanostructure surface on implant osteointegration was examined by in vivo experiment. The results showed that the formation of bone-like apatite was accelerated on the micro-nanostructured Ti surface after immersion in simulated body fluid, and the proliferation, spreading, and BSP gene expression of the MC3T3-E1 cells were also upregulated on the modified surface. The micro-nanostructured Ti surface displayed decreased friction coefficient, stiffness value, and Young's modulus which were much closer to those of the cortical bone, compared to the polished Ti surface. This suggested much better mechanical match to the surrounding bone tissue of the micro-nanostructured Ti surface. Furthermore, the in vivo animal experiment showed that after implantation in the rat femora, the micro-nanostructure surface displayed higher bonding strength between bone tissues and implant; hematoxylin and eosin (H&E) staining suggested that much compact osteoid tissue was observed at the interface of Micro-nano-Ti-bone than polished Ti-bone interface after implantation. Based on these results mentioned above, it was concluded that the improved biological and mechanical properties of the micro-nanostructure endowed Ti surface with good biocompatibility and better osteointegration, implying the enlarged application of the micro-nanostructure surface Ti implants in future.

Physical Attributes and NFL Combine Performance Tests Between Italian National League and American Football Players: A Comparative Study.

PubMed

Vitale, Jacopo A; Caumo, Andrea; Roveda, Eliana; Montaruli, Angela; La Torre, Antonio; Battaglini, Claudio L; Carandente, Franca

2016-10-01

Vitale, JA, Caumo, A, Roveda, E, Montaruli, A, La Torre, A, Battaglini, CL, and Carandente, F. Physical attributes and NFL Combine performance tests between Italian National League and American football players: a comparative study. J Strength Cond Res 30(10): 2802-2808, 2016-The purpose of this study was to examine anthropometric measurements and the results of a battery of performance tests administered during the National Football League (NFL) Combine between American football players who were declared eligible to participate in the NFL Combine and football players of a top Italian team (Rhinos Milan). Participants (N = 50) were categorized by position into 1 of 3 groups based on playing position: skill players (SP) included wide receivers, cornerbacks, free safeties, strong safeties, and running backs; big skill players (BSP) consisted of fullbacks, linebackers, tight ends, and defensive ends; lineman (LM) included centers, offensive guards, offensive tackles, and defensive tackles. A 1-way analysis of variance followed by the Tukey-Kramer post hoc test was used for comparisons between Italian players by playing position. Ninety-five percent CIs were used for comparisons between American and Italian football for the NFL Combine performance tests. Significant differences for all the variables between the 3 playing categories were observed among the Italian players; LM had higher anthropometric and body composition values than SP (p < 0.001) and BSP (p < 0.001), whereas LM performed significantly worse in the physical tests, except for the 225-lb bench press test when compared with SP (p < 0.002). American football players presented significantly higher anthropometric values and test performance scores when compared with Italian players. Administrators of professional football teams in Italy need to improve the player's physical attributes, so the gap that currently exists between American and Italian players can be reduced, which could significantly improve the quality of American football in Italy.

Short term sodium alendronate administration improves the peri-implant bone quality in osteoporotic animals

PubMed Central

de OLIVEIRA, Danila; HASSUMI, Jaqueline Suemi; GOMES-FERREIRA, Pedro Henrique da Silva; POLO, Tárik Ocon Braga; FERREIRA, Gabriel Ramalho; FAVERANI, Leonardo Perez; OKAMOTO, Roberta

2017-01-01

Abstract Sodium alendronate is a bisphosphonate drug that exerts antiresorptive action and is used to treat osteoporosis. Objective The aim of this study was to evaluate the bone repair process at the bone/implant interface of osteoporotic rats treated with sodium alendronate through the analysis of microtomography, real time polymerase chain reactions and immunohistochemistry (RUNX2 protein, bone sialoprotein (BSP), alkaline phosphatase, osteopontin and osteocalcin). Material and Methods A total of 42 rats were used and divided in to the following experimental groups: CTL: control group (rats submitted to fictitious surgery and fed with a balanced diet), OST: osteoporosis group (rats submitted to a bilateral ovariectomy and fed with a low calcium diet) and ALE: alendronate group (rats submitted to a bilateral ovariectomy, fed with a low calcium diet and treated with sodium alendronate). A surface treated implant was installed in both tibial metaphyses of each rat. Euthanasia of the animals was conducted at 14 (immunhostochemistry) and 42 days (immunohistochemistry, micro CT and PCR). Data were subjected to statistical analysis with a 5% significance level. Results Bone volume (BV) and total pore volume were higher for ALE group (P<0.05). Molecular data for RUNX2 and BSP proteins were significantly expressed in the ALE group (P<0.05), in comparison with the other groups. ALP expression was higher in the CTL group (P<0.05). The immunostaining for RUNX2 and osteopontin was positive in the osteoblastic lineage cells of neoformed bone for the CTL and ALE groups in both periods (14 and 42 days). Alkaline phosphatase presented a lower staining area in the OST group compared to the CTL in both periods and the ALE at 42 days. Conclusion There was a decrease of osteocalcin precipitation at 42 days for the ALE and OST groups. Therefore, treatment with short-term sodium alendronate improved bone repair around the implants installed in the tibia of osteoporotic rats. PMID:28198975

The differential effect of basic fibroblast growth factor and stromal cell‑derived factor‑1 pretreatment on bone morrow mesenchymal stem cells osteogenic differentiation potency.

