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

Heralded single-photon generation using imperfect single-photon sources and a two-photon-absorbing medium

We propose a setup for a heralded, i.e. announced generation of a pure single-photon state given two imperfect sources whose outputs are represented by mixtures of the single-photon Fock state $\ket{1}$ with the vacuum $\ket{0}$. Our purification scheme uses beam splitters, photodetection and a two-photon-absorbing medium. The admixture of the vacuum is fully eliminated. We discuss two potential realizations of the scheme.Comment: 22 pages, 8 figures (LaTeX). In version v2 we have slightly modified our setup so as to increase the success probability of single-photon generation by a factor of two. In addition, in an appendix we discuss alternative realizations of single-photon generation without a Mach-Zehnder interferometer. Three new figures have been added. Version v3 is a revised version published in Phys. Rev. A. It contains numerous minor corrections and clarifications. A new figure has been added in order to clarify our convention regarding labelling the field modes. The action of the beam splitters in the Schroedinger picture is introduced. A new reference has been include

Cluster spacecraft observations of a ULF wave enhanced by Space Plasma Exploration by Active Radar (SPEAR)

Space Plasma Exploration by Active Radar (SPEAR) is a high-latitude ionospheric heating facility capable of exciting ULF waves on local magnetic field lines. We examine an interval from 1 February 2006 when SPEAR was transmitting a 1 Hz modulation signal with a 10 min on-off cycle. Ground magnetometer data indicated that SPEAR modulated currents in the local ionosphere at 1 Hz, and enhanced a natural field line resonance with a 10 min period. During this interval the Cluster spacecraft passed over the heater site. Signatures of the SPEAR-enhanced field line resonance were present in the magnetic field data measured by the magnetometer on-board Cluster-2. These are the first joint ground- and space-based detections of field line tagging by SPEAR

Microstructural strain energy of α-uranium determined by calorimetry and neutron diffractometry

The microstructural contribution to the heat capacity of α-uranium was determined by measuring the heat-capacity difference between polycrystalline and single-crystal samples from 77 to 320 K. When cooled to 77 K and then heated to about 280 K, the uranium microstructure released (3±1) J/mol of strain energy. On further heating to 300 K, the microstructure absorbed energy as it began to redevelop microstrains. Anisotropic strain-broadening parameters were extracted from neutron-diffraction measurements on polycrystals. Combining the strain-broadening parameters with anisotropic elastic constants from the literature, the microstructural strain energy is predicted in the two limiting cases of statistically isotropic stress and statistically isotropic strain. The result calculated in the limit of statistically isotropic stress was (3.7±0.5) J/mol K at 77 K and (1±0.5) J/mol at room temperature. In the limit of statistically isotropic strain, the values were (7.8±0.5) J/mol K at 77 K and (4.5±0.5) J/mol at room temperature. In both cases the changes in the microstructural strain energy showed good agreement with the calorimetry

Genetic fuzzy system predicting contractile reactivity patterns of small arteries

Monitoring of physiological surrogate end points in drug development generates dynamic time-domain data reflecting the state of the biological system. Conventional data analysis often reduces the information in these data by extracting specific data points, thereby discarding potentially useful information. We developed a genetic fuzzy system (GFS) algorithm that is capable of learning all information in time-domain physiological data. Data on isometric force development of isolated small arteries were used as a framework for developing and optimizing a GFS. GFS performance was improved by several strategies. Results show that optimized fuzzy systems (OFSs) predict contractile reactivity of arteries accurately. In addition, OFSs identified significant differences that were undetectable using conventional analysis in the responses of arteries between groups. We concluded that OFSs may be used in clustering or classification tasks as aids in the objective identification or prediction of dynamic physiological behavior

Optical Polarization and Spectral Variability in the M87 Jet

During the last decade, M87's jet has been the site of an extraordinary variability event, with one knot (HST-1) increasing by over a factor 100 in brightness. Variability was also seen on timescales of months in the nuclear flux. Here we discuss the optical-UV polarization and spectral variability of these components, which show vastly different behavior. HST-1 shows a highly significant correlation between flux and polarization, with P increasing from $\sim 20$ at minimum to >40% at maximum, while the orientation of its electric vector stayed constant. HST-1's optical-UV spectrum is very hard ($\alpha_{UV-O}\sim0.5$, $F_\nu\propto\nu^{-\alpha}$), and displays "hard lags" during epochs 2004.9-2005.5, including the peak of the flare, with soft lags at later epochs. We interpret the behavior of HST-1 as enhanced particle acceleration in a shock, with cooling from both particle aging and the relaxation of the compression. We set 2$\sigma$ upper limits of $0.5 \delta$ parsecs and 1.02$c$ on the size and advance speed of the flaring region. The slight deviation of the electric vector orientation from the jet PA, makes it likely that on smaller scales the flaring region has either a double or twisted structure. By contrast, the nucleus displays much more rapid variability, with a highly variable electric vector orientation and 'looping' in the $(I,P)$ plane. The nucleus has a much steeper spectrum ($\alpha_{UV-O} \sim 1.5$) but does not show UV-optical spectral variability. Its behavior can be interpreted as either a helical distortion to a steady jet or a shock propagating through a helical jet.Comment: 14 pages, 7 figures, ApJ, in pres

Upper bounds on success probabilities in linear optics

We develop an abstract way of defining linear-optics networks designed to perform quantum information tasks such as quantum gates. We will be mainly concerned with the nonlinear sign shift gate, but it will become obvious that all other gates can be treated in a similar manner. The abstract scheme is extremely well suited for analytical as well as numerical investigations since it reduces the number of parameters for a general setting. With that we show numerically and partially analytically for a wide class of states that the success probability of generating a nonlinear sign shift gate does not exceed 1/4 which to our knowledge is the strongest bound to date.Comment: 8 pages, typeset using RevTex4, 5 EPS figure

Entanglement purification of multi-mode quantum states

An iterative random procedure is considered allowing an entanglement purification of a class of multi-mode quantum states. In certain cases, a complete purification may be achieved using only a single signal state preparation. A physical implementation based on beam splitter arrays and non-linear elements is suggested. The influence of loss is analyzed in the example of a purification of entangled N-mode coherent states.Comment: 6 pages, 3 eps-figures, using revtex