Internal states of model isotropic granular packings. I. Assembling process, geometry and contact networks

This is the first paper of a series of three, reporting on numerical simulation studies of geometric and mechanical properties of static assemblies of spherical beads under an isotropic pressure. Frictionless systems assemble in the unique random close packing (RCP) state in the low pressure limit if the compression process is fast enough, slower processes inducing traces of crystallization, and exhibit specific properties directly related to isostaticity of the force-carrying structure. The different structures of frictional packings assembled by various methods cannot be classified by the sole density. While lubricated systems approach RCP densities and coordination number z^*~=6 on the backbone in the rigid limit, an idealized "vibration" procedure results in equally dense configurations with z^*~=4.5. Near neighbor correlations on various scales are computed and compared to available laboratory data, although z^* values remain experimentally inaccessible. Low coordination packings have many rattlers (more than 10% of the grains carry no force), which should be accounted for on studying position correlations, and a small proportion of harmless "floppy modes" associated with divalent grains. Frictional packings, however slowly assembled under low pressure, retain a finite level of force indeterminacy, except in the limit of infinite friction.Comment: 29 pages. Published in Physical Review

Improving EGM2008 by GPS and leveling data at local scale

The development of the Earth Gravitational Model 2008 (EGM2008) model is a significant contribution for modeling the Earth's gravity and geoid. Recently, it can be confidently used versus geometric models following a simple refinement procedure. Several studies show that, EGM2008 can reach the accuracy of regional or local geoid models after modeling the differences between the GPS-leveling geoid heights and EGM2008 derived geoid heights at identified control points. The study focuses on a corrector surface fitting (CSF) approach based on radial basis functions (RBF) as improvement procedure for EGM2008. A detailed mathematical model and solution algorithm of the proposed model is given, and it has been applied in different test areas covering the city borders of Bursa, Konya, Denizli and Gaziantep in Turkey. Accuracy of the improved model was evaluated in scattered check points within test regions. The geoid heights of all check points obtained by GPS-leveling measurements were compared with the geoid heights obtained from improved model. The discrepancies between the calculated and measured geoid heights were analyzed and discussed

Micromechanical features of jet erosion - A numerical perspective

The erosion mechanisms driving the particle detachment of a soil under an impinging jet are here analysed from a micromechanical perspective combining the numerical Discrete Element and Lattice Boltzmann methods (DEM-LBM). Firstly, the local hydrodynamic conditions of both free and impinging jets are examined and briefly discussed, particularly on the relevance of the superficial irregularities of the granular assembly, which can dominate the local distribution of hydrodynamic variables over the impingement area. Profiles of both macromechanic and discrete (micromechanic) variables will be put forward. Then, the onset of erosion is reviewed from a topological point of view (locality of first grain motion) on the basis of a parametric study. Finally, the variation of the critical inflow velocity for the initiation of erosion in dependence on the particle size is also examined and briefly discussed

Leukemia Inhibitory Factor Is a Key Signal for Injury-Induced Neurogenesis in the Adult Mouse Olfactory Epithelium

The mammalian olfactory epithelium (OE) is composed of primary olfactory sensory neurons (OSNs) that are renewed throughout adulthood by local, restricted neuronal progenitor cells. The molecular signals that control this neurogenesis in vivo are unknown. Using olfactory bulb ablation (OBX) in adult mice to trigger synchronous mitotic stimulation of neuronal progenitors in the OE, we show the in vivo involvement of a cytokine in the cellular events leading to the regeneration of the OE. We find that, of many potential mitogenic signals, only leukemia inhibitory factor (LIF) is induced before the onset of neuronal progenitor proliferation. The rise in LIF mRNA expression peaks at 8 hr after OBX, and in situ RT-PCR and immunocytochemistry indicate that LIF is upregulated, in part, in the injured neurons themselves. This rise in LIF is necessary for injury-induced neurogenesis, as OBX in the LIF knock-out mouse fails to stimulate cell proliferation in the OE. Moreover, delivery of exogenous LIF to the intact adult OE using an adenoviral vector stimulates BrdU labeling in the apical OE. Taken together, these results suggest that injured OSNs release LIF as a stimulus to initiate their own replacement

Population Pharmacokinetic and Pharmacogenetic Analysis of Nevirapine in Hypersensitive and Tolerant HIV-Infected Patients from Malawi

