Effects of geometric anisotropy on local field distribution: Ewald-Kornfeld formulation

We have applied the Ewald-Kornfeld formulation to a tetragonal lattice of point dipoles, in an attempt to examine the effects of geometric anisotropy on the local field distribution. The various problems encountered in the computation of the conditionally convergent summation of the near field are addressed and the methods of overcoming them are discussed. The results show that the geometric anisotropy has a significant impact on the local field distribution. The change in the local field can lead to a generalized Clausius-Mossotti equation for the anisotropic case.Comment: Accepted for publications, Journal of Physics: Condensed Matte

Field-induced structure transformation in electrorheological solids

We have computed the local electric field in a body-centered tetragonal (BCT) lattice of point dipoles via the Ewald-Kornfeld formulation, in an attempt to examine the effects of a structure transformation on the local field strength. For the ground state of an electrorheological solid of hard spheres, we identified a novel structure transformation from the BCT to the face-centered cubic (FCC) lattices by changing the uniaxial lattice constant c under the hard sphere constraint. In contrast to the previous results, the local field exhibits a non-monotonic transition from BCT to FCC. As c increases from the BCT ground state, the local field initially decreases rapidly towards the isotropic value at the body-centered cubic lattice, decreases further, reaching a minimum value and increases, passing through the isotropic value again at an intermediate lattice, reaches a maximum value and finally decreases to the FCC value. An experimental realization of the structure transformation is suggested. Moreover, the change in the local field can lead to a generalized Clausius-Mossotti equation for the BCT lattices.Comment: Submitted to Phys. Rev.

X-linked agammaglobulinemia diagnosed late in life: case report and review of the literature

<p>Abstract</p> <p>Background</p> <p>Common variable immune deficiency (CVID), one of the most common primary immunodeficiency diseases presents in adults, whereas X-linked agammaglobulinemia (XLA), an inherited humoral immunodeficiency, is usually diagnosed early in life after maternal Igs have waned. However, there have been several reports in the world literature in which individuals have either had a delay in onset of symptoms or have been misdiagnosed with CVID and then later found to have mutations in Bruton's tyrosine kinase (BTK) yielding a reclassification as adult-onset variants of XLA. The typical finding of absent B cells should suggest XLA rather than CVID and may be a sensitive test to detect this condition, leading to the more specific test (Btk mutational analysis). Further confirmation may be by mutational analyses.</p> <p>Methods</p> <p>The records of 2 patients were reviewed and appropriate clinical data collected. BTK mutational analysis was carried out to investigate the suspicion of adult-presentation of XLA. A review of the world literature on delayed diagnosis of XLA and mild or "leaky" phenotype was performed.</p> <p>Results</p> <p>2 patients previously diagnosed with CVID associated with virtual absence of CD19⁺B cells were reclassified as having a delayed diagnosis and adult-presentation of XLA. <b>Patient 1</b>, a 64 yr old male with recurrent sinobronchial infections had a low level of serum IgG of 360 mg/dl (normal 736–1900), IgA <27 mg/dl (normal 90–474), and IgM <25 mg/dl (normal 50–415). <b>Patient 2</b>, a 46 yr old male with recurrent sinopulmonary infections had low IgG of 260 mg/dl, low IgA <16 mg/dl, and normal IgM. Mutational analysis of BTK was carried out in both patients and confirmed the diagnosis of XLA</p> <p>Conclusion</p> <p>These two cases represent an unusual adult-presentation of XLA, a humoral immunodeficiency usually diagnosed in childhood and the need to further investigate a suspicion of XLA in adult males with CVID particularly those associated with low to absent CD19⁺B cells. A diagnosis of XLA can have significant implications including family counseling, detecting female carriers, and early intervention and treatment of affected male descendents.</p

Synaptic Cleft Segmentation in Non-Isotropic Volume Electron Microscopy of the Complete Drosophila Brain

Neural circuit reconstruction at single synapse resolution is increasingly recognized as crucially important to decipher the function of biological nervous systems. Volume electron microscopy in serial transmission or scanning mode has been demonstrated to provide the necessary resolution to segment or trace all neurites and to annotate all synaptic connections. Automatic annotation of synaptic connections has been done successfully in near isotropic electron microscopy of vertebrate model organisms. Results on non-isotropic data in insect models, however, are not yet on par with human annotation. We designed a new 3D-U-Net architecture to optimally represent isotropic fields of view in non-isotropic data. We used regression on a signed distance transform of manually annotated synaptic clefts of the CREMI challenge dataset to train this model and observed significant improvement over the state of the art. We developed open source software for optimized parallel prediction on very large volumetric datasets and applied our model to predict synaptic clefts in a 50 tera-voxels dataset of the complete Drosophila brain. Our model generalizes well to areas far away from where training data was available

