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

The bend stiffness of S-DNA

We formulate and solve a two-state model for the elasticity of nicked, double-stranded DNA that borrows features from both the Worm Like Chain and the Bragg--Zimm model. Our model is computationally simple, and gives an excellent fit to recent experimental data through the entire overstretching transition. The fit gives the first value for the bending stiffness of the overstretched state as about 10 nm*kbt, a value quite different from either B-form or single-stranded DNA.Comment: 7 pages, 1 figur

Quantum state conversion by cross-Kerr interaction

A generalized Mach-Zehnder-type interferometer equipped with cross-Kerr elements is proposed to convert N-photon truncated single-mode quantum states into (N+1)-mode single-photon states, which are suitable for further state manipulation by means of beam splitter arrays and ON/OFF-detections, and vice versa. Applications to the realization of unitary and non-unitary transformations, quantum state reconstruction, and quantum telemanipulation are studied.Comment: 22 pages, 4 figures, using a4.st

Conditional quantum-state transformation at a beam splitter

Using conditional measurement on a beam splitter, we study the transformation of the quantum state of the signal mode within the concept of two-port non-unitary transformation. Allowing for arbitrary quantum states of both the input reference mode and the output reference mode on which the measurement is performed, we show that the non-unitary transformation operator can be given as an $s$-ordered operator product, where the value of $s$ is entirely determined by the absolute value of the beam splitter reflectance (or transmittance). The formalism generalizes previously obtained results that can be recovered by simple specification of the non-unitary transformation operator. As an application, we consider the generation of Schr\"odinger-cat-like states. An extension to mixed states and imperfect detection is outlined.Comment: 7 Postscript figures, using Late

Detector imperfections in photon-pair source characterization

We analyze how imperfections in single-photon detectors impact the characterization of photon-pair sources. We perform exact calculations to reveal the effects of multi-pair emissions and of noisy, non-unit efficiency, non photon-number resolving detections on the Cauchy-Schwarz parameter, on the second order auto-correlation and cross-correlation functions, and on the visibilities of both Hong-Ou-Mandel and Bell-like interferences. We consider sources producing either two-mode squeezed states or states with a Poissonian photon distribution. The proposed formulas are useful in practice to determine the impacts of multi-pair emissions and dark counts in standard tests used in quantum optics.Comment: 9 pages, 11 figure

Changes in intracellular ion activities induced by adrenaline in human and rat skeletal muscle

To study the stimulating effect of adrenaline (ADR) on active Na+/K+ transport we used double-barrelled ion-sensitive micro-electrodes to measure the activities of extracellular K+ (aKe) and intracellular Na+ (aNai) in isolated preparations of rat soleus muscle, normal human intercostal muscle and one case of hyperkalemic periodic paralysis (h.p.p.). In these preparations bath-application of ADR (10−6 M) resulted in a membrane hyperpolarization and transient decreasesaKe andaNai which could be blocked by ouabain (3×10−4 M). In the h.p.p. muslce a continuous rise ofaNai induced by elevation ofaKe to 5.2 mM could be stopped by ADR. In addition, the intracellular K+ activity (aKi), the free intracellular Ca2+ concentration (pCai) and intracellular pH (pHi) were monitored in rat soleus muscle. During ADRaKi increased, pHi remained constant and intracellular Ca2+ apparently decreased. In conclusion, our data show that ADR primarily stimulates the Na+/K+ pump in mammalian skeletal muscle. This stimulating action is not impaired in the h.p.p. muscle

Production of superpositions of coherent states in traveling optical fields with inefficient photon detection

We develop an all-optical scheme to generate superpositions of macroscopically distinguishable coherent states in traveling optical fields. It non-deterministically distills coherent state superpositions (CSSs) with large amplitudes out of CSSs with small amplitudes using inefficient photon detection. The small CSSs required to produce CSSs with larger amplitudes are extremely well approximated by squeezed single photons. We discuss some remarkable features of this scheme: it effectively purifies mixed initial states emitted from inefficient single photon sources and boosts negativity of Wigner functions of quantum states.Comment: 13 pages, 9 figures, to be published in Phys. Rev.