VeRNAl: Mining RNA Structures for Fuzzy Base Pairing Network Motifs

RNA 3D motifs are recurrent substructures, modelled as networks of base pair interactions, which are crucial for understanding structure-function relationships. The task of automatically identifying such motifs is computationally hard, and remains a key challenge in the field of RNA structural biology and network analysis. State of the art methods solve special cases of the motif problem by constraining the structural variability in occurrences of a motif, and narrowing the substructure search space. Here, we relax these constraints by posing the motif finding problem as a graph representation learning and clustering task. This framing takes advantage of the continuous nature of graph representations to model the flexibility and variability of RNA motifs in an efficient manner. We propose a set of node similarity functions, clustering methods, and motif construction algorithms to recover flexible RNA motifs. Our tool, VeRNAl can be easily customized by users to desired levels of motif flexibility, abundance and size. We show that VeRNAl is able to retrieve and expand known classes of motifs, as well as to propose novel motifs

Traitement de données à retour d'onde complète : modélisation du signal brut

International audienceUnlike airborne multi-echo laser scanner systems, full-waveform systems are able to digitize and record the entire backscattered signal of each laser pulse. It has been demonstrated that decomposing the return waveforms into a mixture of Gaussian components was suitable. In this paper, we focus on the improvement of peak detection and of raw signal modelling. Refined peak detection greatly increased the number of detected targets as well as their positional accuracy. Models more complex than the Gaussian model, such as the Lognormal or generalized Gaussian functions, were introduced and their contribution to waveform processing was studied. In this way, fitting of asymmetric, peaked or flattened echoes located both in urban and forested areas could be improved. Moreover, introduction of new echo parameters allowed the extraction of additional information on the target shape. This should make easier the decorrelation of geometric and radiometric influences on the signal and, as a consequence, the improvement of point cloud classification algorithms

The Role of Robo3 in the Development of Cortical Interneurons

A number of studies in recent years have shown that members of the Roundabout (Robo) receptor family, Robo1 and Robo2, play significant roles in the formation of axonal tracks in the developing forebrain and in the migration and morphological differentiation of cortical interneurons. Here, we investigated the expression and function of Robo3 in the developing cortex. We found that this receptor is strongly expressed in the preplate layer and cortical hem of the early cortex where it colocalizes with markers of Cajal–Retzius cells and interneurons. Analysis of Robo3 mutant mice at early (embryonic day [E] 13.5) and late (E18.5) stages of corticogenesis revealed no significant change in the number of interneurons, but a change in their morphology at E13.5. However, preliminary analysis on a small number of mice that lacked all 3 Robo receptors indicated a marked reduction in the number of cortical interneurons, but only a limited effect on their morphology. These observations and the results of other recent studies suggest a complex interplay between the 3 Robo receptors in regulating the number, migration and morphological differentiation of cortical interneurons

HelioSwarm: A Multipoint, Multiscale Mission to Characterize Turbulence

HelioSwarm (HS) is a NASA Medium-Class Explorer mission of the Heliophysics Division designed to explore the dynamic three-dimensional mechanisms controlling the physics of plasma turbulence, a ubiquitous process occurring in the heliosphere and in plasmas throughout the universe. This will be accomplished by making simultaneous measurements at nine spacecraft with separations spanning magnetohydrodynamic and sub-ion spatial scales in a variety of near-Earth plasmas. In this paper, we describe the scientific background for the HS investigation, the mission goals and objectives, the observatory reference trajectory and instrumentation implementation before the start of Phase B. Through multipoint, multiscale measurements, HS promises to reveal how energy is transferred across scales and boundaries in plasmas throughout the universe

Introgressive Hybridization of Schistosoma haematobium Group Species in Senegal: Species Barrier Break Down between Ruminant and Human Schistosomes

The file attached is the Published/publisher’s pdf version of the article.Copyright: © 2013 Webster et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Dopamine acting at D1-like, D2-like and α1-adrenergic receptors differentially modulates theta and gamma oscillatory activity in primary motor cortex