PubMed

Wang, Ruolin; Liu, Wenhua; Du, Mi; Yang, Chengzhe; Li, Xuefen; Yang, Pishan

2018-03-01

In situ tissue engineering has become a novel strategy to repair periodontal/bone tissue defects. The choice of cytokines that promote the recruitment and proliferation, and potentiate and maintain the osteogenic differentiation ability of mesenchymal stem cells (MSCs) is the key point in this technique. Stromal cell‑derived factor‑1 (SDF‑1) and basic fibroblast growth factor (bFGF) have the ability to promote the recruitment, and proliferation of MSCs; however, the differential effect of SDF‑1 and bFGF pretreatment on MSC osteogenic differentiation potency remains to be explored. The present study comparatively observed osteogenic differentiation of bone morrow MSCs (BMMSCs) pretreated by bFGF or SDF‑1 in vitro. The gene and protein expression levels of alkaline phosphatase (ALP), runt related transcription factor 2 (Runx‑2) and bone sialoprotein (BSP) were detected using reverse transcription‑quantitative polymerase chain reaction and western blotting. The results showed that the expression of ALP mRNA on day 3, and BSP and Runx‑2 mRNA on day 7 in the bFGF pretreatment group was significantly higher than those in SDF‑1 pretreatment group. Expression levels of Runx‑2 mRNA, and ALP and Runx‑2 protein on day 3 in the SDF‑1 pretreatment group were higher than those in the bFGF pretreatment group. However, there was no significant difference in osteogenic differentiation ability on day 14 and 28 between the bFGF‑ or SDF‑1‑pretreatment groups and the control. In conclusion, bFGF and SDF‑1 pretreatment inhibits osteogenic differentiation of BMMSCs at the early stage, promotes it in the medium phase, and maintains it in the later stage during osteogenic induction, particularly at the mRNA level. Out of the two cytokines, bFGF appeared to have a greater effect on osteogenic differentiation.

Exosomal tumor microRNA modulates premetastatic organ cells.

PubMed

Rana, Sanyukta; Malinowska, Kamilla; Zöller, Margot

2013-03-01

Tumor exosomes educate selected host tissues toward a prometastatic phenotype. We demonstrated this for exosomes of the metastatic rat adenocarcinoma BSp73ASML (ASML), which modulate draining lymph nodes and lung tissue to support settlement of poorly metastatic BSp73ASML-CD44v4-v7 knockdown (ASML-CD44v(kd)) cells. Now, we profiled mRNA and microRNA (miRNA) of ASML(wt) and ASML-CD44v(kd) exosomes to define the pathway(s), whereby exosomes prepare the premetastatic niche. ASML exosomes, recovered in draining lymph nodes after subcutaneous injection, preferentially are taken up by lymph node stroma cells (LnStr) and lung fibroblasts (LuFb) that were chosen as exosome targets. ASML(wt) and ASML-CD44v(kd) exosomes contain a restricted mRNA and miRNA repertoire that differs significantly between the two lines and exosomes thereof due to CD44v6 influencing gene and miRNA transcription/posttranscriptional regulation. Exosomal mRNA and miRNA are recovered in target cells, where transferred miRNA significantly affected mRNA translation. Besides others, this was exemplified for abundant ASML(wt)-exosomal miR-494 and miR-542-3p, which target cadherin-17 (cdh17). Concomitantly, matrix metalloproteinase transcription, accompanying cdh17 down-regulation, was upregulated in LnStr transfected with miR-494 or miR-542-3p or co-cultured with tumor exosomes. Thus, tumor exosomes target non-transformed cells in premetastatic organs and modulate premetastatic organ cells predominantly through transferred miRNA, where miRNA from a metastasizing tumor prepares premetastatic organ stroma cells for tumor cell hosting. Fitting the demands of metastasizing tumor cells, transferred exosomal miRNA mostly affected proteases, adhesion molecules, chemokine ligands, cell cycle- and angiogenesis-promoting genes, and genes engaged in oxidative stress response. The demonstration of function-competent exosomal miRNA in host target cells encourages exploiting exosomes as a therapeutic gene delivery system.

Wnt signaling inhibits cementoblast differentiation and promotes proliferation.

PubMed

Nemoto, Eiji; Koshikawa, Yohei; Kanaya, Sousuke; Tsuchiya, Masahiro; Tamura, Masato; Somerman, Martha J; Shimauchi, Hidetoshi

2009-05-01

Cementoblasts, tooth root lining cells, are responsible for laying down cementum on the root surface, a process that is indispensable for establishing a functional periodontal ligament. Cementoblasts share phenotypical features with osteoblasts. Wnt signaling has been implicated in increased bone formation by controlling mesenchymal stem cell or osteoblastic cell functions; however the role of Wnt signaling on cementogenesis has not been examined. In this study, we have identified a consistent expression profile of Wnt signaling molecules in cementoblasts, in vitro by RT-PCR. Exposure of cells to LiCl, which promotes canonical Wnt signaling by inhibiting GSK-3beta, increased beta-catenin nuclear translocation and up-regulated the transcriptional activity of a canonical Wnt-responsive promoters, suggesting that an endogenous canonical Wnt pathway functions in cementoblasts. Activation of endogenous canonical Wnt signaling with LiCl suppressed alkaline phosphatase (ALP) activity and expression of genes associated with cementum function; ALP, bone sialoprotein (BSP), and osteocalcin (OCN). Exposure to Wnt3a, as a representative canonical Wnt member, also inhibited the expression of ALP, BSP, and OCN gene. This effect was accompanied by decreased gene expression of Runx2 and Osterix and by increased gene expression of lymphoid enhancer factor-1. Pretreatment with Dickkopf (Dkk)-1, a potent canonical Wnt antagonist, which binds to a low-density lipoprotein-receptor-related protein (LRP)-5/6 co-receptor, attenuated the suppressive effects of Wnt3a on mRNA expression of Runx2 and OCN on cementoblasts. These findings suggest that canonical Wnt signaling inhibits cementoblast differentiation via regulation of expression of selective transcription factors. Wnt3a also increased the expression of cyclin D1, known as a cell cycle regulator, as well as cell proliferation. In conclusion, these observations suggest that Wnt signaling inhibits cementoblast differentiation and promotes cell proliferation. Elucidating the role of Wnt in controlling cementoblast function will provide new tools needed to improve on existing periodontal regeneration therapies.