We modeled nevirapine (NVP) pharmacokinetics in HIV-infected Malawian patients to assess the relationship between drug exposure and patient characteristics, genetic polymorphisms, and development of hypersensitivity reaction (HSR). One thousand one hundred seventeen patients were prospectively recruited and followed for 26 weeks with multiple or single serum samples obtained in a subset of patients for NVP quantification. Single nucleotide polymorphisms (SNPs) within CYP2B6 and CYP3A4 genes were typed. Nonlinear mixed effects modeling was utilized to assess the influence of patient characteristics and host genetics on NVP apparent oral clearance (CL/F) and to explore the relationship between NVP CL/F and HSR. Published haplotype distributions were used to simulate NVP concentrations in Caucasians versus Africans. One hundred eighty patients (101 female) were included in the model; 25 experienced HSR. No associations between patient demographics or HSR and NVP CL/F were evident. A significant relationship between CYP2B6 c.983T>C and CYP2B6 c.516G>T and NVP CL/F was observed (P < 0.01). NVP CL/F was reduced by 23% and 36% in patients with CYP2B6 983TT/516TT and 983TC/516GG or GT, respectively, compared to the reference genotype. Simulated exposures suggested similar proportions (13 to 17%) of patients with subtherapeutic NVP among Caucasians and an African population. Influence of CYP2B6 polymorphisms on NVP CL/F in this population is in agreement with other reports. Our data indicate a lack of association between NVP exposure and HSR. Based on these data, dose optimization based solely on ethnicity (without individual gene testing) is unlikely to impact on risk of treatment failure or toxicity even in an African population with high carriage of poor metabolizer mutations

The effect of starch-based biomaterials on leukocyte adhesion and activation in vitro

Leukocyte adhesion to biomaterials has long been recognised as a key element to determine their inflammatory potential. Results regarding leukocyte adhesion and activation are contradictory in some aspects of the material’s effect in determining these events. It is clear that together with the wettability or hydrophilicity/hydrophobicity, the roughness of a substrate has a major effect on leukocyte adhesion. Both the chemical and physical properties of a material influence the adsorbed proteins layer which in turn determines the adhesion of cells. In this work polymorphonuclear (PMN) cells and a mixed population of monocytes/macrophages and lymphocytes (mononuclear cells) were cultured separately with a range of starch-based materials and composites with hydroxyapatite (HA). A combination of both reflected light microscopy and scanning electron microscopy (SEM) was used in order to study the leukocyte morphology. The quantification of the enzyme lactate dehydrogenase (LDH) was used to determine the number of viable cells adhered to the polymers. Cell adhesion and activation was characterised by immunocytochemistry based on the expression of several adhesion molecules, crucial in the progress of an inflammatory response. This work supports previous in vitro studies with PMN and monocytes/macrophages, which demonstrated that there are several properties of the materials that can influence and determine their biological response. From our study, monocytes/macrophages and lymphocytes adhere in similar amounts to more hydrophobic (SPCL) and to moderately hydrophilic (SEVA-C) surfaces and do not preferentially adhere to rougher substrates (SCA). Contrarily, more hydrophilic surfaces (SCA) induced higher PMN adhesion and lower activation. In addition, the hydroxyapatite reinforcement induces changes in cell behaviour for some materials but not for others. The observed response to starch-based biodegradable polymers was not significantly different from the control materials. Thus, the results reported herein indicate the low potential of the starch-based biodegradable polymers to induce inflammation especially the HA reinforced composite materials

Mapping of HNF4α target genes in intestinal epithelial cells

© 2009 Boyd et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Study of FoxA Pioneer Factor at Silent Genes Reveals Rfx-Repressed Enhancer at Cdx2 and a Potential Indicator of Esophageal Adenocarcinoma Development

Understanding how silent genes can be competent for activation provides insight into development as well as cellular reprogramming and pathogenesis. We performed genomic location analysis of the pioneer transcription factor FoxA in the adult mouse liver and found that about one-third of the FoxA bound sites are near silent genes, including genes without detectable RNA polymerase II. Virtually all of the FoxA-bound silent sites are within conserved sequences, suggesting possible function. Such sites are enriched in motifs for transcriptional repressors, including for Rfx1 and type II nuclear hormone receptors. We found one such target site at a cryptic “shadow” enhancer 7 kilobases (kb) downstream of the Cdx2 gene, where Rfx1 restricts transcriptional activation by FoxA. The Cdx2 shadow enhancer exhibits a subset of regulatory properties of the upstream Cdx2 promoter region. While Cdx2 is ectopically induced in the early metaplastic condition of Barrett's esophagus, its expression is not necessarily present in progressive Barrett's with dysplasia or adenocarcinoma. By contrast, we find that Rfx1 expression in the esophageal epithelium becomes gradually extinguished during progression to cancer, i.e, expression of Rfx1 decreased markedly in dysplasia and adenocarcinoma. We propose that this decreased expression of Rfx1 could be an indicator of progression from Barrett's esophagus to adenocarcinoma and that similar analyses of other transcription factors bound to silent genes can reveal unanticipated regulatory insights into oncogenic progression and cellular reprogramming