Ab initio and template-based prediction of multi-class distance maps by two-dimensional recursive neural networks

Background: Prediction of protein structures from their sequences is still one of the open grand challenges of computational biology. Some approaches to protein structure prediction, especially ab initio ones, rely to some extent on the prediction of residue contact maps. Residue contact map predictions have been assessed at the CASP competition for several years now. Although it has been shown that exact contact maps generally yield correct three-dimensional structures, this is true only at a relatively low resolution (3–4 Å from the native structure). Another known weakness of contact maps is that they are generally predicted ab initio, that is not exploiting information about potential homologues of known structure. Results: We introduce a new class of distance restraints for protein structures: multi-class distance maps. We show that C trace reconstructions based on 4-class native maps are significantly better than those from residue contact maps. We then build two predictors of 4-class maps based on recursive neural networks: one ab initio, or relying on the sequence and on evolutionary information; one template-based, or in which homology information to known structures is provided as a further input. We show that virtually any level of sequence similarity to structural templates (down to less than 10%) yields more accurate 4-class maps than the ab initio predictor. We show that template-based predictions by recursive neural networks are consistently better than the best template and than a number of combinations of the best available templates. We also extract binary residue contact maps at an 8 Å threshold (as per CASP assessment) from the 4-class predictors and show that the template-based version is also more accurate than the best template and consistently better than the ab initio one, down to very low levels of sequence identity to structural templates. Furthermore, we test both ab-initio and template-based 8 Å predictions on the CASP7 targets using a pre-CASP7 PDB, and find that both predictors are state-of-the-art, with the template-based one far outperforming the best CASP7 systems if templates with sequence identity to the query of 10% or better are available. Although this is not the main focus of this paper we also report on reconstructions of C traces based on both ab initio and template-based 4-class map predictions, showing that the latter are generally more accurate even when homology is dubious. Conclusion: Accurate predictions of multi-class maps may provide valuable constraints for improved ab initio and template-based prediction of protein structures, naturally incorporate multiple templates, and yield state-of-the- art binary maps. Predictions of protein structures and 8 Å contact maps based on the multi-class distance map predictors described in this paper are freely available to academic users at the url http://distill.ucd.ie/.Science Foundation IrelandHealth Research BoardUCD President's Award 2004au, ti, sp, ke, ab - kpw16/12/1

Optimization of an Impact-Based Frequency Up-Converted Piezoelectric Vibration Energy Harvester for Wearable Devices

This work presents a novel development of the impact-based mechanism for piezoelectric vibration energy harvesters. More precisely, the effect of an impacting mass on a cantilever piezoelectric transducer is studied both in terms of the tip mass value attached to the cantilever and impact position to find an optimal condition for power extraction. At first, the study is carried out by means of parametric analyses at varying tip mass and impact position on a unimorph MEMS cantilever, and a suitable physical interpretation of the associated electromechanical response is given. The effect of multiple impacts is also considered. From the analysis, it emerges that the most effective configuration, in terms of power output, is an impact at the cantilever tip without a tip mass. By changing the value of the tip mass, a sub-optimal impact position along the beam axis can also be identified. Moreover, the effect of a tip mass is deleterious on the power performance, contrary to the well-known case of a resonant energy harvester. A mesoscale prototype with a bimorph transducer is fabricated and tested to validate the computational models. The comparison shows a good agreement between numerical models and the experiments. The proposed approach is promising in the field of consumer electronics, such as wearable devices, in which the impact-based device moves at the frequencies of human movement and is much lower than those of microsystems

The STRIP instrument of the Large Scale Polarization Explorer: microwave eyes to map the Galactic polarized foregrounds

In this paper we discuss the latest developments of the STRIP instrument of the "Large Scale Polarization Explorer" (LSPE) experiment. LSPE is a novel project that combines ground-based (STRIP) and balloon-borne (SWIPE) polarization measurements of the microwave sky on large angular scales to attempt a detection of the "B-modes" of the Cosmic Microwave Background polarization. STRIP will observe approximately 25% of the Northern sky from the "Observatorio del Teide" in Tenerife, using an array of forty-nine coherent polarimeters at 43 GHz, coupled to a 1.5 m fully rotating crossed-Dragone telescope. A second frequency channel with six-elements at 95 GHz will be exploited as an atmospheric monitor. At present, most of the hardware of the STRIP instrument has been developed and tested at sub-system level. System-level characterization, starting in July 2018, will lead STRIP to be shipped and installed at the observation site within the end of the year. The on-site verification and calibration of the whole instrument will prepare STRIP for a 2-years campaign for the observation of the CMB polarization.Comment: 17 pages, 15 figures, proceedings of the SPIE Astronomical Telescopes + Instrumentation conference "Millimeter, Submillimeter, and Far-Infrared Detectors and Instrumentation for Astronomy IX", on June 15th, 2018, Austin (TX