Realizing high-rate sulfur reduction under sulfate-rich conditions in a biological sulfide production system to treat metal-laden wastewater deficient in organic matter.

PubMed

Sun, Rongrong; Zhang, Liang; Zhang, Zefeng; Chen, Guang-Hao; Jiang, Feng

2017-12-22

Biological sulfur reduction can theoretically produce sufficient sulfide to effectively remove and recover heavy metals in the treatment of organics-deficient sulfate-rich metal-laden wastewater such as acid mine drainage and metallurgic wastewater, using 75% less organics than biological sulfate reduction. However, it is still unknown whether sulfur reduction can indeed compete with sulfate reduction, particularly under high-strength sulfate conditions. The aim of this study was to investigate the long-term feasibility of biological sulfur reduction under high sulfate conditions in a lab-scale sulfur-reducing biological sulfide production (BSP) system with sublimed sulfur added. In the 169-day trial, an average sulfide production rate (SPR) as high as 47 ± 9 mg S/L-h was achieved in the absence of sulfate, and the average SPR under sulfate-rich conditions was similar (53 ± 10 mg S/L-h) when 1300 mg S/L sulfate were fed with the influent. Interestingly, sulfate was barely reduced even at such a high strength and contributed to only 1.5% of total sulfide production. Desulfomicrobium was identified as the predominant sulfidogenic bacterium in the bioreactor. Batch tests further revealed that this sulfidogenic bacteria used elemental sulfur as the electron acceptor instead of the highly bioavailable sulfate, during which polysulfide acted as an intermediate, leading to an even higher bioavailability of sulfur than sulfate. The pathway of sulfur to sulfide conversion via polysulfide in the presence of both sulfur and sulfate was discussed. Collectively, when conditions favor polysulfide formation, sulfur reduction can be a promising and attractive technology to realize a high-rate and low-cost BSP process for treating sulfate-rich metal-laden wastewater. Copyright © 2017 Elsevier Ltd. All rights reserved.

Polymer-Ceramic Spiral Structured Scaffolds for Bone Tissue Engineering: Effect of Hydroxyapatite Composition on Human Fetal Osteoblasts

PubMed Central

Zhang, Xiaojun; Chang, Wei; Lee, Paul; Wang, Yuhao; Yang, Min; Li, Jun; Kumbar, Sangamesh G.; Yu, Xiaojun

2014-01-01

For successful bone tissue engineering, a scaffold needs to be osteoconductive, porous, and biodegradable, thus able to support attachment and proliferation of bone cells and guide bone formation. Recently, hydroxyapatites (HA), a major inorganic component of natural bone, and biodegrade polymers have drawn much attention as bone scaffolds. The present study was designed to investigate whether the bone regenerative properties of nano-HA/polycaprolactone (PCL) spiral scaffolds are augmented in an HA dose dependent manner, thereby establishing a suitable composition as a bone formation material. Nano-HA/PCL spiral scaffolds were prepared with different weight ratios of HA and PCL, while porosity was introduced by a modified salt leaching technique. Human fetal osteoblasts (hFOBs) were cultured on the nano-HA/PCL spiral scaffolds up to 14 days. Cellular responses in terms of cell adhesion, viability, proliferation, differentiation, and the expression of bone-related genes were investigated. These scaffolds supported hFOBs adhesion, viability and proliferation. Cell proliferation trend was quite similar on polymer-ceramic and neat polymer spiral scaffolds on days 1, 7, and 14. However, the significantly increased amount of alkaline phosphatase (ALP) activity and mineralized matrix synthesis was evident on the nano-HA/PCL spiral scaffolds. The HA composition in the scaffolds showed a significant effect on ALP and mineralization. Bone phenotypic markers such as bone sialoprotein (BSP), osteonectin (ON), osteocalcin (OC), and type I collagen (Col-1) were semi-quantitatively estimated by reverse transcriptase polymerase chain reaction analysis. All of these results suggested the osteoconductive characteristics of HA/PCL nanocomposite and cell maturation were HA dose dependent. For instance, HA∶PCL = 1∶4 group showed significantly higher ALP mineralization and elevated levels of BSP, ON, OC and Col-I expression as compared other lower or higher ceramic ratios. Amongst the different nano-HA/PCL spiral scaffolds, the 1∶4 weight ratio of HA and PCL is shown to be the most optimal composition for bone tissue regeneration. PMID:24475056

Regeneration of dental pulp/dentine complex with a three-dimensional and scaffold-free stem-cell sheet-derived pellet.

