Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM.

Understanding how structure and function meet to drive biological processes is progressively shifting the cryoEM field towards a more advanced analysis of macromolecular flexibility. Thanks to techniques such as single-particle analysis and electron tomography, it is possible to image a macromolecule in different states, information that can subsequently be extracted through advanced image-processing methods to build a richer approximation of a conformational landscape. However, the interoperability of all of these algorithms remains a challenging task that is left to users, preventing them from defining a single flexible workflow in which conformational information can be addressed by different algorithms. Therefore, in this work, a new framework integrated into Scipion is proposed called the Flexibility Hub. This framework automatically handles intercommunication between different heterogeneity software, simplifying the task of combining the software into workflows in which the quality and the amount of information extracted from flexibility analysis is maximized.

ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation.

Image processing in cryogenic electron tomography (cryoET) is currently at a similar state as Single Particle Analysis (SPA) in cryogenic electron microscopy (cryoEM) was a few years ago. Its data processing workflows are far from being well defined and the user experience is still not smooth. Moreover, file formats of different software packages and their associated metadata are not standardized, mainly since different packages are developed by different groups, focusing on different steps of the data processing pipeline. The Scipion framework, originally developed for SPA (de la Rosa-Trevín et al., 2016), has a generic python workflow engine that gives it the versatility to be extended to other fields, as demonstrated for model building (Martínez et al., 2020). In this article, we provide an extension of Scipion based on a set of tomography plugins (referred to as ScipionTomo hereafter), with a similar purpose: to allow users to be focused on the data processing and analysis instead of having to deal with multiple software installation issues and the inconvenience of switching from one to another, converting metadata files, managing possible incompatibilities, scripting (writing a simple program in a language that the computer must convert to machine language each time the program is run), etcetera. Additionally, having all the software available in an integrated platform allows comparing the results of different algorithms trying to solve the same problem. In this way, the commonalities and differences between estimated parameters shed light on which results can be more trusted than others. ScipionTomo is developed by a collaborative multidisciplinary team composed of Scipion team engineers, structural biologists, and in some cases, the developers whose software packages have been integrated. It is open to anyone in the field willing to contribute to this project. The result is a framework extension that combines the acquired knowledge of Scipion developers in close collaboration with third-party developers, and the on-demand design of functionalities requested by beta testers applying this solution to actual biological problems.

On bias, variance, overfitting, gold standard and consensus in single-particle analysis by cryo-electron microscopy.

Cryo-electron microscopy (cryoEM) has become a well established technique to elucidate the 3D structures of biological macromolecules. Projection images from thousands of macromolecules that are assumed to be structurally identical are combined into a single 3D map representing the Coulomb potential of the macromolecule under study. This article discusses possible caveats along the image-processing path and how to avoid them to obtain a reliable 3D structure. Some of these problems are very well known in the community. These may be referred to as sample-related (such as specimen denaturation at interfaces or non-uniform projection geometry leading to underrepresented projection directions). The rest are related to the algorithms used. While some have been discussed in depth in the literature, such as the use of an incorrect initial volume, others have received much less attention. However, they are fundamental in any data-analysis approach. Chiefly among them, instabilities in estimating many of the key parameters that are required for a correct 3D reconstruction that occur all along the processing workflow are referred to, which may significantly affect the reliability of the whole process. In the field, the term overfitting has been coined to refer to some particular kinds of artifacts. It is argued that overfitting is a statistical bias in key parameter-estimation steps in the 3D reconstruction process, including intrinsic algorithmic bias. It is also shown that common tools (Fourier shell correlation) and strategies (gold standard) that are normally used to detect or prevent overfitting do not fully protect against it. Alternatively, it is proposed that detecting the bias that leads to overfitting is much easier when addressed at the level of parameter estimation, rather than detecting it once the particle images have been combined into a 3D map. Comparing the results from multiple algorithms (or at least, independent executions of the same algorithm) can detect parameter bias. These multiple executions could then be averaged to give a lower variance estimate of the underlying parameters.

Cryo-EM and Single-Particle Analysis with Scipion.

Cryo-electron microscopy has become one of the most important tools in biological research to reveal the structural information of macromolecules at near-atomic resolution. In single-particle analysis, the vitrified sample is imaged by an electron beam and the detectors at the end of the microscope column produce movies of that sample. These movies contain thousands of images of identical particles in random orientations. The data need to go through an image processing workflow with multiple steps to obtain the final 3D reconstructed volume. The goal of the image processing workflow is to identify the acquisition parameters to be able to reconstruct the specimen under study. Scipion provides all the tools to create this workflow using several image processing packages in an integrative framework, also allowing the traceability of the results. In this article the whole image processing workflow in Scipion is presented and discussed with data coming from a real test case, giving all the details necessary to go from the movies obtained by the microscope to a high resolution final 3D reconstruction. Also, the power of using consensus tools that allow combining methods, and confirming results along every step of the workflow, improving the accuracy of the obtained results, is discussed.

Algorithmic robustness to preferred orientations in single particle analysis by CryoEM.

The presence of preferred orientations in single particle analysis (SPA) by cryo-Electron Microscopy (cryoEM) is currently one of the hurdles preventing many structural analyses from yielding high-resolution structures. Although the existence of preferred orientations is mostly related to the grid preparation, in this technical note, we show that some image processing algorithms used for angular assignment and three-dimensional (3D) reconstruction are more robust than others to these detrimental conditions. We exemplify this argument with three different data sets in which the presence of preferred orientations hindered achieving a 3D reconstruction without artifacts or, even worse, a 3D reconstruction could never be achieved.