Differential physiological responses to environmental change promote woody shrub expansion

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ecology and Evolution 3 (2013): 1149–1162, doi:10.1002/ece3.525.Direct and indirect effects of warming are increasingly modifying the carbon-rich vegetation and soils of the Arctic tundra, with important implications for the terrestrial carbon cycle. Understanding the biological and environmental influences on the processes that regulate foliar carbon cycling in tundra species is essential for predicting the future terrestrial carbon balance in this region. To determine the effect of climate change impacts on gas exchange in tundra, we quantified foliar photosynthesis (Anet), respiration in the dark and light (RD and RL, determined using the Kok method), photorespiration (PR), carbon gain efficiency (CGE, the ratio of photosynthetic CO2 uptake to total CO2 exchange of photosynthesis, PR, and respiration), and leaf traits of three dominant species – Betula nana, a woody shrub; Eriophorum vaginatum, a graminoid; and Rubus chamaemorus, a forb – grown under long-term warming and fertilization treatments since 1989 at Toolik Lake, Alaska. Under warming, B. nana exhibited the highest rates of Anet and strongest light inhibition of respiration, increasing CGE nearly 50% compared with leaves grown in ambient conditions, which corresponded to a 52% increase in relative abundance. Gas exchange did not shift under fertilization in B. nana despite increases in leaf N and P and near-complete dominance at the community scale, suggesting a morphological rather than physiological response. Rubus chamaemorus, exhibited minimal shifts in foliar gas exchange, and responded similarly to B. nana under treatment conditions. By contrast, E. vaginatum, did not significantly alter its gas exchange physiology under treatments and exhibited dramatic decreases in relative cover (warming: −19.7%; fertilization: −79.7%; warming with fertilization: −91.1%). Our findings suggest a foliar physiological advantage in the woody shrub B. nana that is further mediated by warming and increased soil nutrient availability, which may facilitate shrub expansion and in turn alter the terrestrial carbon cycle in future tundra environments.This study was supported by the National Science Foundation #0732664; Australian Research Council DP0986823; and Marsden Fund of the Royal Society of New Zealand

Identification of residues and domains of Raf important for function in vivo and in vitro

Random mutagenesis and genetic screens for impaired Raf function in Caenorhabditis elegans were used to identify six loss-of-function alleles of lin-45 raf that result in a substitution of a single amino acid. The mutations were classified as weak, intermediate, and strong based on phenotypic severity. We engineered these mutations into the homologous residues of vertebrate Raf-1 and analyzed the mutant proteins for their underlying biochemical defects. Surprisingly, phenotype strength did not correlate with the catalytic activity of the mutant proteins. Amino acid substitutions Val-589 and Ser-619 severely compromised Raf kinase activity, yet these mutants displayed weak phenotypes in the genetic screen. Interestingly, this is because these mutant Raf proteins efficiently activate the MAPK (mitogen-activated protein kinase) cascade in living cells, a result that may inform the analysis of knockout mice. Equally intriguing was the observation that mutant proteins with non-functional Ras-binding domains, and thereby deficient in Ras-mediated membrane recruitment, displayed only intermediate strength phenotypes. This confirms that secondary mechanisms exist to couple Ras to Raf in vivo. The strongest phenotype in the genetic screens was displayed by a S508N mutation that again did not correlate with a significant loss of kinase activity or membrane recruitment by oncogenic Ras in biochemical assays. Ser-508 lies within the Raf-1 activation loop, and mutation of this residue in Raf-1 and the equivalent Ser-615 in B-Raf revealed that this residue regulates Raf binding to MEK. Further characterization revealed that in response to activation by epidermal growth factor, the Raf-S508N mutant protein displayed both reduced catalytic activity and aberrant activation kinetics: characteristics that may explain the C. elegans phenotype

Fractional Systems and Fractional Bogoliubov Hierarchy Equations

We consider the fractional generalizations of the phase volume, volume element and Poisson brackets. These generalizations lead us to the fractional analog of the phase space. We consider systems on this fractional phase space and fractional analogs of the Hamilton equations. The fractional generalization of the average value is suggested. The fractional analogs of the Bogoliubov hierarchy equations are derived from the fractional Liouville equation. We define the fractional reduced distribution functions. The fractional analog of the Vlasov equation and the Debye radius are considered.Comment: 12 page

Fractional Liouville and BBGKI Equations

We consider the fractional generalizations of Liouville equation. The normalization condition, phase volume, and average values are generalized for fractional case.The interpretation of fractional analog of phase space as a space with fractal dimension and as a space with fractional measure are discussed. The fractional analogs of the Hamiltonian systems are considered as a special class of non-Hamiltonian systems. The fractional generalization of the reduced distribution functions are suggested. The fractional analogs of the BBGKI equations are derived from the fractional Liouville equation.Comment: 20 page