Integrative structural and dynamical biology with PLUMED-ISDB

Accurate structural models of biological systems can be obtained by properly combining experimental data with a priori physico-chemical knowledge. Here we present PLUMED-ISDB, an open-source, freely-available module of the popular PLUMED library, which enables the simultaneous determination of structure and dynamics of conformationally heterogeneous systems by integrating experimental data with a priori information. This integration is achieved using metainference, a general Bayesian framework that accounts for both noise in the data and their ensemble-averaged nature. PLUMED-ISDB implements different types of experimental data, such as several NMR observables, FRET, SAXS and cryo-electron microscopy data, and enables modelling structure and dynamics of individual proteins, protein complexes, membrane proteins, RNA and DNA, using a variety of enhanced sampling methods and resolutions of the system

High-power test results of a 3 GHz single-cell cavity

Compact, reliable and little consuming accelerators are required for the treatment of tumours with ions. TERA proposes the "cyclinac", composed of a high-frequency, fast-cycling linac which boosts the energy of the particles previously accelerated in a cyclotron. The dimensions of the linac can be reduced if high gradients are used. TERA initiated a high-gradient test program to understand the operational limit of such structures. The program foresees the design, prototyping and high-power test of several high-gradient structures operating at 3 and 5.7 GHz. The high-power tests of the 3 GHz single-cell cavity were completed in Winter 2012. The maximum BDR threshold measured for Emax of 170 MV/m and RF pulses of 2.5 \mu s was 3 x 10-6 bpp/m

Early indication of decompensated heart failure in patients on home-telemonitoring: a comparison of prediction algorithms based on daily weight and noninvasive transthoracic bio-impedance

Background: Heart Failure (HF) is a common reason for hospitalization. Admissions might be prevented by early detection of and intervention for decompensation. Conventionally, changes in weight, a possible measure of fluid accumulation, have been used to detect deterioration. Transthoracic impedance may be a more sensitive and accurate measure of fluid accumulation. Objective: In this study, we review previously proposed predictive algorithms using body weight and noninvasive transthoracic bio-impedance (NITTI) to predict HF decompensations. Methods: We monitored 91 patients with chronic HF for an average of 10 months using a weight scale and a wearable bio-impedance vest. Three algorithms were tested using either simple rule-of-thumb differences (RoT), moving averages (MACD), or cumulative sums (CUSUM). Results: Algorithms using NITTI in the 2 weeks preceding decompensation predicted events (P<.001); however, using weight alone did not. Cross-validation showed that NITTI improved sensitivity of all algorithms tested and that trend algorithms provided the best performance for either measurement (Weight-MACD: 33%, NITTI-CUSUM: 60%) in contrast to the simpler rules-of-thumb (Weight-RoT: 20%, NITTI-RoT: 33%) as proposed in HF guidelines. Conclusions: NITTI measurements decrease before decompensations, and combined with trend algorithms, improve the detection of HF decompensation over current guideline rules; however, many alerts are not associated with clinically overt decompensation

TrustShadow: Secure Execution of Unmodified Applications with ARM TrustZone

The rapid evolution of Internet-of-Things (IoT) technologies has led to an emerging need to make it smarter. A variety of applications now run simultaneously on an ARM-based processor. For example, devices on the edge of the Internet are provided with higher horsepower to be entrusted with storing, processing and analyzing data collected from IoT devices. This significantly improves efficiency and reduces the amount of data that needs to be transported to the cloud for data processing, analysis and storage. However, commodity OSes are prone to compromise. Once they are exploited, attackers can access the data on these devices. Since the data stored and processed on the devices can be sensitive, left untackled, this is particularly disconcerting. In this paper, we propose a new system, TrustShadow that shields legacy applications from untrusted OSes. TrustShadow takes advantage of ARM TrustZone technology and partitions resources into the secure and normal worlds. In the secure world, TrustShadow constructs a trusted execution environment for security-critical applications. This trusted environment is maintained by a lightweight runtime system that coordinates the communication between applications and the ordinary OS running in the normal world. The runtime system does not provide system services itself. Rather, it forwards requests for system services to the ordinary OS, and verifies the correctness of the responses. To demonstrate the efficiency of this design, we prototyped TrustShadow on a real chip board with ARM TrustZone support, and evaluated its performance using both microbenchmarks and real-world applications. We showed TrustShadow introduces only negligible overhead to real-world applications.Comment: MobiSys 201

