1,721,159 research outputs found
Automatic extension of Gene Ontology with flexible identification of candidate terms
No full textThis is a pre-copy-editing, author-produced PDF of an article accepted for publication in Bioinformatics following peer review. The definitive publisher-authenticated version is available online at: http://bioinformatics.oxfordjournals.org/cgi/reprint/22/6/665Motivation: Gene Ontology (GO) has been manually developed to provide a controlled vocabulary for gene product attributes. It continues to evolve with new concepts that are compiled mostly from existing concepts in a compositional way. If we consider the relatively slow growth rate of GO in the face of the fast accumulation of the biological data, it is much desirable to provide an automatic means for predicting new concepts from the existing ones. Results: We present a novel method that predicts more detailed concepts by utilizing syntactic relations among the existing concepts. We propose a validation measure for the automatically predicted concepts by matching the concepts to biomedical articles. We also suggest how to find a suitable direction for the extension of a constantly growing ontology such as GO.This work was supported by MOST/KOSEF through AITrc
Effects of synchronous vibration of bearing on stability of externally pressurized air journal bearings
No full textAn active control of bearing is proposed as a new method to improve the stability characteristics of the externally pressurized nir journal bearing and the results of numerical investigations of the stability characteristics of the actively controlled air journal bearing are presented. The synchronous control, where the bearing center whirls with the same frequency as the journal center with respect to the position in the steady state, is proposed as a control algorithm of the active air bearing. The step jump method is used to calculate the locus of the journal center which whirls or vibrates relative to the whirling bearing. The stability characteristics of the high speed rotor supported by actively controlled bearing system for zero steady-state eccentricity are investigated for various phase difference between the bearing and journal. It is shown that the stability of the air bearing can be greatly increased by the controlled synchronous motion of the bearing, and there is an optimum phase difference, which gives the maximum stability limit of the system
Role of electrostatics in the texture of islands in free-standing ferroelectric liquid crystal films
No full textCurved textures of ferroelectric smectic-C-* liquid crystals produce space charge when they involve divergence of the spontaneous polarization field. Impurity ions can partially screen this space charge, reducing long-range interactions to local ones. Through studies of the textures of islands on very thin free-standing smectic films, we see evidence of this effect, in which materials with a large spontaneous polarization have static structures described by a large effective bend elastic constant. To address this issue, we calculated the electrostatic free energy of a free-standing film of ferroelectric liquid crystal, showing how the screened Coulomb interaction contributes a term to the effective bend elastic constant, in the static long-wavelength limit. We report experiments which support the main features of this model.open1127sciescopu
DYNAMICS OF THE MOLECULAR ORIENTATION FIELD COUPLED TO IONS IN TWO-DIMENSIONAL FERROELECTRIC LIQUID CRYSTALS
No full textMolecular orientation fluctuations in ferroelectric smectic liquid crystals produce space charges, due to the divergence of the spontaneous polarization. These space charges interact with mobile ions, so that one must consider the coupled dynamics of the orientation and ionic degrees of freedom. Previous theory and light scattering experiments on thin free-standing films of ferroelectric liquid crystals have not included this coupling, possibly invalidating their quantitative conclusions. We consider the most important case of very slow ionic dynamics, compared to rapid orientational fluctuations, and focus on the use of a short electric field pulse to quench orientational fluctuations. We find that the resulting change in scattered light intensity must include a term due to the quasistatic ionic configuration, which has previously been ignored. In addition to developing the general theory, we present a simple model to demonstrate the role of this added term.open113sciescopu
TEXTURAL TRANSFORMATIONS IN ISLANDS ON FREE STANDING SMECTIC-C-* LIQUID CRYSTAL FILMS