Detection chain and electronic readout of the QUBIC instrument

The Q and U Bolometric Interferometer for Cosmology (QUBIC) Technical Demonstrator (TD) aiming to shows the feasibility of the combination of interferometry and bolometric detection. The electronic readout system is based on an array of 128 NbSi Transition Edge Sensors cooled at 350mK readout with 128 SQUIDs at 1K controlled and amplified by an Application Specific Integrated Circuit at 40K. This readout design allows a 128:1 Time Domain Multiplexing. We report the design and the performance of the detection chain in this paper. The technological demonstrator unwent a campaign of test in the lab. Evaluation of the QUBIC bolometers and readout electronics includes the measurement of I-V curves, time constant and the Noise Equivalent Power. Currently the mean Noise Equivalent Power is ~ 2 x 10⁻¹⁶ W/√Hz

Detection chain and electronic readout of the QUBIC instrument

The Q and U Bolometric Interferometer for Cosmology (QUBIC) Technical Demonstrator (TD) aiming to shows the feasibility of the combination of interferometry and bolometric detection. The electronic readout system is based on an array of 128 NbSi Transition Edge Sensors cooled at 350mK readout with 128 SQUIDs at 1K controlled and amplified by an Application Specific Integrated Circuit at 40K. This readout design allows a 128:1 Time Domain Multiplexing. We report the design and the performance of the detection chain in this paper. The technological demonstrator unwent a campaign of test in the lab. Evaluation of the QUBIC bolometers and readout electronics includes the measurement of I-V curves, time constant and the Noise Equivalent Power. Currently the mean Noise Equivalent Power is ~ 2 x 10⁻¹⁶ W/√Hz

Science and innovation with stratospheric balloons: the Olimpo & Lspe/swipe projects

The measurement of the Cosmic Microwave Background (CMB) polarization and the spectral distortions produced on this radiation field by clusters of galaxies (Sunyaev-Zeldovich Effect, SZE) are the current frontiers in cosmology. In this paper, we report on two stratospheric balloon experiments aimed to study the research fields mentioned above. OLIMPO is a mm/submm waves telescope, with 2.6 m primary mirror coupled to four arrays of Kinetic Inductance Detectors (KID), centered at 150, 250, 350, and 460 GHz, to match the SZ spectrum, and operating at 0.3 K. The payload, flown in 2018 producing a very successful technology demonstration, includes a plug-in Differential Fourier-Transform Spectrometer. LSPE (Large Scale Polarization Explorer) is a combined balloon-borne and ground-based program dedicated to the measurement of the CMB polarization at large angular scales. LSPE/SWIPE (Short Wavelength Instrument for the Polarization Explorer), the balloon-borne instrument, includes a refractive telescope with a 50 cm optical aperture feeding three arrays of 330 multi-mode TES bolometers at 145, 210, e 240 GHz. The polarization of the incoming radiation will be modulated by a rotating Half Wave Plate (HWP), that is maintained levitating by an innovative magnetic suspension system. The detectors and the optical elements are cooled at cryogenic temperatures. The cryogenic system is designed to have a duration of 14 days with a flight performed during the polar night, to allow a coverage of a large fraction of the sky. In the paper, we describe the configuration of the two instruments, the modifications to be implemented on OLIMPO for a second scientific flight and the status of the different sub-system for LSPE/SWIPE

‘Una vera arte e un’arte difficile’: Gian Dàuli editore moderno tra le due guerre