Integration of Cryo-EM Model Building Software in Scipion.

Advances in cryo-electron microscopy (cryo-EM) have made it possible to obtain structures of large biological macromolecules at near-atomic resolution. This "resolution revolution" has encouraged the use and development of modeling tools able to produce high-quality atomic models from cryo-EM density maps. Unfortunately, many practical problems appear when combining different packages in the same processing workflow, which make difficult the use of these tools by non-experts and, therefore, reduce their utility. We present here a major extension of the image processing framework Scipion that provides inter-package integration in the model building area and full tracking of the complete workflow, from image processing to structure validation.

Flexible workflows for on-the-fly electron-microscopy single-particle image processing using Scipion.

Electron microscopy of macromolecular structures is an approach that is in increasing demand in the field of structural biology. The automation of image acquisition has greatly increased the potential throughput of electron microscopy. Here, the focus is on the possibilities in Scipion to implement flexible and robust image-processing workflows that allow the electron-microscope operator and the user to monitor the quality of image acquisition, assessing very simple acquisition measures or obtaining a first estimate of the initial volume, or the data resolution and heterogeneity, without any need for programming skills. These workflows can implement intelligent automatic decisions and they can warn the user of possible acquisition failures. These concepts are illustrated by analysis of the well known 2.2 Šresolution ß-galactosidase data set.

Sunscreen protection against ultraviolet-induced oxidative stress: evaluation of reduced glutathione levels, metalloproteinase secretion, and myeloperoxidase activity.

Several studies have demonstrated the skin protection by sunscreens considering the aspects skin penetration, photostability, and protection against erythema and sunburn. However, little is known about the effect of topically applied sunscreen formulations on the antioxidant defense, metalloproteinases, and inflammatory processes of skin in response to UVR exposure. Therefore, this study aimed to investigate the use of a cream gel formulation containing the UV filters benzophenone-3, octyl methoxycinnamate, and octyl salicylate to prevent skin damage from a single dose of UVR (2.87 J/cm2). This protective effect was evaluated in vivo by measuring the following biochemical parameters: reduced glutathione levels, secretion of matrix metalloproteinases, and myeloperoxidase activity. The results showed that the sunscreen formulation, despite having sun protection factor (SPF) 15, was not completely effective to protect the skin against GSH depletion, MMP-9 secretion and the inflammatory process induced by UVR. These results demonstrate the importance of analyzing UV-altered biochemical parameters of skin in order to propose new sunscreen formulations that can completely protect skin against UVR-induced damage.

[Analysis of the patient safety culture in hospitals of the Spanish National Health System]. / Análisis de la cultura sobre seguridad del paciente en los hospitales del Sistema Nacional de Salud español.

BACKGROUND AND OBJECTIVES: A safety culture is essential to minimize errors and adverse events. Its measurement is needed to design activities in order to improve it. This paper describes the methods and main results of a study on safety climate in a nation-wide representative sample of public hospitals of the Spanish NHS. MATERIAL AND METHOD: The Hospital Survey on Patient Safety Culture questionnaire was distributed to a random sample of health professionals in a representative sample of 24 hospitals, proportionally stratified by hospital size. Results are analyzed to provide a description of safety climate, its strengths and weaknesses. Differences by hospital size, type of health professional and service are analyzed using ANOVA. RESULTS: A total of 2503 responses are analyzed (response rate: 40%, (93% from professionals with direct patient contact). A total of 50% gave patient safety a score from 6 to 8 (on a 10-point scale); 95% reported < 2 events last year. Dimensions "Teamwork within hospital units" (71.8 [1.8]) and "Supervisor/Manager expectations and actions promoting safety" (61.8 [1.7]) have the highest percentage of positive answers. "Staffing", "Teamwork across hospital units", "Overall perceptions of safety" and "Hospital management support for patient safety" could be identified as weaknesses. Significant differences by hospital size, type of professional and service suggest a generally more positive attitude in small hospitals and Pharmacy services, and a more negative one in physicians. CONCLUSIONS: Strengths and weaknesses of the safety climate in the hospitals of the Spanish NHS have been identified and they are used to design appropriate strategies for improvement.

Development of topical functionalized formulations added with propolis extract: stability, cutaneous absorption and in vivo studies.

Propolis, which is a natural product widely consumed in the folk medicine, is a serious candidate to be applied topically due to its outstanding antioxidant properties. So, the purpose of this study was to develop stable topical formulations added with propolis extract in an attempt to prevent and/or treat the diseases occurring in skin caused by UV radiation. The antioxidant activity using a chemiluminescent method was used to evaluate the functional stability and the permeation/retention in skin of these formulations. In the long-term stability study, the formulations were stored at 25+/-2 degrees C/AH and at 40+/-2 degrees C/70% RH for 360 days. It was found in this study, that the formulations prepared with Polawax showed functional and physical stability in the period of study. In addition, this formulation presented good results in the percutaneous study, allowing the antioxidant compounds present in the propolis extract to reach lower layers in pig ear skin and in the whole hairless mice skin (retention=0.12 and 0.13 microL of propolis/g of skin, respectively). In the in vivo study, it was also suggested that this formulation may be effective in protecting skin from UVB photodamage, nevertheless other assays need to be done in order to have a complete understanding of the protective effect of formulations added with propolis extract.