PubMed

Na, Sijia; Zhang, Hao; Huang, Fang; Wang, Weiqi; Ding, Yin; Li, Dechao; Jin, Yan

2016-03-01

Dental pulp/dentine complex regeneration is indispensable to the construction of biotissue-engineered tooth roots and represents a promising approach to therapy for irreversible pulpitis. We used a tissue-engineering method based on odontogenic stem cells to design a three-dimensional (3D) and scaffold-free stem-cell sheet-derived pellet (CSDP) with the necessary physical and biological properties. Stem cells were isolated and identified and stem cells from root apical papilla (SCAPs)-based CSDPs were then fabricated and examined. Compact cell aggregates containing a high proportion of extracellular matrix (ECM) components were observed, and the CSDP culture time was prolonged. The expression of alkaline phosphatase (ALP), dentine sialoprotein (DSPP), bone sialoprotein (BSP) and runt-related gene 2 (RUNX2) mRNA was higher in CSDPs than in cell sheets (CSs), indicating that CSDPs have greater odonto/osteogenic potential. To further investigate this hypothesis, CSDPs and CSs were inserted into human treated dentine matrix fragments (hTDMFs) and transplanted into the subcutaneous space in the backs of immunodeficient mice, where they were cultured in vivo for 6 weeks. The root space with CSDPs was filled entirely with a dental pulp-like tissue with well-established vascularity, and a continuous layer of dentine-like tissue was deposited onto the existing dentine. A layer of odontoblast-like cells was found to express DSPP, ALP and BSP, and human mitochondria lined the surface of the newly formed dentine-like tissue. These results clearly indicate that SCAP-CSDPs with a mount of endogenous ECM have a strong capacity to form a heterotopic dental pulp/dentine complex in empty root canals; this method can be used in the fabrication of bioengineered dental roots and also provides an alternative treatment approach for pulp disease. Copyright © 2013 John Wiley & Sons, Ltd.

A Systems Approach to Scalable Transportation Network Modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perumalla, Kalyan S

2006-01-01

Emerging needs in transportation network modeling and simulation are raising new challenges with respect to scal-ability of network size and vehicular traffic intensity, speed of simulation for simulation-based optimization, and fidel-ity of vehicular behavior for accurate capture of event phe-nomena. Parallel execution is warranted to sustain the re-quired detail, size and speed. However, few parallel simulators exist for such applications, partly due to the challenges underlying their development. Moreover, many simulators are based on time-stepped models, which can be computationally inefficient for the purposes of modeling evacuation traffic. Here an approach is presented to de-signing a simulator with memory andmore » speed efficiency as the goals from the outset, and, specifically, scalability via parallel execution. The design makes use of discrete event modeling techniques as well as parallel simulation meth-ods. Our simulator, called SCATTER, is being developed, incorporating such design considerations. Preliminary per-formance results are presented on benchmark road net-works, showing scalability to one million vehicles simu-lated on one processor.« less

Distributed parallel computing in stochastic modeling of groundwater systems.

PubMed

Dong, Yanhui; Li, Guomin; Xu, Haizhen

2013-03-01

Stochastic modeling is a rapidly evolving, popular approach to the study of the uncertainty and heterogeneity of groundwater systems. However, the use of Monte Carlo-type simulations to solve practical groundwater problems often encounters computational bottlenecks that hinder the acquisition of meaningful results. To improve the computational efficiency, a system that combines stochastic model generation with MODFLOW-related programs and distributed parallel processing is investigated. The distributed computing framework, called the Java Parallel Processing Framework, is integrated into the system to allow the batch processing of stochastic models in distributed and parallel systems. As an example, the system is applied to the stochastic delineation of well capture zones in the Pinggu Basin in Beijing. Through the use of 50 processing threads on a cluster with 10 multicore nodes, the execution times of 500 realizations are reduced to 3% compared with those of a serial execution. Through this application, the system demonstrates its potential in solving difficult computational problems in practical stochastic modeling. © 2012, The Author(s). Groundwater © 2012, National Ground Water Association.

Reversible Parallel Discrete-Event Execution of Large-scale Epidemic Outbreak Models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perumalla, Kalyan S; Seal, Sudip K

2010-01-01

The spatial scale, runtime speed and behavioral detail of epidemic outbreak simulations together require the use of large-scale parallel processing. In this paper, an optimistic parallel discrete event execution of a reaction-diffusion simulation model of epidemic outbreaks is presented, with an implementation over themore » $$\\mu$$sik simulator. Rollback support is achieved with the development of a novel reversible model that combines reverse computation with a small amount of incremental state saving. Parallel speedup and other runtime performance metrics of the simulation are tested on a small (8,192-core) Blue Gene / P system, while scalability is demonstrated on 65,536 cores of a large Cray XT5 system. Scenarios representing large population sizes (up to several hundred million individuals in the largest case) are exercised.« less

Regional-scale calculation of the LS factor using parallel processing

NASA Astrophysics Data System (ADS)

Liu, Kai; Tang, Guoan; Jiang, Ling; Zhu, A.-Xing; Yang, Jianyi; Song, Xiaodong

2015-05-01

With the increase of data resolution and the increasing application of USLE over large areas, the existing serial implementation of algorithms for computing the LS factor is becoming a bottleneck. In this paper, a parallel processing model based on message passing interface (MPI) is presented for the calculation of the LS factor, so that massive datasets at a regional scale can be processed efficiently. The parallel model contains algorithms for calculating flow direction, flow accumulation, drainage network, slope, slope length and the LS factor. According to the existence of data dependence, the algorithms are divided into local algorithms and global algorithms. Parallel strategy are designed according to the algorithm characters including the decomposition method for maintaining the integrity of the results, optimized workflow for reducing the time taken for exporting the unnecessary intermediate data and a buffer-communication-computation strategy for improving the communication efficiency. Experiments on a multi-node system show that the proposed parallel model allows efficient calculation of the LS factor at a regional scale with a massive dataset.