Efectos de la calidad de luz en la reproducción, crecimiento y contenido pigmentario de Gracilaria birdiae (Rhodophyta: Gracilariales)

Gracilaria species are the main source of agar worldwide. Since laboratory cultivation is an important means of sustaining such production, this study aimed to assess the influence of two fundamental strategies of physiological algae adjustment, photoacclimation and photomorphogenesis, on G. birdiae physiology. Specifically, the effects of different spectral light qualities on reproduction, growth, and pigment content in two distinct photoperiods (8 and 14 hours) were examined. Tetrasporophytes and gametophytes were submitted to different light qualities: white, green, red, and blue over the course of nine weeks. At the end of this period, chlorophyll a, allophycocyanin, phycocyanin, and phycoerythrin contents were analysed. Gametophytes showed reproductive structures only under monochromatic radiation. A stimulatory effect on tetrasporangium differentiation was mainly observed under red light, but this high fertility was negatively correlated with growth rate, i.e. algae cultivated under red light showed the lowest growth rate. However, while growth rates were higher in algae exposed to white light, they were similar to those observed in algae subjected to green light and 14 hours of daylight. PE was the predominant pigment, irrespective of light quality. Phycocyanin and phycoerythrin concentration increased when algae were cultivated under green and blue light. Therefore, considering future management prospects for G. birdiae mariculture, we suggest that red light could be utilized as a reproductive inductor to produce tetraspores. Furthermore, if the aim is to achieve high phycoerythrin content, continuous blue light could be applied during a short photoperiod. Indeed, the combination of different wavelengths could allow better economic resource exploitation.Las especies del género Gracilaria son la principal fuente de agar en el mundo. El desarrollo de técnicas de cultivo en laboratorio es importante para mejorar la producción, y por ello, este estudio tuvo como objetivo la evaluación de la influencia de dos estrategias de ajuste fisiológico de las algas, la fotoaclimatación y la fotomorfogénesis en G. birdiae. De modo más específico, se evaluaron los efectos de diferentes calidades espectrales de luz sobre la reproducción, crecimiento y contenido pigmentario bajo dos fotoperiodos (8 y 14 horas). Tetrasporofitos y gametofitos fueron sometidos a las siguientes calidades de luz: blanca (WH), verde (GR), rojo (RD) y azul (BL) a lo largo de nueve semanas. Al final del periodo, se analizaron los contenidos de clorofila a (Chl a), aloficocianina (APC), ficocianina (PC) y ficoeritrina (PE). Los gametofitos carecieron de estructuras reproductivas exclusivamente en radiación blanca. La diferenciación de tetrasporangios fue obtenida bajo estímulo de luz roja, pero fue negativamente correlacionado con las tasas de crecimiento (GRTs), presentando las tasas más bajas. Por otro lado, mientras las tasas de crecimiento fueron más altas en algas expuestas a luz WH, éstas fueron similares en algas mantenidas bajo luz GR y 14 horas de fotoperiodo. PE fue el pigmento predominante en G. birdiae, independientemente de la calidad de la luz aplicada. La concentración de PC y PE aumentaron cuando las algas recibieron luz GR y BL. De esa manera, considerando las perspectivas de manejo en la maricultura de G. birdiae, se sugiere que la luz roja puede ser utilizada como factor de inducción de la producción de tetrasporas. Por otro lado, las algas cultivadas en fotoperiodos cortos y luz BL alcanzaron altos contenidos de PE. La combinación de diferentes longitudes de onda puede permitir una mayor valorización en la explotación económica de los recursos algales