547 research outputs found
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
Structural analysis and corrosion studies on an ISO 5832-9 biomedical alloy with TiO2 sol–gel 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
sol–gel 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
Tyrode’s 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 substrate–layer interaction. From the point of
view of corrosion, the best TiO2 sol–gel 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
Cytoplasmic Intron Sequence-Retaining Transcripts Can Be Dendritically Targeted via ID Element Retrotransposons
SummaryRNA precursors give rise to mRNA after splicing of intronic sequences traditionally thought to occur in the nucleus. Here, we show that intron sequences are retained in a number of dendritically-targeted mRNAs, by using microarray and Illumina sequencing of isolated dendritic mRNA as well as in situ hybridization. Many of the retained introns contain ID elements, a class of SINE retrotransposon. A portion of these SINEs confers dendritic targeting to exogenous and endogenous transcripts showing the necessity of ID-mediated mechanisms for the targeting of different transcripts to dendrites. ID elements are capable of selectively altering the distribution of endogenous proteins, providing a link between intronic SINEs and protein function. As such, the ID element represents a common dendritic targeting element found across multiple RNAs. Retention of intronic sequence is a more general phenomenon than previously thought and plays a functional role in the biology of the neuron, partly mediated by co-opted repetitive sequences
Initial Rotor Position Estimation of an Interior Permanent-Magnet Synchronous Machine Using Carrier-Frequency Injection Methods
Interrogating the Genetic Determinants of Tourette\u27s Syndrome and Other Tic Disorders Through Genome-Wide Association Studies
Ultrathin compound semiconductor on insulator layers for high performance nanoscale transistors
Over the past several years, the inherent scaling limitations of electron
devices have fueled the exploration of high carrier mobility semiconductors as
a Si replacement to further enhance the device performance. In particular,
compound semiconductors heterogeneously integrated on Si substrates have been
actively studied, combining the high mobility of III-V semiconductors and the
well-established, low cost processing of Si technology. This integration,
however, presents significant challenges. Conventionally, heteroepitaxial
growth of complex multilayers on Si has been explored. Besides complexity, high
defect densities and junction leakage currents present limitations in the
approach. Motivated by this challenge, here we utilize an epitaxial transfer
method for the integration of ultrathin layers of single-crystalline InAs on
Si/SiO2 substrates. As a parallel to silicon-on-insulator (SOI) technology14,we
use the abbreviation "XOI" to represent our compound semiconductor-on-insulator
platform. Through experiments and simulation, the electrical properties of InAs
XOI transistors are explored, elucidating the critical role of quantum
confinement in the transport properties of ultrathin XOI layers. Importantly, a
high quality InAs/dielectric interface is obtained by the use of a novel
thermally grown interfacial InAsOx layer (~1 nm thick). The fabricated FETs
exhibit an impressive peak transconductance of ~1.6 mS/{\mu}m at VDS=0.5V with
ON/OFF current ratio of greater than 10,000 and a subthreshold swing of 107-150
mV/decade for a channel length of ~0.5 {\mu}m
Cytoplasmic BK\u3csub\u3eCa\u3c/sub\u3e channel intron-containing mRNAs contribute to the intrinsic excitability of hippocampal neurons
High single-channel conductance K+ channels, which respond jointly to membrane depolarization and micromolar concentrations of intracellular Ca2+ ions, arise from extensive cell-specific alternative splicing of pore-forming α-subunit mRNAs. Here, we report the discovery of an endogenous BKCa channel α-subunit intron-containing mRNA in the cytoplasm of hippocampal neurons. This partially processed mRNA, which comprises ≈10% of the total BKCa channel α-subunit mRNAs, is distributed in a gradient throughout the somatodendritic space. We selectively reduced endogenous cytoplasmic levels of this intron-containing transcript by RNA interference without altering levels of the mature splice forms of the BKCa channel mRNAs. In doing so, we could demonstrate that changes in a unique BKCa channel α-subunit introncontaining splice variant mRNA can greatly impact the distribution of the BKCa channel protein to dendritic spines and intrinsic firing properties of hippocampal neurons. These data suggest a new regulatory mechanism for modulating the membrane properties and ion channel gradients of hippocampal neurons
Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution
The standard approach to analyzing 16S tag sequence data, which relies on
clustering reads by sequence similarity into Operational Taxonomic Units
(OTUs), underexploits the accuracy of modern sequencing technology. We present
a clustering-free approach to multi-sample Illumina datasets that can identify
independent bacterial subpopulations regardless of the similarity of their 16S
tag sequences. Using published data from a longitudinal time-series study of
human tongue microbiota, we are able to resolve within standard 97% similarity
OTUs up to 20 distinct subpopulations, all ecologically distinct but with 16S
tags differing by as little as 1 nucleotide (99.2% similarity). A comparative
analysis of oral communities of two cohabiting individuals reveals that most
such subpopulations are shared between the two communities at 100% sequence
identity, and that dynamical similarity between subpopulations in one host is
strongly predictive of dynamical similarity between the same subpopulations in
the other host. Our method can also be applied to samples collected in
cross-sectional studies and can be used with the 454 sequencing platform. We
discuss how the sub-OTU resolution of our approach can provide new insight into
factors shaping community assembly.Comment: Updated to match the published version. 12 pages, 5 figures +
supplement. Significantly revised for clarity, references added, results not
change
The biocompatibility of titanium in a buffer solution: compared effects of a thin film of TiO2 deposited by MOCVD and of collagen deposited from a gel
This study aims at evaluating the biocompatibility of titanium surfaces modified according two different ways: (i) deposition of a bio-inert, thin film of rutile TiO2 by chemical vapour deposition (MOCVD), and (ii) biochemical treatment with collagen gel, in order to obtain a bio-interactive coating. Behind the comparison is the idea that either the bio-inert or the bio-active coating has specific advantages when applied to implant treatment, such as the low price of the collagen treatment for instance. The stability in buffer solution was evaluated by open circuit potential (OCP) for medium time and cyclic voltametry. The OCP stabilized after 5104 min for all the specimens except the collagen treated sample which presented a stable OCP from the first minutes. MOCVD treated samples stabilized to more electropositive values. Numeric results were statistically analysed to obtain the regression equations for long time predictable evolution. The corrosion parameters determined from cyclic curves revealed that the MOCVD treatment is an efficient way to improve corrosion resistance. Human dermal fibroblasts were selected for cell culture tests, taking into account that these cells are present in all bio-interfaces, being the main cellular type of connective tissue. The cells grew on either type of surface without phenotype modification. From the reduction of yellow, water-soluble 3-(4,5-dimethyldiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT cytotoxicity test), MOCVD treated samples offer better viability than mechanically polished Ti and collagen treated samples as well. Cell spreading, as evaluated from microscope images processed by the program Sigma Scan, showed also enhancement upon surface modification. Depending on the experimental conditions, MOCVD deposited TiO2 exhibits different nanostructures that may influence biological behaviour. The results demonstrate the capacity of integration in simulated physiologic liquids for an implant pretreated by either method
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