Parallel implementation of a Lagrangian-based model on an adaptive mesh in C++: Application to sea-ice

NASA Astrophysics Data System (ADS)

Samaké, Abdoulaye; Rampal, Pierre; Bouillon, Sylvain; Ólason, Einar

2017-12-01

We present a parallel implementation framework for a new dynamic/thermodynamic sea-ice model, called neXtSIM, based on the Elasto-Brittle rheology and using an adaptive mesh. The spatial discretisation of the model is done using the finite-element method. The temporal discretisation is semi-implicit and the advection is achieved using either a pure Lagrangian scheme or an Arbitrary Lagrangian Eulerian scheme (ALE). The parallel implementation presented here focuses on the distributed-memory approach using the message-passing library MPI. The efficiency and the scalability of the parallel algorithms are illustrated by the numerical experiments performed using up to 500 processor cores of a cluster computing system. The performance obtained by the proposed parallel implementation of the neXtSIM code is shown being sufficient to perform simulations for state-of-the-art sea ice forecasting and geophysical process studies over geographical domain of several millions squared kilometers like the Arctic region.

PARAMO: A Parallel Predictive Modeling Platform for Healthcare Analytic Research using Electronic Health Records

PubMed Central

Ng, Kenney; Ghoting, Amol; Steinhubl, Steven R.; Stewart, Walter F.; Malin, Bradley; Sun, Jimeng

2014-01-01

Objective Healthcare analytics research increasingly involves the construction of predictive models for disease targets across varying patient cohorts using electronic health records (EHRs). To facilitate this process, it is critical to support a pipeline of tasks: 1) cohort construction, 2) feature construction, 3) cross-validation, 4) feature selection, and 5) classification. To develop an appropriate model, it is necessary to compare and refine models derived from a diversity of cohorts, patient-specific features, and statistical frameworks. The goal of this work is to develop and evaluate a predictive modeling platform that can be used to simplify and expedite this process for health data. Methods To support this goal, we developed a PARAllel predictive MOdeling (PARAMO) platform which 1) constructs a dependency graph of tasks from specifications of predictive modeling pipelines, 2) schedules the tasks in a topological ordering of the graph, and 3) executes those tasks in parallel. We implemented this platform using Map-Reduce to enable independent tasks to run in parallel in a cluster computing environment. Different task scheduling preferences are also supported. Results We assess the performance of PARAMO on various workloads using three datasets derived from the EHR systems in place at Geisinger Health System and Vanderbilt University Medical Center and an anonymous longitudinal claims database. We demonstrate significant gains in computational efficiency against a standard approach. In particular, PARAMO can build 800 different models on a 300,000 patient data set in 3 hours in parallel compared to 9 days if running sequentially. Conclusion This work demonstrates that an efficient parallel predictive modeling platform can be developed for EHR data. This platform can facilitate large-scale modeling endeavors and speed-up the research workflow and reuse of health information. This platform is only a first step and provides the foundation for our ultimate goal of building analytic pipelines that are specialized for health data researchers. PMID:24370496

PARAMO: a PARAllel predictive MOdeling platform for healthcare analytic research using electronic health records.

PubMed

Ng, Kenney; Ghoting, Amol; Steinhubl, Steven R; Stewart, Walter F; Malin, Bradley; Sun, Jimeng

2014-04-01

Healthcare analytics research increasingly involves the construction of predictive models for disease targets across varying patient cohorts using electronic health records (EHRs). To facilitate this process, it is critical to support a pipeline of tasks: (1) cohort construction, (2) feature construction, (3) cross-validation, (4) feature selection, and (5) classification. To develop an appropriate model, it is necessary to compare and refine models derived from a diversity of cohorts, patient-specific features, and statistical frameworks. The goal of this work is to develop and evaluate a predictive modeling platform that can be used to simplify and expedite this process for health data. To support this goal, we developed a PARAllel predictive MOdeling (PARAMO) platform which (1) constructs a dependency graph of tasks from specifications of predictive modeling pipelines, (2) schedules the tasks in a topological ordering of the graph, and (3) executes those tasks in parallel. We implemented this platform using Map-Reduce to enable independent tasks to run in parallel in a cluster computing environment. Different task scheduling preferences are also supported. We assess the performance of PARAMO on various workloads using three datasets derived from the EHR systems in place at Geisinger Health System and Vanderbilt University Medical Center and an anonymous longitudinal claims database. We demonstrate significant gains in computational efficiency against a standard approach. In particular, PARAMO can build 800 different models on a 300,000 patient data set in 3h in parallel compared to 9days if running sequentially. This work demonstrates that an efficient parallel predictive modeling platform can be developed for EHR data. This platform can facilitate large-scale modeling endeavors and speed-up the research workflow and reuse of health information. This platform is only a first step and provides the foundation for our ultimate goal of building analytic pipelines that are specialized for health data researchers. Copyright © 2013 Elsevier Inc. All rights reserved.

