A new algorithm for particle weighted subtraction to decrease signals from unwanted components in single particle analysis

Single particle analysis (SPA) in cryo-electron microscopy (cryo-EM) is highly used to obtain the near-atomic structure of biological macromolecules. The current methods allow users to produce high-resolution maps from many samples. However, there are still challenging cases that require extra processing to obtain high resolution. This is the case when the macromolecule of the sample is composed of different components and we want to focus just on one of them. For example, if the macromolecule is composed of several flexible subunits and we are interested in a specific one, if it is embedded in a viral capsid environment, or if it has additional components to stabilize it, such as nanodiscs. The signal from these components, which in principle we are not interested in, can be removed from the particles using a projection subtraction method. Currently, there are two projection subtraction methods used in practice and both have some limitations. In fact, after evaluating their results, we consider that the problem is still open to new solutions, as they do not fully remove the signal of the components that are not of interest. Our aim is to develop a new and more precise projection subtraction method, improving the performance of state-of-the-art methods. We tested our algorithm with data from public databases and an in–house data set. In this work, we show that the performance of our algorithm improves the results obtained by others, including the localization of small ligands, such as drugs, whose binding location is unknown a prioriThe authors acknowledge the economic support from MICIN to the Instruct Image Processing Center (I2PC) as part of the Spanish participation in Instruct-ERIC, the European Strategic Infrastructure Project (ESFRI) in Structural Biology. Grant PID2019-104757RB-I00 is funded by MCIN/AEI/ 10.13039/ 501100011033 and “ERDF A way of making Europe”, by the European Union. The “Comunidad Autónoma de Madrid” through Grant S2022/BMD-7232, the European Union (EU) and Horizon 2020 through grant HighResCells (ERC-2018-SyG, Proposal: 810057). The authors also acknowledge grant PID2019-104098 GB-I00/AEI/10.13039/501100011033, cofunded by the Spanish State Research Agency and the European Regional Development and grant 2023AEP082 by Agencia Estatal CSIC. Ruben Sanchez-Garcia is funded by an Astex Pharmaceuticals Sustaining Innovation Post-Doctoral Awar

Influence of Ca/Si ratio on the microstructure and properties of blended cements elaborated with kaolinite based waste

ICCC 2015, Beijing, China, 13~16 October 2015; http://iccc2015.csp.escience.cn/dct/page/1To reduce the environmental impact of cement industries, cementitious materials are added to the manufacture of eco-efficient cements, focusing in industrial wastes. In this paper metakaolinite (MK) based industrial wastes have been mixed with cement in order to study the effect of the chemical composition of the raw material in both microstructural and mechanical properties of the pastes. Frattini test was also determined. The selected metakaolin based industrial wastes were previously activated for two hours at temperatures around 600ºC to transform the inert waste into a cementing material. The industrial wastes materials used were coal mining and paper sludge. The second one was mixed with fly ash (50/50 w/w) in order to evaluate the performance of ternary blended cements. The mixtures were prepared with OPC and both 6 and 20% of activated industrial waste (coal mining and paper sludge + fly ash). Prismatic samples (1x1x6 cm) were prepared with water/cement ratio of 0.5 and cured 28 days. After this time, mineralogical composition of the samples was determined by XRD as well as mechanical properties (compressive and flexural strength, total porosity, etc). Besides, portlandite and ettringite, both monocarboaluminate and C4AH13 have been formed in the samples after 28 days of hydration. It can be observed that C4AH13 decreases as Ca/Si ratio decreases; with the opposite behaviour for the monocarboaluminate. From the mechanical properties, porosity decreases from 1 to 28 days of curing as compressive strength increases.To the Ministry of Economy and Competiveness by the financial support (MAT2012-37005-C03-01-02-03).Peer Reviewe

Histological evidence for a supraspinous ligament in sauropod dinosaurs

Supraspinous ossified rods have been reported in the sacra of some derived sauropod dinosaurs. Although different hypotheses have been proposed to explain the origin ofthis structure, histological evidence has never been provided to support or reject any of them. In order to establish its origin, we analyse and characterize the microstructure of thesupraspinous rod of two sauropod dinosaurs from the Upper Cretaceous of Argentina. The supraspinous ossified rod is almost entirely formed by dense Haversian bone. Remains ofprimary bone consist entirely of an avascular tissue composed of two types of fibre-like structures, which are coarse and longitudinally (parallel to the main axis of the element) oriented. These structures are differentiated on the basis of their optical properties under polarized light. Very thin fibrous strands are also observed in some regions. These small fibres are all oriented parallel to one another but perpendicular to the element main axis. Histological features of the primary bone tissue indicate that the sacral supraspinous rod corresponds to an ossified supraspinous ligament. The formation of this structure appears to have been a non-pathological metaplastic ossification, possibly induced by the continuous tensile forces applied to the element.Fil: Cerda, Ignacio Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigación en Paleobiología y Geología; Argentina. Universidad Nacional de Río Negro; ArgentinaFil: Casal, Gabriel. Universidad Nacional de la Patagonia; ArgentinaFil: Martínez, Rubén Darío. Universidad Nacional de la Patagonia ; ArgentinaFil: Ibiricu, Lucio Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentin

Veinte años de seguimiento poblacional de ungulados silvestres de Aragón

The remarkable increase of wild ungulates populations in Aragon during the last 50 years, both in numbers and distribution, has made population monitoring a need for effective management of these species. In parallel to their raising numbers, problems related to crop damage and collisions with vehicles are growing. In this situation there has been a shift in the management goals from conservation to population control. Different methods have been used in the surveys: postal enquiries for distribution, battues, distance sampling, night spotlight surveys and indirect ones based on transect and plot counts of pellet groups. Surveys started in 1985 for red deer, 1990 for wild boar and Iberian wild goat, 1995 for chamois and 2002 for roe deer, gradually becoming a population monitoring program. The surveys are carried out by rangers and wildlife consultants under the coordination and supervision of the Fish and Game Service of the Aragon Government. The ungulate populations are still growing (wild boar, wild goat, red and roe deer), are relatively stabilised (fallow deer, feral goat), fluctuate due to diseases (chamois) or show small populations limited to fenced states (Barbary sheep, mouflon). Hunting bags went from 1,100 to 36,000 during an eleven-year period (1990-2009): 303 chamois, 1,173 wild goats, 2,141 roe deer, 2,424 red deer and 29,595 wild boars, showing a trend which is still increasing. The main tool is therefore hunting quota and its verification through hunting bags declarations, damages to crops and car crashes, and population trend and abundance.La importante expansión de las poblaciones de ungulados silvestres en Aragón desde los años 50 del siglo XX hasta la actualidad, tanto en superficie ocupada como en abundancia de ejemplares, ha hecho necesario el seguimiento de las mismas para su adecuada gestión. Su incremento en las dos últimas décadas, junto con el importante aumento de daños agrícolas y colisiones con vehículos, ha motivado un importante cambio en los criterios gestores; pasando de la conservación y fomento al control e incluso reducción de efectivos. Los métodos utilizados para el seguimiento de las poblaciones fueron: encuestas quincenales de distribución, batidas, muestreos de distancia, captura – recaptura, fareos nocturnos y muestreos indirectos basados en el conteo de grupos de excrementos en transectos y parcelas fijas. Los seguimientos se comenzaron a realizar en 1985 en el caso del ciervo, 1990 en el jabalí y cabra montesa, 1995 en el sarrio y 2002 en el corzo, habiéndose convertido paulatinamente en una verdadera monitorización poblacional. Los seguimientos son realizados por Agentes de Protección de la Naturaleza del Gobierno de Aragón y asistencias técnicas externas, bajo la supervisión y coordinación de los responsables administrativos. Los resultados obtenidos muestran que, algunas poblaciones continúan su expansión e incremento (jabalí, ciervo, corzo, cabra montesa), otras se encuentran relativamente estabilizadas (gamo, cabra doméstica asilvestrada), y unas pocas fluctúan debido a enfermedades (sarrio) o muestran presencias testimoniales prácticamente reducidas a cercados (arruí, muflón). Las capturas declaradas han pasado de 1.100 a 36.000 en 11 años (1999-2009): 303 sarrios, 1.173 cabras montesas, 2.141 corzos, 2.424 ciervos y 29.595 jabalíes, con una tendencia al incremento que aún no ha finalizado. El instrumento fundamental por lo tanto son los cupos de caza y su verificación se realiza a partir de las declaraciones de capturas, los daños a la agricultura y accidentes automovilísticos y la tendencia y abundancia poblacional

Programa de Atención al Ictus en Aragón (PAIA). Estrategia del cambio y resultados en el periodo 2009-2014

