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

Synthesis of Heterogeneous Li4Ti5O12 Nanostructured Anodes with Long-Term Cycle Stability

The 0D-1D Lithium titanate (Li4Ti5O12) heterogeneous nanostructures were synthesized through the solvothermal reaction using lithium hydroxide monohydrate (Li(OH)·H2O) and protonated trititanate (H2Ti3O7) nanowires as the templates in an ethanol/water mixed solvent with subsequent heat treatment. A scanning electron microscope (SEM) and a high resolution transmission electron microscope (HRTEM) were used to reveal that the Li4Ti5O12 powders had 0D-1D heterogeneous nanostructures with nanoparticles (0D) on the surface of wires (1D). The composition of the mixed solvents and the volume ratio of ethanol modulated the primary particle size of the Li4Ti5O12 nanoparticles. The Li4Ti5O12 heterogeneous nanostructures exhibited good capacity retention of 125 mAh/g after 500 cycles at 1C and a superior high-rate performance of 114 mAh/g at 20C

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

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

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

Rare Copy Number Variants in \u3cem\u3eNRXN1\u3c/em\u3e and \u3cem\u3eCNTN6\u3c/em\u3e Increase Risk for Tourette Syndrome

Tourette syndrome (TS) is a model neuropsychiatric disorder thought to arise from abnormal development and/or maintenance of cortico-striato-thalamo-cortical circuits. TS is highly heritable, but its underlying genetic causes are still elusive, and no genome-wide significant loci have been discovered to date. We analyzed a European ancestry sample of 2,434 TS cases and 4,093 ancestry-matched controls for rare (\u3c 1% frequency) copy-number variants (CNVs) using SNP microarray data. We observed an enrichment of global CNV burden that was prominent for large (\u3e 1 Mb), singleton events (OR = 2.28, 95% CI [1.39–3.79], p = 1.2 × 10−3) and known, pathogenic CNVs (OR = 3.03 [1.85–5.07], p = 1.5 × 10−5). We also identified two individual, genome-wide significant loci, each conferring a substantial increase in TS risk (NRXN1 deletions, OR = 20.3, 95% CI [2.6–156.2]; CNTN6 duplications, OR = 10.1, 95% CI [2.3–45.4]). Approximately 1% of TS cases carry one of these CNVs, indicating that rare structural variation contributes significantly to the genetic architecture of TS