The work is centered on the activity of the Vicentinian publisher Gian Dàuli, (p Ugo Giuseppe Nalato) born in Vicenza on December 9, 1894. The intellectual training and the entire professional career of Gian Dàuli were unraveled during the most controversial phases of the first forty years of the twentieth century. Dàuli is best known for being the first of Jack London's translators (1924) and for creating the editorial series 'Writers of the World' (1928). The work, which is the result of systematic archive research, assumes the burden to an in depth evaluation of the professional life of Dàuli. What emerges is that he was not, as IT has been widely affirmed, a confusing publisher, a man of disorder. The catalogues he set up were not only the result of his eccentric genius. To animate the efforts of Dàuli were firm values, passions and ideals pursued during the long stay in England, the European travels, the Great War. Democracy, social reformism, universal brotherhood, solidarity with the disadvantaged classes were elements that oriented the entire career of the publisher. While the Fascist regime increasingly influenced the spaces of freedom, Dàuli introduced European works of great intellectual inspiration in Italy, anticipating the 'decade of translation' and hoping that foreign literature would stimulate Italian writers to overcome academicism and art prose. Publishing was for Dàuli the means to educate people to beauty and to provide them with conceptual instruments for interpreting reality. He was mocked, despised by critics and excluded from the literary associations that counted. He paid a heavy price for his opposition to the Regime; he was viewed with suspicion by the ecclesiastical hierarchy for his humanitarian laicism. Since 1934 he ceased collaborations with luxury publishing houses, and after many catastrophic failures, he became a consultant editor of the Lucchi publishing house, specialized in low cost editions. He died in Milan on December 29, 1945

Flexural Plate Wave Piezoelectric MEMS Transducer for Cell Alignment in Aqueous Solution

Part of the Lecture Notes in Electrical Engineering book series (LNEE, volume 1005)International audienceIn this work, the possibility to align cells dispersed in water by means of standing flexural plate waves (FPWs) in an underlying substrate has been explored by designing and fabricating a piezoelectric MEMS transducer. The MEMS exhibits a 6x6 mm2 cavity etched out in a silicon substrate forming a volume where cells dispersed in liquid can be steered under electronic control. The diaphragm of the cavity is composed of silicon (Si) and an aluminum nitride (AlN) layer. The generation of FPWs of the A0 mode in the diaphragm is achieved by applying proper excitation voltages to two metal interdigital transducers (IDTs). In turn, acoustic waves are transferred in the liquid, generating a one-dimensional acoustic field pattern thus steering and trapping the dispersed cells in distinct positions. The MEMS device has been fabricated by using the PiezoMUMPs process and experimentally tested by exploiting a tailored front-end circuit. The cavity has been loaded with inert fibroblasts cells with an approximate diameter of 15&nbsp;&mu;m dispersed in demineralized water with a concentration in the order of 105 cells/ml. By properly driving two IDTs, lines of cells spaced by half wavelength &lambda;/2&thinsp;=&thinsp;56&nbsp;&mu;m have been achieved at 12.5&nbsp;MHz, in good agreement with theoretical expectations.</p

Distill : a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins

We describe Distill, a suite of servers for the prediction of protein structural features: secondary structure; relative solvent accessibility; contact density; backbone structural motifs; residue contact maps at 6, 8 and 12 Angstrom; coarse protein topology. The servers are based on large-scale ensembles of recursive neural networks and trained on large, up-to-date, non- redundant subsets of the Protein Data Bank. Together with structural feature predictions, Distill includes a server for prediction of Cα traces for short proteins (up to 200 amino acids). The servers are state-of-the-art, with secondary structure predicted correctly for nearly 80% of residues (currently the top performance on EVA), 2-class solvent accessibility nearly 80% correct, and contact maps exceeding 50% precision on the top non-diagonal contacts. A preliminary implementation of the predictor of protein Cα traces featured among the top 20 Novel Fold predictors at the last CASP6 experiment as group Distill (ID 0348). The majority of the servers, including the Cα trace predictor, now take into account homology information from the PDB, when available, resulting in greatly improved reliability. All predictions are freely available through a simple joint web interface and the results are returned by email. In a single submission the user can send protein sequences for a total of up to 32k residues to all or a selection of the servers. Distill is accessible at the address: http://distill.ucd.ie/distill/.Science Foundation IrelandIrish Research Council for Science, Engineering and TechnologyHealth Research BoardOther funderUCD President\u27s Award 2004au, da, sp, ke, ab - kpw13/1/1