miROrtho: computational survey of microRNA genes

MicroRNAs (miRNAs) are short, non-protein coding RNAs that direct the widespread phenomenon of post-transcriptional regulation of metazoan genes. The mature ∼22-nt long RNA molecules are processed from genome-encoded stem-loop structured precursor genes. Hundreds of such genes have been experimentally validated in vertebrate genomes, yet their discovery remains challenging, and substantially higher numbers have been estimated. The miROrtho database (http://cegg.unige.ch/mirortho) presents the results of a comprehensive computational survey of miRNA gene candidates across the majority of sequenced metazoan genomes. We designed and applied a three-tier analysis pipeline: (i) an SVM-based ab initio screen for potent hairpins, plus homologs of known miRNAs, (ii) an orthology delineation procedure and (iii) an SVM-based classifier of the ortholog multiple sequence alignments. The web interface provides direct access to putative miRNA annotations, ortholog multiple alignments, RNA secondary structure conservation, and sequence data. The miROrtho data are conceptually complementary to the miRBase catalog of experimentally verified miRNA sequences, providing a consistent comparative genomics perspective as well as identifying many novel miRNA genes with strong evolutionary suppor

Carbon−Phosphorus Bond Activation of Tri(2-thienyl)phosphine at Dirhenium and Dimanganese Centers

Reaction of [Re2(CO)9(NCMe)] with tri(2-thienyl)phosphine (PTh3) in refluxing cyclohexane affords three substituted dirhenium complexes: [Re2(CO)9(PTh3)] (1), [Re2(CO)8(NCMe)(PTh3)] (2), and [Re2(CO)8(PTh3)2] (3). Complex 2 was also obtained from the room-temperature reaction of [Re2(CO)8(NCMe)2] with PTh3 and is an unusual example in which the acetonitrile and phosphine ligands are coordinated to the same rhenium atom. Thermolysis of 1 and 3 in refluxing xylene affords [Re2(CO)8(μ-PTh2)(μ-η1:κ1-C4H3S)] (4) and [Re2(CO)7(PTh3)(μ-PTh2)(μ-H)] (5), respectively, both resulting from carbon−phosphorus bond cleavage of a coordinated PTh3 ligand. Reaction of [Re2(CO)10] and PTh3 in refluxing xylene gives a complex mixture of products. These products include 3−5, two further binuclear products, [Re2(CO)7(PTh3)(μ-PTh2)(μ-η1:κ1-C4H3S)] (6) and [Re2(CO)7(μ-κ1:κ2-Th2PC4H2SPTh)(μ-η1:κ1-C4H3S)] (7), and the mononuclear hydrides [ReH(CO)4(PTh3)] (8) and trans-[ReH(CO)3(PTh3)2] (9). Binuclear 6 is structurally similar to 4 and can be obtained from reaction of the latter with 1 equiv of PTh3. Formation of 7 involves a series of rearrangements resulting in the formation of a unique new diphosphine ligand, Th2PC4H2SPTh. Reaction of [Mn2(CO)10] with PTh3 in refluxing toluene affords the phosphine-substituted product [Mn2(CO)9(PTh3)] (10) and two carbon−phosphorus bond cleavage products, [Mn2(CO)6(μ-PTh2)(μ-η1:η5-C4H3S)] (11) and [Mn2(CO)5(PTh3)(μ-PTh2)(μ-η1:η5-C4H3S)] (12). Both 11 and 12 contain a bridging thienyl ligand that is bonded to one manganese atom in a η5-fashion. The molecular structures of eight of these new complexes were established by single-crystal X-ray diffraction studies, allowing a detailed analysis of the disposition of the coordinated ligands

Puffed Noncommutative Nonabelian Vortices

We present new solutions of noncommutative gauge theories in which coincident unstable vortices expand into unstable circular shells. As the theories are noncommutative, the naive definition of the locations of the vortices and shells is gauge-dependent, and so we define and calculate the profiles of these solutions using the gauge-invariant noncommutative Wilson lines introduced by Gross and Nekrasov. We find that charge 2 vortex solutions are characterized by two positions and a single nonnegative real number, which we demonstrate is the radius of the shell. We find that the radius is identically zero in all 2-dimensional solutions. If one considers solutions that depend on an additional commutative direction, then there are time-dependent solutions in which the radius oscillates, resembling a braneworld description of a cyclic universe. There are also smooth BIon-like space-dependent solutions in which the shell expands to infinity, describing a vortex ending on a domain wall.Comment: 21 pages, 3 eps figures. v2: published version, analytic solution adde

Elemental Diffusion Behaviour of Biomedical Grade Titanium Alloy through Thermal Oxidation

Major issues related to implant failure are wear debris and metal ions release where Titanium-Aluminium-Niobium alloys still face those problems despite of better biocompatibility. Surface modification is one of the alternatives in order to reduce those wear as well as ion release problems to the host tissue. In this study, experiments were carried out to investigate the element diffusion behaviour of Ti-6Al-7Nb alloy through thermal oxidation in order to obtain coating on the surfaces for diminishing those effects. Thermal oxidation was carried out at 650°C for three different durations 6, 12 and 24 hours. It is found that at prolong time, Niobium diffusion occurs where short duration Aluminium dominates. This suggests that longer heating time promotes heavy metal diffusion by restricting diffusion of light metal and hence, dominates the heavy metal oxide layer formation. The oxide layer formed on the substrate may lead to increase the lifespan of the implant and reduces the harmful effects caused by wear debris or toxic ion from metal alloys