National Centers for Environmental Prediction

Science.gov Websites

Operational Forecast Graphics Experimental Forecast Graphics Verification and Diagnostics Model Configuration /EXPERIMENTAL MODEL FORECAST GRAPHICS OPERATIONAL VERIFICATION / DIAGNOSTICS PARALLEL VERIFICATION / DIAGNOSTICS Developmental Air Quality Forecasts and Verification Back to Table of Contents 2. PARALLEL/EXPERIMENTAL GRAPHICS

3D printed soft parallel actuator

NASA Astrophysics Data System (ADS)

Zolfagharian, Ali; Kouzani, Abbas Z.; Khoo, Sui Yang; Noshadi, Amin; Kaynak, Akif

2018-04-01

This paper presents a 3-dimensional (3D) printed soft parallel contactless actuator for the first time. The actuator involves an electro-responsive parallel mechanism made of two segments namely active chain and passive chain both 3D printed. The active chain is attached to the ground from one end and constitutes two actuator links made of responsive hydrogel. The passive chain, on the other hand, is attached to the active chain from one end and consists of two rigid links made of polymer. The actuator links are printed using an extrusion-based 3D-Bioplotter with polyelectrolyte hydrogel as printer ink. The rigid links are also printed by a 3D fused deposition modelling (FDM) printer with acrylonitrile butadiene styrene (ABS) as print material. The kinematics model of the soft parallel actuator is derived via transformation matrices notations to simulate and determine the workspace of the actuator. The printed soft parallel actuator is then immersed into NaOH solution with specific voltage applied to it via two contactless electrodes. The experimental data is then collected and used to develop a parametric model to estimate the end-effector position and regulate kinematics model in response to specific input voltage over time. It is observed that the electroactive actuator demonstrates expected behaviour according to the simulation of its kinematics model. The use of 3D printing for the fabrication of parallel soft actuators opens a new chapter in manufacturing sophisticated soft actuators with high dexterity and mechanical robustness for biomedical applications such as cell manipulation and drug release.

The design of multi-core DSP parallel model based on message passing and multi-level pipeline

NASA Astrophysics Data System (ADS)

Niu, Jingyu; Hu, Jian; He, Wenjing; Meng, Fanrong; Li, Chuanrong

2017-10-01

Currently, the design of embedded signal processing system is often based on a specific application, but this idea is not conducive to the rapid development of signal processing technology. In this paper, a parallel processing model architecture based on multi-core DSP platform is designed, and it is mainly suitable for the complex algorithms which are composed of different modules. This model combines the ideas of multi-level pipeline parallelism and message passing, and summarizes the advantages of the mainstream model of multi-core DSP (the Master-Slave model and the Data Flow model), so that it has better performance. This paper uses three-dimensional image generation algorithm to validate the efficiency of the proposed model by comparing with the effectiveness of the Master-Slave and the Data Flow model.

Multiprocessor speed-up, Amdahl's Law, and the Activity Set Model of parallel program behavior

NASA Technical Reports Server (NTRS)

Gelenbe, Erol

1988-01-01

An important issue in the effective use of parallel processing is the estimation of the speed-up one may expect as a function of the number of processors used. Amdahl's Law has traditionally provided a guideline to this issue, although it appears excessively pessimistic in the light of recent experimental results. In this note, Amdahl's Law is amended by giving a greater importance to the capacity of a program to make effective use of parallel processing, but also recognizing the fact that imbalance of the workload of each processor is bound to occur. An activity set model of parallel program behavior is then introduced along with the corresponding parallelism index of a program, leading to upper and lower bounds to the speed-up.

Xyce™ Parallel Electronic Simulator Users' Guide, Version 6.5.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keiter, Eric R.; Aadithya, Karthik V.; Mei, Ting

This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to developmore » new types of analysis without requiring the implementation of analysis-specific device models. Device models that are specifically tailored to meet Sandia's needs, including some radiation- aware devices (for Sandia users only). Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase -- a message passing parallel implementation -- which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. The information herein is subject to change without notice. Copyright © 2002-2016 Sandia Corporation. All rights reserved.« less

Stiffness modeling of compliant parallel mechanisms and applications in the performance analysis of a decoupled parallel compliant stage

NASA Astrophysics Data System (ADS)

Jiang, Yao; Li, Tie-Min; Wang, Li-Ping

2015-09-01

This paper investigates the stiffness modeling of compliant parallel mechanism (CPM) based on the matrix method. First, the general compliance matrix of a serial flexure chain is derived. The stiffness modeling of CPMs is next discussed in detail, considering the relative positions of the applied load and the selected displacement output point. The derived stiffness models have simple and explicit forms, and the input, output, and coupling stiffness matrices of the CPM can easily be obtained. The proposed analytical model is applied to the stiffness modeling and performance analysis of an XY parallel compliant stage with input and output decoupling characteristics. Then, the key geometrical parameters of the stage are optimized to obtain the minimum input decoupling degree. Finally, a prototype of the compliant stage is developed and its input axial stiffness, coupling characteristics, positioning resolution, and circular contouring performance are tested. The results demonstrate the excellent performance of the compliant stage and verify the effectiveness of the proposed theoretical model. The general stiffness models provided in this paper will be helpful for performance analysis, especially in determining coupling characteristics, and the structure optimization of the CPM.

Parallel performance of TORT on the CRAY J90: Model and measurement

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barnett, A.; Azmy, Y.Y.

