925 research outputs found
Localized States and Resultant Band Bending in Graphene Antidot Superlattices
We fabricated dye sensitized graphene antidot superlattices with the purpose
of elucidating the role of the localized edge state density. The fluorescence
from deposited dye molecules was found to strongly quench as a function of
increasing antidot filling fraction, whereas it was enhanced in unpatterned but
electrically back-gated samples. This contrasting behavior is strongly
indicative of a built-in lateral electric field that accounts for fluorescence
quenching as well as p-type doping. These findings are of great interest for
light-harvesting applications that require field separation of electron-hole
pairs.Comment: NanoLetters, 201
MrsRF: an efficient MapReduce algorithm for analyzing large collections of evolutionary trees
<p>Abstract</p> <p>Background</p> <p>MapReduce is a parallel framework that has been used effectively to design large-scale parallel applications for large computing clusters. In this paper, we evaluate the viability of the MapReduce framework for designing phylogenetic applications. The problem of interest is generating the all-to-all Robinson-Foulds distance matrix, which has many applications for visualizing and clustering large collections of evolutionary trees. We introduce MrsRF (<it>MapReduce Speeds up RF</it>), a multi-core algorithm to generate a <it>t </it>Ć <it>t </it>Robinson-Foulds distance matrix between <it>t </it>trees using the MapReduce paradigm.</p> <p>Results</p> <p>We studied the performance of our MrsRF algorithm on two large biological trees sets consisting of 20,000 trees of 150 taxa each and 33,306 trees of 567 taxa each. Our experiments show that MrsRF is a scalable approach reaching a speedup of over 18 on 32 total cores. Our results also show that achieving top speedup on a multi-core cluster requires different cluster configurations. Finally, we show how to use an RF matrix to summarize collections of phylogenetic trees visually.</p> <p>Conclusion</p> <p>Our results show that MapReduce is a promising paradigm for developing multi-core phylogenetic applications. The results also demonstrate that different multi-core configurations must be tested in order to obtain optimum performance. We conclude that RF matrices play a critical role in developing techniques to summarize large collections of trees.</p
Medial Prefrontal Cortical Thinning Mediates Shifts in Other-Regarding Preferences during Adolescence
Adolescence is a time of significant cortical changes in the āsocial brainā, a set of brain regions involved in sophisticated social inference. However, there is limited evidence linking the structural changes in social brain to development of social behavior. The present study investigated how cortical development of the social brain relates to other-regarding behavior, in the context of fairness concerns. Participants aged between 9 to 23 years old responded to multiple rounds of ultimatum game proposals. The degree to which each participant considers fairness of intention (i.e., intention-based reciprocity) vs. outcome (i.e., egalitarianism) was quantified using economic utility models. We observed a gradual shift in other-regarding preferences from simple rule-based egalitarianism to complex intention-based reciprocity from early childhood to young adulthood. The preference shift was associated with cortical thinning of the dorsomedial prefrontal cortex and posterior temporal cortex. Meta-analytic reverse-inference analysis showed that these regions were involved in social inference. Importantly, the other-regarding preference shift was statistically mediated by cortical thinning in the dorsomedial prefrontal cortex. Together these findings suggest that development of the ability to perform sophisticated other-regarding social inference is associated with the structural changes of specific social brain regions in late adolescence
Structural analysis and corrosion studies on an ISO 5832-9 biomedical alloy with TiO2 solāgel layers
The aim of this study was to demonstrate the
relationship between the structural and corrosion properties
of an ISO 5832-9 biomedical alloy modified with titanium
dioxide (TiO2) layers. These layers were obtained via the
solāgel method by acid-catalyzed hydrolysis of titanium
isopropoxide in isopropanol solution. To obtain TiO2 layers
with different structural properties, the coated samples
were annealed at temperatures of 200, 300, 400, 450, 500,
600 and 800 C for 2 h. For all the prepared samples,
accelerated corrosion measurements were performed in
Tyrodeās physiological solution using electrochemical
methods. The most important corrosion parameters were
determined: corrosion potential, polarization resistance,
corrosion rate, breakdown and repassivation potentials.
Corrosion damage was analyzed using scanning electron
microscopy. Structural analysis was carried out for selected
TiO2 coatings annealed at 200, 400, 600 and 800 C. In
addition, the morphology, chemical composition, crystallinity,
thickness and density of the deposited TiO2 layers
were determined using suitable electron and X-ray measurement
methods. It was shown that the structure and
character of interactions between substrate and deposited
TiO2 layers depended on annealing temperature. All the
obtained TiO2 coatings exhibit anticorrosion properties, but
these properties are related to the crystalline structure and
character of substrateālayer interaction. From the point of
view of corrosion, the best TiO2 solāgel coatings for stainless steel intended for biomedical applications seem to
be those obtained at 400 C.This study was supported by Grant No. N N507
501339 of the National Science Centre. The authors wish to express
their thanks to J. Borowski (MEDGAL, Poland) for the Rex 734 alloy
Effectively identifying regulatory hotspots while capturing expression heterogeneity in gene expression studies
Expression quantitative trait loci (eQTL) mapping is a tool that can systematically identify genetic variation affecting gene expression. eQTL mapping studies have shown that certain genomic locations, referred to as regulatory hotspots, may affect the expression levels of many genes. Recently, studies have shown that various confounding factors may induce spurious regulatory hotspots. Here, we introduce a novel statistical method that effectively eliminates spurious hotspots while retaining genuine hotspots. Applied to simulated and real datasets, we validate that our method achieves greater sensitivity while retaining low false discovery rates compared to previous methods
The generalized Robinson-Foulds metric
The Robinson-Foulds (RF) metric is arguably the most widely used measure of
phylogenetic tree similarity, despite its well-known shortcomings: For example,
moving a single taxon in a tree can result in a tree that has maximum distance
to the original one; but the two trees are identical if we remove the single
taxon. To this end, we propose a natural extension of the RF metric that does
not simply count identical clades but instead, also takes similar clades into
consideration. In contrast to previous approaches, our model requires the
matching between clades to respect the structure of the two trees, a property
that the classical RF metric exhibits, too. We show that computing this
generalized RF metric is, unfortunately, NP-hard. We then present a simple
Integer Linear Program for its computation, and evaluate it by an
all-against-all comparison of 100 trees from a benchmark data set. We find that
matchings that respect the tree structure differ significantly from those that
do not, underlining the importance of this natural condition.Comment: Peer-reviewed and presented as part of the 13th Workshop on
Algorithms in Bioinformatics (WABI2013
Neighborhood Homogeneous Labelings of Graphs
Given a labeling of the vertices and edges of a graph, we define a type of homogeneity that requires that the neighborhood of every vertex contains the same number of each of the labels. This homogeneity constraint is a generalization of regularity ā all such graphs are regular. We consider a specific condition in which both the edge and vertex label sets have two elements and every neighborhood contains two of each label. We show that vertex homogeneity implies edge homogeneity (so long as the number of edges in any neighborhood is four), and give two theorems describing how to build new homogeneous graphs (or multigraphs) from others. Keywords: vertex labeling; edge labeling; homogenous graph; regular graph 1
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