Improved ontology for eukaryotic single-exon coding sequences in biological databases

Indexación: Scopus.Efficient extraction of knowledge from biological data requires the development of structured vocabularies to unambiguously define biological terms. This paper proposes descriptions and definitions to disambiguate the term 'single-exon gene'. Eukaryotic Single-Exon Genes (SEGs) have been defined as genes that do not have introns in their protein coding sequences. They have been studied not only to determine their origin and evolution but also because their expression has been linked to several types of human cancer and neurological/developmental disorders and many exhibit tissue-specific transcription. Unfortunately, the term 'SEGs' is rife with ambiguity, leading to biological misinterpretations. In the classic definition, no distinction is made between SEGs that harbor introns in their untranslated regions (UTRs) versus those without. This distinction is important to make because the presence of introns in UTRs affects transcriptional regulation and post-transcriptional processing of the mRNA. In addition, recent whole-transcriptome shotgun sequencing has led to the discovery of many examples of single-exon mRNAs that arise from alternative splicing of multi-exon genes, these single-exon isoforms are being confused with SEGs despite their clearly different origin. The increasing expansion of RNA-seq datasets makes it imperative to distinguish the different SEG types before annotation errors become indelibly propagated in biological databases. This paper develops a structured vocabulary for their disambiguation, allowing a major reassessment of their evolutionary trajectories, regulation, RNA processing and transport, and provides the opportunity to improve the detection of gene associations with disorders including cancers, neurological and developmental diseases. © The Author(s) 2018. Published by Oxford University Press.https://academic.oup.com/database/article/doi/10.1093/database/bay089/509943

Glass transitions and shear thickening suspension rheology

We introduce a class of simple models for shear thickening and/ or `jamming' in colloidal suspensions. These are based on schematic mode coupling theory (MCT) of the glass transition, having a memory term that depends on a density variable, and on both the shear stress and the shear rate. (Tensorial aspects of the rheology, such as normal stresses, are ignored for simplicity.) We calculate steady-state flow curves and correlation functions. Depending on model parameters, we find a range of rheological behaviours, including `S-shaped' flow curves, indicating discontinuous shear thickening, and stress-induced transitions from a fluid to a nonergodic (jammed) state, showing zero flow rate in an interval of applied stress. The shear thickening and jamming scenarios that we explore appear broadly consistent with experiments on dense colloids close to the glass transition, despite the fact that we ignore hydrodynamic interactions. In particular, the jamming transition we propose is conceptually quite different from various hydrodynamic mechanisms of shear thickening in the literature, although the latter might remain pertinent at lower colloid densities. Our jammed state is a stress-induced glass, but its nonergodicity transitions have an analytical structure distinct from that of the conventional MCT glass transition.Comment: 33 pages; 19 figure

An experimental and theoretical investigation of deposition patterns from an agricultural airplane

A flight test program has been conducted with a representative agricultural airplane to provide data for validating a computer program model which predicts aerially applied particle deposition. Test procedures and the data from this test are presented and discussed. The computer program features are summarized, and comparisons of predicted and measured particle deposition are presented. Applications of the computer program for spray pattern improvement are illustrated

Natural laminar flow experiments on modern airplane surfaces

Flight and wind-tunnel natural laminar flow experiments have been conducted on various lifting and nonlifting surfaces of several airplanes at unit Reynolds numbers between 0.63 x 10 to the 6th power/ft and 3.08 x 10 to the 6th power/ft, at Mach numbers from 0.1 to 0.7, and at lifting surface leading-edge sweep angles from 0 deg to 63 deg. The airplanes tested were selected to provide relatively stiff skin conditions, free from significant roughness and waviness, on smooth modern production-type airframes. The observed transition locations typically occurred downstream of the measured or calculated pressure peak locations for the test conditions involved. No discernible effects on transition due to surface waviness were observed on any of the surfaces tested. None of the measured heights of surface waviness exceeded the empirically predicted allowable surface waviness. Experimental results consistent with spanwise contamination criteria were observed. Large changes in flight-measured performance and stability and control resulted from loss of laminar flow by forced transition. Rain effects on the laminar boundary layer caused stick-fixed nose-down pitch-trim changes in two of the airplanes tested. No effect on transition was observed for flight through low-altitude liquid-phase clouds. These observations indicate the importance of fixed-transition tests as a standard flight testing procedure for modern smooth airframes

Ultra-wide detuning planar Bragg grating fabrication technique based on direct UV grating writing with electro-optic phase modulation

A direct UV grating writing technique based on phase-controlled interferometry is proposed and demonstrated in a silica-on-silicon platform, with a wider wavelength detuning range than any previously reported UV writing technology. Electro-optic phase modulation of one beam in the interferometer is used to manipulate the fringe pattern and thus control the parameters of the Bragg gratings and waveguides. Various grating structures with refractive index apodization, phase shifts and index contrasts of up to 0.8×10-3 have been demonstrated. The method offers significant time/energy efficiency as well as simplified optical layout and fabrication process. We have shown Bragg gratings can be made from 1200 nm to 1900 nm exclusively under software control and the maximum peak grating reflectivity only decreases by 3dB over a 250 nm (~32THz) bandwidth

The multisensory attentional consequences of tool use : a functional magnetic resonance imaging study

Background: Tool use in humans requires that multisensory information is integrated across different locations, from objects seen to be distant from the hand, but felt indirectly at the hand via the tool. We tested the hypothesis that using a simple tool to perceive vibrotactile stimuli results in the enhanced processing of visual stimuli presented at the distal, functional part of the tool. Such a finding would be consistent with a shift of spatial attention to the location where the tool is used. Methodology/Principal Findings: We tested this hypothesis by scanning healthy human participants’ brains using functional magnetic resonance imaging, while they used a simple tool to discriminate between target vibrations, accompanied by congruent or incongruent visual distractors, on the same or opposite side to the tool. The attentional hypothesis was supported: BOLD response in occipital cortex, particularly in the right hemisphere lingual gyrus, varied significantly as a function of tool position, increasing contralaterally, and decreasing ipsilaterally to the tool. Furthermore, these modulations occurred despite the fact that participants were repeatedly instructed to ignore the visual stimuli, to respond only to the vibrotactile stimuli, and to maintain visual fixation centrally. In addition, the magnitude of multisensory (visual-vibrotactile) interactions in participants’ behavioural responses significantly predicted the BOLD response in occipital cortical areas that were also modulated as a function of both visual stimulus position and tool position. Conclusions/Significance: These results show that using a simple tool to locate and to perceive vibrotactile stimuli is accompanied by a shift of spatial attention to the location where the functional part of the tool is used, resulting in enhanced processing of visual stimuli at that location, and decreased processing at other locations. This was most clearly observed in the right hemisphere lingual gyrus. Such modulations of visual processing may reflect the functional importance of visuospatial information during human tool use

Unstable recurrent patterns in Kuramoto-Sivashinsky dynamics

We undertake a systematic exploration of recurrent patterns in a 1-dimensional Kuramoto-Sivashinsky system. For a small, but already rather turbulent system, the long-time dynamics takes place on a low-dimensional invariant manifold. A set of equilibria offers a coarse geometrical partition of this manifold. A variational method enables us to determine numerically a large number of unstable spatiotemporally periodic solutions. The attracting set appears surprisingly thin - its backbone are several Smale horseshoe repellers, well approximated by intrinsic local 1-dimensional return maps, each with an approximate symbolic dynamics. The dynamics appears decomposable into chaotic dynamics within such local repellers, interspersed by rapid jumps between them.Comment: 11 pages, 11 figure