1997-10-01

A limitation on the parallel performance of TORT on the CRAY J90 is the amount of extra work introduced by the multitasking algorithm itself. The extra work beyond that of the serial version of the code, called overhead, arises from the synchronization of the parallel tasks and the accumulation of results by the master task. The goal of recent updates to TORT was to reduce the time consumed by these activities. To help understand which components of the multitasking algorithm contribute significantly to the overhead, a parallel performance model was constructed and compared to measurements of actual timings of themore » code.« less

A Parallel Adaboost-Backpropagation Neural Network for Massive Image Dataset Classification

NASA Astrophysics Data System (ADS)

Cao, Jianfang; Chen, Lichao; Wang, Min; Shi, Hao; Tian, Yun

2016-12-01

Image classification uses computers to simulate human understanding and cognition of images by automatically categorizing images. This study proposes a faster image classification approach that parallelizes the traditional Adaboost-Backpropagation (BP) neural network using the MapReduce parallel programming model. First, we construct a strong classifier by assembling the outputs of 15 BP neural networks (which are individually regarded as weak classifiers) based on the Adaboost algorithm. Second, we design Map and Reduce tasks for both the parallel Adaboost-BP neural network and the feature extraction algorithm. Finally, we establish an automated classification model by building a Hadoop cluster. We use the Pascal VOC2007 and Caltech256 datasets to train and test the classification model. The results are superior to those obtained using traditional Adaboost-BP neural network or parallel BP neural network approaches. Our approach increased the average classification accuracy rate by approximately 14.5% and 26.0% compared to the traditional Adaboost-BP neural network and parallel BP neural network, respectively. Furthermore, the proposed approach requires less computation time and scales very well as evaluated by speedup, sizeup and scaleup. The proposed approach may provide a foundation for automated large-scale image classification and demonstrates practical value.

A Parallel Adaboost-Backpropagation Neural Network for Massive Image Dataset Classification.

PubMed

Cao, Jianfang; Chen, Lichao; Wang, Min; Shi, Hao; Tian, Yun

2016-12-01

Image classification uses computers to simulate human understanding and cognition of images by automatically categorizing images. This study proposes a faster image classification approach that parallelizes the traditional Adaboost-Backpropagation (BP) neural network using the MapReduce parallel programming model. First, we construct a strong classifier by assembling the outputs of 15 BP neural networks (which are individually regarded as weak classifiers) based on the Adaboost algorithm. Second, we design Map and Reduce tasks for both the parallel Adaboost-BP neural network and the feature extraction algorithm. Finally, we establish an automated classification model by building a Hadoop cluster. We use the Pascal VOC2007 and Caltech256 datasets to train and test the classification model. The results are superior to those obtained using traditional Adaboost-BP neural network or parallel BP neural network approaches. Our approach increased the average classification accuracy rate by approximately 14.5% and 26.0% compared to the traditional Adaboost-BP neural network and parallel BP neural network, respectively. Furthermore, the proposed approach requires less computation time and scales very well as evaluated by speedup, sizeup and scaleup. The proposed approach may provide a foundation for automated large-scale image classification and demonstrates practical value.

A Parallel Adaboost-Backpropagation Neural Network for Massive Image Dataset Classification

PubMed Central

Cao, Jianfang; Chen, Lichao; Wang, Min; Shi, Hao; Tian, Yun

2016-01-01

Image classification uses computers to simulate human understanding and cognition of images by automatically categorizing images. This study proposes a faster image classification approach that parallelizes the traditional Adaboost-Backpropagation (BP) neural network using the MapReduce parallel programming model. First, we construct a strong classifier by assembling the outputs of 15 BP neural networks (which are individually regarded as weak classifiers) based on the Adaboost algorithm. Second, we design Map and Reduce tasks for both the parallel Adaboost-BP neural network and the feature extraction algorithm. Finally, we establish an automated classification model by building a Hadoop cluster. We use the Pascal VOC2007 and Caltech256 datasets to train and test the classification model. The results are superior to those obtained using traditional Adaboost-BP neural network or parallel BP neural network approaches. Our approach increased the average classification accuracy rate by approximately 14.5% and 26.0% compared to the traditional Adaboost-BP neural network and parallel BP neural network, respectively. Furthermore, the proposed approach requires less computation time and scales very well as evaluated by speedup, sizeup and scaleup. The proposed approach may provide a foundation for automated large-scale image classification and demonstrates practical value. PMID:27905520

A Neurally Plausible Parallel Distributed Processing Model of Event-Related Potential Word Reading Data

ERIC Educational Resources Information Center

Laszlo, Sarah; Plaut, David C.

2012-01-01

The Parallel Distributed Processing (PDP) framework has significant potential for producing models of cognitive tasks that approximate how the brain performs the same tasks. To date, however, there has been relatively little contact between PDP modeling and data from cognitive neuroscience. In an attempt to advance the relationship between…

Fast I/O for Massively Parallel Applications

NASA Technical Reports Server (NTRS)

OKeefe, Matthew T.

1996-01-01

The two primary goals for this report were the design, contruction and modeling of parallel disk arrays for scientific visualization and animation, and a study of the IO requirements of highly parallel applications. In addition, further work in parallel display systems required to project and animate the very high-resolution frames resulting from our supercomputing simulations in ocean circulation and compressible gas dynamics.

Modeling Cooperative Threads to Project GPU Performance for Adaptive Parallelism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meng, Jiayuan; Uram, Thomas; Morozov, Vitali A.

