D2P2: database of disordered protein predictions

We present the Database of Disordered Protein Prediction (D2P2), available at http://d2p2.pro (including website source code). A battery of disorder predictors and their variants, VL-XT, VSL2b, PrDOS, PV2, Espritz and IUPred, were run on all protein sequences from 1765 complete proteomes (to be updated as more genomes are completed). Integrated with these results are all of the predicted (mostly structured) SCOP domains using the SUPERFAMILY predictor. These disorder/structure annotations together enable comparison of the disorder predictors with each other and examination of the overlap between disordered predictions and SCOP domains on a large scale. D2P2 will increase our understanding of the interplay between disorder and structure, the genomic distribution of disorder, and its evolutionary history. The parsed data are made available in a unified format for download as flat files or SQL tables either by genome, by predictor, or for the complete set. An interactive website provides a graphical view of each protein annotated with the SCOP domains and disordered regions from all predictors overlaid (or shown as a consensus). There are statistics and tools for browsing and comparing genomes and their disorder within the context of their position on the tree of life. © The Author(s) 2012. Published by Oxford University Press

Free vibrations of simply-supported beam bridges under moving loads: Maximum resonance, cancellation and resonant vertical acceleration

The advent of high-speed railways has raised many concerns regarding the behaviour of bridges. Particularly, the analysis of the free vibrations generated by each load is of great interest because they can possibly accumulate and create resonance phenomena. Regarding simply supported beams, earlier contributions showed that the free vibrations created by a single moving force are of maximum or zero amplitude (cancellation) for certain speeds. In the present paper new closed-form expressions are given for the cancellation speeds of a generic mode, as well as for the most representative points of maximum amplitude. Similar new results are provided for elastically supported beams as well. A simpler, closed-form approximate expression of the cancellation condition for an elastically supported beam is also derived from the analysis of a single passing load; this approximate formula is in good agreement with the exact results. Knowing a priori the speeds of maximum free vibrations or cancellation is of great interest for experimental tests on bridges, particularly as regards the evaluation of amplitude-dependent magnitudes such as structural damping. Regarding the resonance phenomena, if the resonance speeds coincide with either a maximum free vibration or a cancellation speed, then a maximum resonance or a cancellation of resonance will occur. The most relevant cases thereof have been investigated, and new expressions which allow predicting them for a generic mode are given. Finally, a new approximate formula is proposed for estimating the maximum acceleration of simply supported bridges caused by resonances of the fundamental mode. After extensive numerical testing, the formula has proved to be a useful tool for a first assessment of simply supported bridges according to building codes such as Eurocodes. (C) 2012 Elsevier Ltd. All rights reserved.The authors acknowledge the financial support of the State Secretariat for Research of the Spanish Ministry of Science and Innovation (Secretaria de Estado de Investigacion, Ministerio de Ciencia e Innovacion, MICINN) in the framework of the Research Project BIA2008-04111.Museros Romero, P.; Moliner, E.; Martinez-Rodrigo, M. (2013). Free vibrations of simply-supported beam bridges under moving loads: Maximum resonance, cancellation and resonant vertical acceleration. Journal of Sound and Vibration. 332(2):326-345. https://doi.org/10.1016/j.jsv.2012.08.008326345332

Dynamic performance of existing double track railway bridges at resonance with the increase of the operational line speed

[EN] This article addresses the dynamic behaviour of double track simply supported bridges of short to medium span lengths (10 m < L< 25 m) belonging to conventional railway lines. These structures are susceptible to experience inadmissible levels of vertical vibrations when traversed by trains at high speeds, and in certain cases their dynamic performance may require to be re-evaluated in case of an increase of the traffic velocity above 200 km/h. In engineering consultancies, these structures have been traditionally analysed under the passage of trains at different speeds using planar models, neglecting the contribution of transverse vibration modes and also the flexibility of the elastomeric bearings. The study presented herein endeavours to evaluate the influence of these two aspects in the verification of the Serviceability Limit State of vertical accelerations, which is of great interest in order to guarantee a conservative prediction of the dynamic behaviour. In the present study, the dynamic response of representative slab and girder bridges has been evaluated using an orthotropic plate finite element model, leading to practical conclusions regarding the circumstances under which the above mentioned factors should be considered in order to adequately evaluate the transverse vibration levels of the deck.Moliner, E.; Martínez-Rodrigo, M.; Museros Romero, P. (2017). Dynamic performance of existing double track railway bridges at resonance with the increase of the operational line speed. Engineering Structures. 132:98-109. doi:10.1016/j.engstruct.2016.11.031S9810913