Introducción En 2008, Aragón tenía tasas de morbimortalidad y discapacidad por ictus superiores a las del conjunto de España. Se estableció la necesidad de desarrollar un Programa de Atención al Ictus (PAIA). Material y métodos Damos a conocer la dinámica de planificación, implantación, evaluación y mejora que se ha desarrollado entre los años 2009-2014 y sus resultados a 5 años. Resultados Se ha mejorado en la estructura, en los procesos y en los resultados, con mejoría en los indicadores clave de la asistencia (audit 2008-2010-2012) y otros: tasa ictus 2013: 2, 07 (2008: 2, 36); 78% ictus atendidos en áreas/unidades en 2014 (30%, 2008); tasa fibrinólisis 8, 3% en 2014 (4, 4%, 2010); fibrinólisis hospitales secundarios (30% total); fibrinólisis con teleictus 9%; descenso de la mortalidad por ictus, 38%; años de vida prematura perdidos 67, 7 (2013)/144 (2008); capacitación de enfermería, desarrollo de la neurosonología, trabajo en red, con protocolos y buenas prácticas compartidos entre sectores sanitarios, etc. Conclusiones La gestión por procesos y equipos multidisciplinares desplegados en una distribución territorial integral, con protocolos y referencias establecidas y una dinámica de evaluación y mejora continua, ha demostrado ser una herramienta potente para garantizar la calidad y la equidad. El PAIA, por su dinámica de mejora sostenida y la implicación de los clínicos, es un buen ejemplo de gestión clínica y trabajo en red. Introduction: In 2008, stroke mortality, morbidity, and disability rates in Aragon were higher than the average in Spain. These data underscored the need to develop a stroke care programme (PAIA). Material and methods: We present the dynamics of planning, implementation, evaluation, and improvement developed between 2009 and 2014 as well as the results of the PAIA after that 5-year period. Results: Structure, processes, and outcomes have improved with reference to the key indicators of healthcare (audit: 2008, 2010, 2012) among others: stroke rate in 2013 was 2.07 (2.36 in 2008); 78% of strokes were managed in stroke units in 2014 (30% in 2008); rate of fibrinolysis was 8.3% in 2014 (4.4% in 2010); fibrinolysis was administered in secondary hospitals (30% of the total); fibrinolysis was administered by Telestroke in 9%; stroke mortality decreased (38%); 67.7 years of potential life lost (YPLL) in 2013 (144 in 2008); nurse training; development of neurosonology; networking; sharing protocols and best practices between health sectors, etc. Conclusions: Integrated process management and multidisciplinary teams distributed and deployed over an entire territory with established protocols, references, evaluations, and continuous development, have been proven powerful tools to ensure both quality and equality. The PAIA is a good example of clinical governance and networking due to its dynamic and sustained improvement and cooperation between clinicians

Environmental variables, habitat discontinuity and life history shaping the genetic structure of Pomatoschistus marmoratus

Coastal lagoons are semi-isolated ecosystems exposed to wide fluctuations of environmental conditions and showing habitat fragmentation. These features may play an important role in separating species into different populations, even at small spatial scales. In this study, we evaluate the concordance between mitochondrial (previous published data) and nuclear data analyzing the genetic variability of Pomatoschistus marmoratus in five localities, inside and outside the Mar Menor coastal lagoon (SE Spain) using eight microsatellites. High genetic diversity and similar levels of allele richness were observed across all loci and localities, although significant genic and genotypic differentiation was found between populations inside and outside the lagoon. In contrast to the FST values obtained from previous mitochondrial DNA analyses (control region), the microsatellite data exhibited significant differentiation among samples inside the Mar Menor and between lagoonal and marine samples. This pattern was corroborated using Cavalli-Sforza genetic distances. The habitat fragmentation inside the coastal lagoon and among lagoon and marine localities could be acting as a barrier to gene flow and contributing to the observed genetic structure. Our results from generalized additive models point a significant link between extreme lagoonal environmental conditions (mainly maximum salinity) and P. marmoratus genetic composition. Thereby, these environmental features could be also acting on genetic structure of coastal lagoon populations of P. marmoratus favoring their genetic divergence. The mating strategy of P. marmoratus could be also influencing our results obtained from mitochondrial and nuclear DNA. Therefore, a special consideration must be done in the selection of the DNA markers depending on the reproductive strategy of the species

Image processing tools for the validation of CryoEM maps

The number of maps deposited in public databases (Electron Microscopy Data Bank, EMDB) determined by cryo-electron microscopy has quickly grown in recent years. With this rapid growth, it is critical to guarantee their quality. So far, map validation has primarily focused on the agreement between maps and models. From the image processing perspective, the validation has been mostly restricted to using two half-maps and the measurement of their internal consistency. In this article, we suggest that map validation can be taken much further from the point of view of image processing if 2D classes, particles, angles, coordinates, defoci, and micrographs are also provided. We present a progressive validation scheme that qualifies a result validation status from 0 to 5 and offers three optional qualifiers (A, W, and O) that can be added. The simplest validation state is 0, while the most complete would be 5AWO. This scheme has been implemented in a website https://biocomp.cnb.csic.es/EMValidationService/ to which reconstructed maps and their ESI can be uploaded

New insights into the neolithisation process in southwest Europe according to spatial density analysis from calibrated radiocarbon dates

The agricultural way of life spreads throughout Europe via two main routes: the Danube corridor and the Mediterranean basin. Current archaeological literature describes the arrival to the Western Mediterranean as a rapid process which involves both demic and cultural models, and in this regard, the dispersal movement has been investigated using mathematical models, where the key factors are time and space. In this work, we have created a compilation of all available radiocarbon dates for the whole of Iberia, in order to draw a chronological series of maps to illustrate temporal and spatial patterns in the neolithisation process. The maps were prepared by calculating the calibrated 14C date probability density curves, as a proxy to show the spatial dynamics of the last hunter-gatherers and first farmers. Several scholars have pointed out problems linked with the variability of samples, such as the overrepresentation of some sites, the degree of regional research, the nature of the dated samples and above all the archaeological context, but we are confident that the selected dates, after applying some filters and statistical protocols, constitute a good way to approach settlement spatial patterns in Iberia at the time of the neolithisation process