Unoccupied Topological States on Bismuth Chalcogenides

The unoccupied part of the band structure of topological insulators Bi$_2$Te$_{x}$Se$_{3-x}$ ($x=0,2,3$) is studied by angle-resolved two-photon photoemission and density functional theory. For all surfaces linearly-dispersing surface states are found at the center of the surface Brillouin zone at energies around 1.3 eV above the Fermi level. Theoretical analysis shows that this feature appears in a spin-orbit-interaction induced and inverted local energy gap. This inversion is insensitive to variation of electronic and structural parameters in Bi$_2$Se$_3$ and Bi$_2$Te$_2$Se. In Bi$_2$Te$_3$ small structural variations can change the character of the local energy gap depending on which an unoccupied Dirac state does or does not exist. Circular dichroism measurements confirm the expected spin texture. From these findings we assign the observed state to an unoccupied topological surface state

Silver additions influence on biomedical porous Ti-Ni SMAs fabricated by microwave sintering

Ti-Ni and Ti-Ni-Ag shape memory alloys (SMAs) were prepared by microwave sintering. In Ti (49 -%Ag)-Ni51-Ag (atomic percentage), the silver was added with three percentages of (0.246, 0.5 and 1.51) at. %, respectively. The influence of Ag addition on the microstructure, phase composition, transformation temperatures and mechanical properties were investigated by scanning electron microscopy (SEM), X-ray diffraction (XRD), differential scanning calorimeter (DSC) and compression test. The microstructure shows needles and plates inside Ti-rich region. The R phase appears at the plane (-112) and the plane (300). This phase has appeared during cooling and heating of the baseline of DSC test. The compression strain at maximum strength was improved, while the compression strength was reduced. The highest compressive strain was for the sample with 0.246 at. % Ag. The elastic modulus decreases with the increasing of Ag content. The elastic modulus of these alloys was low that make it proper for biomedical applications such as natural human bone due to the sintering method and also improve by adding silver

Adhesion strength of HFCVD diamond coating on WC substrate seeded with diamond and different ratios of SiC powders

The effect of seeding using different mixtures of diamond and silicon carbide (SiC) powders on the adhesion strength of hot-filament chemical vapor deposition (HFCVD) diamond coating on WC-6% Co substrates was studied. Diamond powders with the average grain size of 0.5 µm mixed with various concentrations of SiC powder of 175µm average grain size were employed. Diamond layers were deposited using a production unit of HFCVD technique. The diamond film morphology and the diamond quality were examined using field emission scanning electron microscope (FESEM), X-ray diffraction (XRD) and Raman spectrometer respectively. It was found that the diamond morphologies produced and the qualities were almost the same for all the seeding mixtures of pretreatment. With the blasting technique employed to determine the adhesion strength it was found that the highest diamond film adhesion strength was achieved from the seeding of a mixture of diamond with 5g/l SiC powder

Should physical activity recommendations be ethnicity-specific? Evidence from a cross-sectional study of south Asian and European men

Background Expert bodies and health organisations recommend that adults undertake at least 150 min.week−1 of moderate-intensity physical activity (MPA). However, the underpinning data largely emanate from studies of populations of European descent. It is unclear whether this level of activity is appropriate for other ethnic groups, particularly South Asians, who have increased cardio-metabolic disease risk compared to Europeans. The aim of this study was to explore the level of MPA required in South Asians to confer a similar cardio-metabolic risk profile to that observed in Europeans undertaking the currently recommended MPA level of 150 min.week−1.<p></p> Methods Seventy-five South Asian and 83 European men, aged 40–70, without cardiovascular disease or diabetes had fasted blood taken, blood pressure measured, physical activity assessed objectively (using accelerometry), and anthropometric measures made. Factor analysis was used to summarise measured risk biomarkers into underlying latent ‘factors’ for glycaemia, insulin resistance, lipid metabolism, blood pressure, and overall cardio-metabolic risk. Age-adjusted regression models were used to determine the equivalent level of MPA (in bouts of ≥10 minutes) in South Asians needed to elicit the same value in each factor as Europeans undertaking 150 min.week−1 MPA.<p></p> Findings For all factors, except blood pressure, equivalent MPA values in South Asians were significantly higher than 150 min.week−1; the equivalent MPA value for the overall cardio-metabolic risk factor was 266 (95% CI 185-347) min.week−1.<p></p> Conclusions South Asian men may need to undertake greater levels of MPA than Europeans to exhibit a similar cardio-metabolic risk profile, suggesting that a conceptual case can be made for ethnicity-specific physical activity guidance. Further study is needed to extend these findings to women and to replicate them prospectively in a larger cohort.<p></p&gt