Real-time evolution of a large-scale relativistic jet

Context. Astrophysical jets are ubiquitous in the Universe on all scales, but their large-scale dynamics and evolution in time are hard to observe since they usually develop at a very slow pace. Aims. We aim to obtain the first observational proof of the expected large-scale evolution and interaction with the environment in an astrophysical jet. Only jets from microquasars offer a chance to witness the real-time, full-jet evolution within a human lifetime, since they combine a 'short', few parsec length with relativistic velocities. Methods. The methodology of this work is based on a systematic recalibraton of interferometric radio observations of microquasars available in public archives. In particular, radio observations of the microquasar GRS 1758-258 over less than two decades have provided the most striking results. Results. Significant morphological variations in the extended jet structure of GRS 1758-258 are reported here that were previously missed. Its northern radio lobe underwent a major morphological variation that rendered the hotspot undetectable in 2001 and reappeared again in the following years. The reported changes confirm the Galactic nature of the source. We tentatively interpret them in terms of the growth of instabilities in the jet flow. There is also evidence of surrounding cocoon. These results can provide a testbed for models accounting for the evolution of jets and their interaction with the environment.Comment: 5 pages, 3 figures, 2 tables. Accepted for publication in Astronomy and Astrophysics Letter

Effects of saline reclaimed waters and deficit irrigation on Citrus physiology assessed by UAV remote sensing

The aim of our research was to discover the effects of the long-term irrigation with saline reclaimed (RW) and transfer (TW) water and different irrigation strategies: control (C) and regulated deficit irrigation (RDI) on yield and fruit quality of grapefruit at harvest and during cold storage. TW-RDI treatment decreased tree canopy (TC) and crop load, resulting in a 21% reduction of fruit yield. Regarding fruit quality, RW notably decreased peel thickness at harvest (about 8%); however, this difference was not remained during cold storage. Sugar/acid ratio was mainly increased by RDI, but also by RW, due to an important increase in soluble solid content (11% of average value for TW-RDI, RW-C and RW-RDI). In addition, RDI combined with RW, significantly increased the number of fruits in small category 5 at the end of cold storage. Finally, neither ratio yield/TC nor irrigation water productivity were affected by any irrigation treatments.This study was supported by two CICYT (AGL2010-17553 and AGL2013-49047-C2-482 515 2-R) projects and SIRRIMED (KBBE-2009-1- 2-03, PROPOSAL N◦245159) 483 project. We are also grateful to SENECA–Excelencia Científica (19903/GERM/15) for 484 providing funds for this research

Are T Tauri stars gamma-ray emitters?

T Tauri stars are young, low mass, pre-main sequence stars surrounded by an accretion disk. These objects present strong magnetic activity and powerful magnetic reconnection events. Strong shocks are likely associated with fast reconnection in the stellar magnetosphere. Such shocks can accelerate particles up to relativistic energies. We aim at developing a simple model to calculate the radiation produced by non-thermal relativistic particles in the environment of T Tauri stars. We want to establish whether this emission is detectable at high energies with the available or forthcoming gamma-ray telescopes. We assume that particles (protons and electrons) pre-accelerated in reconnection events are accelerated at shocks through Fermi mechanism and we study the high-energy emission produced by the dominant radiative processes. We calculate the spectral energy distribution of T Tauri stars up to high-energies and we compare the integrated flux obtained with that from a specific Fermi source, 1FGL J1625.8-2429c, that we tentatively associate with this kind of young stellar objects (YSOs). We suggest that under reasonable general conditions nearby T Tauri stars might be detected at high energies and be responsible for some unidentified Fermi sources on the Galactic plane.Comment: 7 pages, 10 figure

Changes in the Semantic Construction of Compassion after the Cognitively-Based Compassion Training (CBCT®) in Women Breast Cancer Survivors

The growing body of research on compassion has demonstrated its benefits for healthcare and wellbeing. However, there is no clear agreement about a definition for compassion, given the novelty of the research on this construct and its religious roots. The aim of this study is to analyze the mental semantic construction of compassion in Spanish-speaking women breast cancer survivors, and the effects of the Cognitively-Based Compassion Training (CBCT®) on the modification of this definition, compared to treatment-as-usual (TAU), at baseline, post-intervention, and six-month follow-up. Participants were 56 women breast cancer survivors from a randomized clinical trial. The Osgood''s Semantic Differential categories (evaluative, potency, and activity scales) were adapted to assess the semantic construction of compassion. At baseline, participants had an undefined idea about compassion. The CBCT influenced subjects'' semantic construction of what it means to be compassionate. Findings could lead to future investigations and compassion programs that adapt to a specific culture or population. © Universidad Complutense de Madrid and Colegio Oficial de Psicólogos de Madrid 2021