No full textWe report on and analyze the textural transformations in islands, thicker circular domains, floating in very thin free standing chiral Smectic-C-* liquid crystal films. As an island is growing, an initial pure bend texture of the c director changes into a reversing spiral at a critical size. Another distinct spiral texture is induced by changing the boundary condition at the central point defect in the island. To understand these transformations from a pure bend island, a linear stability analysis of the c-director free energy is developed, which predicts a state diagram for the island. Our observations are consistent with the theoretical phase diagram.open1115sciescopu
Loading Dynamics of a sliding DNA clamp
Full text linkSliding DNA clamps are loaded at a ss/dsDNA junction by a clamp loader that depends on ATP binding for clamp opening. Sequential ATP hydrolysis results in closure of the clamp so that it completely encircles and diffuses on dsDNA. We followed events during loading of an E. coli beta clamp in real time by using single-molecule FRET (smFRET). Three successive FRET states were retained for 0.3 s, 0.7 s, and 9 min: Hydrolysis of the first ATP molecule by the g clamp loader resulted in closure of the clamp in 0.3 s, and after 0.7 s in the closed conformation, the clamp was released to diffuse on the dsDNA for at least 9 min. An additional single-molecule polarization study revealed that the interfacial domain of the clamp rotated in plane by approximately 88 during clamp closure. The single-molecule polarization and FRET studies thus revealed the real-time dynamics of the ATP-hydrolysis-dependent 3D conformational change of the b clamp during loading at a ss/dsDNA junction.X1156Ysciescopu
Equilibrium size and textures of islands in free standing Smectic C* films.
No full textIn free standing films of one smectic C* material, Chisso 1015, we observe circular islands, of greater thickness than the background film. These islands, nucleated by smoke particles, grow to an equilibrium diameter that is a function of their thickness. We present data on island size, and a theory attributing the finite equilibrium size to a negative island edge energy arising from a spontaneous bend term in the elastic free energy for the islands. We also observe textural transformations within the islands, attributed to a difference between splay and bend elastic constants, combined with weak anchoring of the director at a point disclination at the center of an island.X1115sciescopu
Effect of the external twist on molecular orientation in antiferroelectric liquid crystals.
No full textWe report on microscopic observations of molecular orientation and layer structure induced by an external twist in antiferroelectric liquid crystals (AFLCs). In a twisted geometry, the smectic layers are formed perpendicular to the surface normal of the cell such that the molecular director experiences twist by twice of intrinsic molecular tilt on going from one surface to the other. It is found that this external twist significantly influences the uniformity of molecular alignment and the characteristics of the double hysteresis inherent to the antiferroelectric order. The resultant electro-optic effect is described within the framework of the field-induced antiferroelectric-ferroelectric phase transition.X111sciescopu
Cascading MutS and MutL sliding clamps control DNA diffusion to activate mismatch repair
No full textMismatched nucleotides arise from polymerase misincorporation errors, recombination between heteroallelic parents and chemical or physical DNA damage(1). Highly conserved MutS (MSH) and MutL (MLH/PMS) homologues initiate mismatch repair and, in higher eukaryotes, act as DNA damage sensors that can trigger apoptosis(2). Defects in human mismatch repair genes cause Lynch syndrome or hereditary non-polyposis colorectal cancer and 10-40% of related sporadic tumours(3). However, the collaborative mechanics of MSH and MLH/PMS proteins have not been resolved in any organism. We visualized Escherichia coli (Ec) ensemble mismatch repair and confirmed that EcMutS mismatch recognition results in the formation of stable ATP-bound sliding clamps that randomly diffuse along the DNA with intermittent backbone contact. The EcMutS sliding clamps act as a platform to recruit EcMutL onto the mismatched DNA, forming an EcMutS-EcMutL search complex that then closely follows the DNA backbone. ATP binding by EcMutL establishes a second long-lived DNA clamp that oscillates between the principal EcMutS-EcMutL search complex and unrestricted EcMutS and EcMutL sliding clamps. The EcMutH endonuclease that targets mismatch repair excision only binds clamped EcMutL, increasing its DNA association kinetics by more than 1,000-fold. The assembly of an EcMutS-EcMutL-EcMutH search complex illustrates how sequential stable sliding clamps can modulate one-dimensional diffusion mechanics along the DNA to direct mismatch repair.11176sciescopu
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