2,272 research outputs found
Nitric oxide as a putative retinal axon pathfinding and target recognition cue in Xenopus laevis
Nitric oxide (NO) is an atypical neurotransmitter synthesized by the enzyme nitric oxide synthase (NOS) during many stages of the Xenopus laevis life cycle. This research investigates whether the gas NO is involved in axon guidance, the neurodevelopmental process in which axons travel through the brain to their appropriate target locations to form functional neural circuitry. Through immunocytochemistry and direct labeling of the NO gas with a fluorescent dye, we have found that NOS expression corresponds spatiotemporally with the beginning of retinal axon innervation of the optic tectum in X. laevis. Our function-blocking studies in which NO is chemically inhibited suggest that NO may be necessary for correct pathfinding and targeting, evidenced by qualitative widening of the optic tract and aberrant target innervation
Combinatorial Characterizations of K-matrices
We present a number of combinatorial characterizations of K-matrices. This
extends a theorem of Fiedler and Ptak on linear-algebraic characterizations of
K-matrices to the setting of oriented matroids. Our proof is elementary and
simplifies the original proof substantially by exploiting the duality of
oriented matroids. As an application, we show that a simple principal pivot
method applied to the linear complementarity problems with K-matrices converges
very quickly, by a purely combinatorial argument.Comment: 17 pages; v2, v3: clarified proof of Thm 5.5, minor correction
Characterizing meteorological forecast impact on microgrid optimization performance and design
A microgrid consists of electrical generation sources, energy storage assets, loads, and the ability to function independently, or connect and share power with other electrical grids. Thefocus of this work is on the behavior of a microgrid, with both diesel generator and photovoltaic resources, whose heating or cooling loads are influenced by local meteorological conditions. Themicrogrid\u27s fuel consumption and energy storage requirement were then examined as a function of the atmospheric conditions used by its energy management strategy (EMS). A fuel-optimal EMS, able to exploit meteorological forecasts, was developed and evaluated using a hybrid microgrid simulation. Weather forecast update periods ranged from 15 min to 24 h. Four representative meteorological sky classifications (clear, partly cloudy, overcast, or monsoon) were considered. Forall four sky classifications, fuel consumption and energy storage requirements increased linearly with the increasing weather forecast interval. Larger forecast intervals lead to degraded weather forecasts, requiring more frequent charging/discharging of the energy storage, increasing both the fuel consumption and energy storage design requirements. The significant contributions of this work include the optimal EMS and an approach for quantifying the meteorological forecast effects on fuel consumption and energy storage requirements on microgrid performance. The findings of this study indicate that the forecast interval used by the EMS affected both fuel consumption and energy storage requirements, and that the sensitivity of these effects depended on the 24-hour sky conditions
Zassenhaus conjecture for central extensions of S5
We confirm a conjecture of Zassenhaus about rational conjugacy of torsion units in
integral group rings for a covering group of the symmetric group S5 and for the general linear
group GLð2; 5Þ. The first result, together with others from the literature, settles the conjugacy
question for units of prime-power order in the integral group ring of a finite Frobenius group
How does conformational flexibility influence key structural features involved in activation of anaplastic lymphoma kinase?
Anaplastic Lymphoma Kinase (ALK) plays a major role in developing tumor processes and therefore has emerged as a validated therapeutic target. Applying atomistic molecular dynamics simulations on the wild type enzyme and the nine most frequently occurring and clinically important activation mutants we revealed important conformational effects on key interactions responsible for the activation of the enzyme
Pairwise running of automated crystallographic model-building pipelines
For the last two decades, researchers have worked independently to automate protein model building, and four widely used software pipelines have been developed for this purpose: ARP/wARP, Buccaneer, Phenix AutoBuild and SHELXE. Here, the usefulness of combining these pipelines to improve the built protein structures by running them in pairwise combinations is examined. The results show that integrating these pipelines can lead to significant improvements in structure completeness and Rfree. In particular, running Phenix AutoBuild after Buccaneer improved structure completeness for 29% and 75% of the data sets that were examined at the original resolution and at a simulated lower resolution, respectively, compared with running Phenix AutoBuild on its own. In contrast, Phenix AutoBuild alone produced better structure completeness than the two pipelines combined for only 7% and 3% of these data sets
Mean-Field Gauge Interactions in Five Dimensions II. The Orbifold
We study Gauge-Higgs Unification in five dimensions on the lattice by means
of the mean-field expansion. We formulate it for the case of an SU(2) pure
gauge theory and orbifold boundary conditions along the extra dimension, which
explicitly break the gauge symmetry to U(1) on the boundaries. Our main result
is that the gauge boson mass computed from the static potential along
four-dimensional hyperplanes is nonzero implying spontaneous symmetry breaking.
This observation supports earlier data from Monte Carlo simulations [12].Comment: 33 pages, 8 figures; text improved; references corrected; version
accepted for publication in Nucl. Phys.
PocketMatch: A new algorithm to compare binding sites in protein structures
Background: Recognizing similarities and deriving relationships among protein molecules is a fundamental
requirement in present-day biology. Similarities can be present at various levels which can be detected through comparison of protein sequences or their structural folds. In some cases similarities obscure at these levels could be present merely in the substructures at their binding sites. Inferring functional similarities between protein molecules by comparing their binding sites is still largely exploratory and not as yet a routine protocol. One of
the main reasons for this is the limitation in the choice of appropriate analytical tools that can compare binding sites with high sensitivity. To benefit from the enormous amount of structural data that is being rapidly accumulated, it is essential to have high throughput tools that enable large scale binding site comparison.

Results: Here we present a new algorithm PocketMatch for comparison of binding sites in a frame invariant
manner. Each binding site is represented by 90 lists of sorted distances capturing shape and chemical nature of the site. The sorted arrays are then aligned using an incremental alignment method and scored to obtain PMScores for pairs of sites. A comprehensive sensitivity analysis and an extensive validation of the algorithm have been carried out. Perturbation studies where the geometry of a given site was retained but the residue types were changed randomly, indicated that chance similarities were virtually non-existent. Our analysis also demonstrates that shape information alone is insufficient to discriminate between diverse binding sites, unless
combined with chemical nature of amino acids.

Conclusions: A new algorithm has been developed to compare binding sites in accurate, efficient and
high-throughput manner. Though the representation used is conceptually simplistic, we demonstrate that along
with the new alignment strategy used, it is sufficient to enable binding comparison with high sensitivity. Novel methodology has also been presented for validating the algorithm for accuracy and sensitivity with respect to geometry and chemical nature of the site. The method is also fast and takes about 1/250th second for one comparison on a single processor. A parallel version on BlueGene has also been implemented
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