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

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

Dark-bellied Brent Geese Branta bernicla bernicla, as recorded by satellite telemetry, do not minimize flight distance during spring migration

Nine Dark-bellied Brent Geese Branta bernicla bernicla were equipped with satellite transmitters during spring staging in the Dutch Wadden Sea in 1998 and 1999. The transmitters (in all cases less than 3% of body mass) were attached to the back by a flexible elastic harness. One juvenile female was tracked to the Yamal peninsula in 1998. Eight adult males were selected from a single catch of 75 to span the range of body mass observed on the date of capture (11 May 1999) and all but the lightest individual completed the first lap of the migratory flight to the White Sea, Russia, according to the time schedule normal for this species. Six birds were successfully tracked to Taymyr for a total distance averaging 5004 km (range 4577-5164) but judging from later movements none bred (although 1999 was breeding year). Although the routes chosen during spring migration were closely similar; none of the tagged birds migrated together. On average the geese used 16 flights to reach their summer destinations on Taymyr. The longest uninterrupted flights during the first half of the journey (Wadden Sea to Kanin) covered 1056 km (mean of seven adult males, range 768-1331), while the corresponding value for the second half of the migration (Kanin-Taymyr) was only 555 km (mean of six adult males). Only 7% of total time during spring migration was spent in active flight, as contrasted to c. 80% at long-term stopovers. Overall average travelling speed was 118 km/day (range 97-148). Including fattening prior to departure the rate of travel falls to 62 km/day (range 49-70), in keeping with theoretical predictions. Routes followed deviated from the great circle route, adding at least 700 km (16%) to the journey from Wadden Sea to Taymyr, and we conclude that the coastal route is chosen to facilitate feeding, drinking and resting en route instead of minimizing total flight distance

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.

Er3+Ylif4 Continuous Wave Cascade Laser Operation At 1620 And 2810 Nm At Room-Temperature

For the first time cw, cascade lasing was demonstrated in 1% Er doped yttrium lithium fluoride (YLF) at room temperature at both 1620 and 2810 nm. In addition, cw lasing in Er[1%]:YLF at 1640 nm and in Er[5%]:YLF at 2810 nm at room temperature is reported for the first time in material of such low concentration

What are the current challenges of managing cancer pain and could digital technologies help?

OBJECTIVES: Pain remains a problem for people with cancer despite effective treatments being available. We aimed to explore current pain management strategies used by patients, caregivers and professionals and to investigate opportunities for digital technologies to enhance cancer pain management. METHODS: A qualitative study comprising semistructured interviews and focus groups. Patients with cancer pain, their caregivers and health professionals from Northeast Scotland were recruited from a purposive sample of general practices. Professionals were recruited from regional networks. RESULTS: Fifty one participants took part in 33 interviews (eight patients alone, six patient/caregiver dyads and 19 professionals) and two focus groups (12 professionals). Living with cancer was hard work for patients and caregivers and comparable to a 'full-time job'. Patients had personal goals which involved controlling pain intensity and balancing this with analgesic use, side effects, overall symptom burden and social/physical activities.Digital technologies were embraced by most patients, and made living life with advanced cancer easier and richer (eg, video calls with family). Technology was underutilised for pain and symptom management. There were suggestions that technology could support self-monitoring and communicating problems to professionals, but patients and professionals were concerned about technological monitoring adding to the work of managing illness. CONCLUSIONS: Cancer pain management takes place in the context of multiple, sometimes competing personal goals. It is possible that technology could be used to help patients share individual symptom experiences and goals, thus enhancing tailored care. The challenge is for digital solutions to add value without adding undue burden

Role of thyroid hormones in early postnatal development of skeletal muscle and its implications for undernutrition

Published online by Cambridge University Press 09 Mar 2007Energy intake profoundly influences many endocrine axes which in turn play a central role in development. The specific influence of a short period of mild hypothyroidism, similar to that induced by undernutrition, in regulating muscle development has been assessed in a large mammal during early postnatal life. Hypothyroidism was induced by providing methimazole and iopanoic acid in the feed of piglets between 4 and 14 d of age, and controls were pair-fed to the energy intake of their hypothyroid littermates. Thyroid status was evaluated, and myofibre differentiation and cation pump concentrations were then assessed in the following functionally distinct muscles: longissimus dorsi (l. dorsi), soleus and rhomboideus. Reductions in plasma concentrations of thyroxine (T4; 32%, P < O·Ol), triiodothyronine (T3;48%, P < 0·001), free T3, (58%, P < 0·001)and hepatic 5'-monodeiodinase (EC 1.11.1.8) activity (74%, P < 0·001) occurred with treatment. Small, although significant, increases in the proportion of type I slow-twitch oxidative fibres occurred with mild hypothyroidism, in l. dorsi (2%, P < 0·01) and soleus(7%, P < 0·01). Nuclear T3-receptor concentration in l. dorsi of hypothyroid animals compared with controls increased by 46% (P < 0·001), a response that may represent a homeostatic mechanism making muscle more sensitive to low levels of circulating thyroid hormones. Nevertheless, Na+, K+-ATPase (EC 3.6.1.37) concentration was reduced by 15–16% in all muscles (l.dorsi P< 0·05,soleus P < 0·001, rhomboideus P < 0·05), and Ca2+-ATPase (EC 3.6.1.38) concentration was significantly reduced in the two slow-twitch muscles: by 22% in rhomboideus (P < 0·001) and 23% in soleus (P < 0·05). It is concluded that during early postnatal development of large mammals a period of mild hypothyroidism, comparable with that found during undernutrition, induces changes in myofibre differentiation and a down-regulation of cation pumps in skeletal muscle. Such changes would result in slowness of movement and muscle weakness, and also reduce ATP hydrolysis with a concomitant improvement in energetic efficiency.A. P. Harrison, D. R. Tivey, T. Clausen, C. Duchamp and M. J. Daunce