Most accelerators, such as graphics processing units (GPUs) and vector processors, are particularly suitable for accelerating massively parallel workloads. On the other hand, conventional workloads are developed for multi-core parallelism, which often scale to only a few dozen OpenMP threads. When hardware threads significantly outnumber the degree of parallelism in the outer loop, programmers are challenged with efficient hardware utilization. A common solution is to further exploit the parallelism hidden deep in the code structure. Such parallelism is less structured: parallel and sequential loops may be imperfectly nested within each other, neigh boring inner loops may exhibit different concurrency patternsmore » (e.g. Reduction vs. Forall), yet have to be parallelized in the same parallel section. Many input-dependent transformations have to be explored. A programmer often employs a larger group of hardware threads to cooperatively walk through a smaller outer loop partition and adaptively exploit any encountered parallelism. This process is time-consuming and error-prone, yet the risk of gaining little or no performance remains high for such workloads. To reduce risk and guide implementation, we propose a technique to model workloads with limited parallelism that can automatically explore and evaluate transformations involving cooperative threads. Eventually, our framework projects the best achievable performance and the most promising transformations without implementing GPU code or using physical hardware. We envision our technique to be integrated into future compilers or optimization frameworks for autotuning.« less

Fast parallel algorithm for slicing STL based on pipeline

NASA Astrophysics Data System (ADS)

Ma, Xulong; Lin, Feng; Yao, Bo

2016-05-01

In Additive Manufacturing field, the current researches of data processing mainly focus on a slicing process of large STL files or complicated CAD models. To improve the efficiency and reduce the slicing time, a parallel algorithm has great advantages. However, traditional algorithms can't make full use of multi-core CPU hardware resources. In the paper, a fast parallel algorithm is presented to speed up data processing. A pipeline mode is adopted to design the parallel algorithm. And the complexity of the pipeline algorithm is analyzed theoretically. To evaluate the performance of the new algorithm, effects of threads number and layers number are investigated by a serial of experiments. The experimental results show that the threads number and layers number are two remarkable factors to the speedup ratio. The tendency of speedup versus threads number reveals a positive relationship which greatly agrees with the Amdahl's law, and the tendency of speedup versus layers number also keeps a positive relationship agreeing with Gustafson's law. The new algorithm uses topological information to compute contours with a parallel method of speedup. Another parallel algorithm based on data parallel is used in experiments to show that pipeline parallel mode is more efficient. A case study at last shows a suspending performance of the new parallel algorithm. Compared with the serial slicing algorithm, the new pipeline parallel algorithm can make full use of the multi-core CPU hardware, accelerate the slicing process, and compared with the data parallel slicing algorithm, the new slicing algorithm in this paper adopts a pipeline parallel model, and a much higher speedup ratio and efficiency is achieved.

Full f-p Shell Calculation of {sup 51}Ca and {sup 51}Sc

DOE Office of Scientific and Technical Information (OSTI.GOV)

Novoselsky, A.; Vallieres, M.; Laadan, O.

The spectra and the electromagnetic transitions of the nuclei {sup 51}Ca and {sup 51}Sc with 11 nucleons in the {ital f-p} shell are described in the nuclear shell-model approach by using two different two-body effective interactions. The full {ital f-p} shell basis functions are used with no truncation. The new parallel shell-model computer code DUPSM (Drexel University parallel shell model), that we recently developed, has been used. The calculations have been done on the MOSIX parallel machine at the Hebrew University of Jerusalem. {copyright} {ital 1997} {ital The American Physical Society}

Parallel computing method for simulating hydrological processesof large rivers under climate change

NASA Astrophysics Data System (ADS)

Wang, H.; Chen, Y.

2016-12-01

Climate change is one of the proverbial global environmental problems in the world.Climate change has altered the watershed hydrological processes in time and space distribution, especially in worldlarge rivers.Watershed hydrological process simulation based on physically based distributed hydrological model can could have better results compared with the lumped models.However, watershed hydrological process simulation includes large amount of calculations, especially in large rivers, thus needing huge computing resources that may not be steadily available for the researchers or at high expense, this seriously restricted the research and application. To solve this problem, the current parallel method are mostly parallel computing in space and time dimensions.They calculate the natural features orderly thatbased on distributed hydrological model by grid (unit, a basin) from upstream to downstream.This articleproposes ahigh-performancecomputing method of hydrological process simulation with high speedratio and parallel efficiency.It combinedthe runoff characteristics of time and space of distributed hydrological model withthe methods adopting distributed data storage, memory database, distributed computing, parallel computing based on computing power unit.The method has strong adaptability and extensibility,which means it canmake full use of the computing and storage resources under the condition of limited computing resources, and the computing efficiency can be improved linearly with the increase of computing resources .This method can satisfy the parallel computing requirements ofhydrological process simulation in small, medium and large rivers.

Solar wind interaction with Venus and Mars in a parallel hybrid code

NASA Astrophysics Data System (ADS)

Jarvinen, Riku; Sandroos, Arto

2013-04-01

We discuss the development and applications of a new parallel hybrid simulation, where ions are treated as particles and electrons as a charge-neutralizing fluid, for the interaction between the solar wind and Venus and Mars. The new simulation code under construction is based on the algorithm of the sequential global planetary hybrid model developed at the Finnish Meteorological Institute (FMI) and on the Corsair parallel simulation platform also developed at the FMI. The FMI's sequential hybrid model has been used for studies of plasma interactions of several unmagnetized and weakly magnetized celestial bodies for more than a decade. Especially, the model has been used to interpret in situ particle and magnetic field observations from plasma environments of Mars, Venus and Titan. Further, Corsair is an open source MPI (Message Passing Interface) particle and mesh simulation platform, mainly aimed for simulations of diffusive shock acceleration in solar corona and interplanetary space, but which is now also being extended for global planetary hybrid simulations. In this presentation we discuss challenges and strategies of parallelizing a legacy simulation code as well as possible applications and prospects of a scalable parallel hybrid model for the solar wind interactions of Venus and Mars.