The loss of dopamine (DA) in Parkinson’s is accompanied by the emergence of exaggerated theta and beta frequency neuronal oscillatory activity in the primary motor cortex (M1) and basal ganglia. DA replacement therapy or deep brain stimulation reduces the power of these oscillations and this is coincident with an improvement in motor performance implying a causal relationship. Here we provide in vitro evidence for the differential modulation of theta and gamma activity in M1 by DA acting at receptors exhibiting conventional and non-conventional DA pharmacology. Recording local field potentials in deep layer V of rat M1, co-application of carbachol (CCh, 5 μM) and kainic acid (KA, 150 nM) elicited simultaneous oscillations at a frequency of 6.49 ± 0.18 Hz (theta, n = 84) and 34.97 ± 0.39 Hz (gamma, n = 84). Bath application of DA resulted in a decrease in gamma power with no change in theta power. However, application of either the D1-like receptor agonist SKF38393 or the D2-like agonist quinpirole increased the power of both theta and gamma suggesting that the DA-mediated inhibition of oscillatory power is by action at other sites other than classical DA receptors. Application of amphetamine, which promotes endogenous amine neurotransmitter release, or the adrenergic α1-selective agonist phenylephrine mimicked the action of DA and reduced gamma power, a result unaffected by prior co-application of D1 and D2 receptor antagonists SCH23390 and sulpiride. Finally, application of the α1-adrenergic receptor antagonist prazosin blocked the action of DA on gamma power suggestive of interaction between α1 and DA receptors. These results show that DA mediates complex actions acting at dopamine D1-like and D2-like receptors, α1 adrenergic receptors and possibly DA/α1 heteromultimeric receptors to differentially modulate theta and gamma activity in M1

Quantum bits with Josephson junctions

Already in the first edition of this book (Barone and Paterno, "Fundamentals and Physics and Applications of the Josephson Effect", Wiley 1982), a great number of interesting and important applications for Josephson junctions were discussed. In the decades that have passed since then, several new applications have emerged. This chapter treats one such new class of applications: quantum optics and quantum information processing (QIP) based on superconducting circuits with Josephson junctions. In this chapter, we aim to explain the basics of superconducting quantum circuits with Josephson junctions and demonstrate how these systems open up new prospects, both for QIP and for the study of quantum optics and atomic physics.Comment: 30 pages, 10 figures. Book chapter for a new edition of Barone and Paterno's "Fundamentals and Physics and Applications of the Josephson Effect". Final versio

The eck fistula in animals and humans

In all species so far studied, including man, portacaval shunt causes the same changes in liver morphology, including hepatocyte atrophy, fatty infiltration, deglycogenation, depletion and disorganization of the rough endoplasmic reticulum (RER) and its lining polyribosomes and variable but less specific damage to other organelles. Many, perhaps all, biosynthetic processes are quickly depressed, largely secondary to the selective damage to the RER, which is the "factory" of the cell. These structural and metabolic changes in the liver after portal diversion are caused by the diversion around the liver of the hepatotrophic substances in portal venous blood, of which endogenous insulin is the most important. In experimental animals, the injury of Eck's fistula can be prevented by infusing insulin into the tied-off hilar portal vein. The subtle but far-reaching changes in hepatic function after portal diversion have made it possible to use this procedure in palliating three inborn errors of metabolism: glycogen storage disease, familial hypercholesterolemia, and α1-antitrypsin deficiency In these three diseases, the abnormalities caused by portal diversion have counteracted abnormalities in the patients that were caused by the inborn errors. In these diseases, amelioration of the inborn errors depends on the completeness of the portal diversion. In contrast, total portal diversion to treat complications of portal hypertension is undesirable and always will degrade hepatic function if a significant amount of hepatopetal portal venous blood is taken from the liver. When total portal diversion is achieved (and this is to be expected after all conventional shunts), the incidence of hepatic failure and hepatic encephalopathy is increased. If portal diversion must be done for the control of variceal hemorrhage, a selective procedure such as the Warren procedure is theoretically superior to the completely diverting shunt. In practice, better patient survival has not been achieved after selective shunts than after conventional shunts, but the incidence of hepatic encephalopathy has been less. © 1983 Year Book Medical Publishers, Inc

Erratum to: Methods for evaluating medical tests and biomarkers

[This corrects the article DOI: 10.1186/s41512-016-0001-y.]