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.

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.

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.

Estudio observacional, prospectivo y multicéntrico sobre el uso de citrato de fentanilo transmucosa en la práctica clínica habitual para el control de las crisis de dolor irruptivo en pacientes oncológicos / Observational, prospective and multicenter study on the use of transmucosal fentanyl citrate in regular clinical practice for the control of breakthrough pain crises in cancer patients

Objetivo: Evaluar el grado de satisfacción de los pacientes y/o cuidadores con el tratamiento de citrato de fentanilo transmucosa en la gestión de las crisis de dolor irruptivo oncológico en términos de facilidad de uso. Métodos: Se realizó un estudio observacional, prospectivo y multicéntrico con 48 pacientes sometidos a tratamiento de mantenimiento con opioides para el dolor crónico basal provocado por el cáncer y que, además, sufrían crisis de dolor irruptivo para las que estaban recibiendo tratamiento con citrato de fentanilo. La variable principal del estudio fue el grado de satisfacción de los pacientes y/o sus cuidadores con el citrato de fentanilo en el manejo de las crisis de dolor irruptivo oncológico, evaluadas mediante cuestionarios Escala Visual Analógica (EVA). Resultados: El 90,6 % de los pacientes/cuidadores muestran un elevado grado de satisfacción con el empleo de citrato de fentanilo en términos de facilidad de uso (valor medio EVA de 8,2). Por su parte, tanto la valoración general por parte de los pacientes/cuidadores como por parte de los sanitarios ha sido muy positiva (valor medio EVA 7,7). Conclusiones: El citrato de fentanilo es una terapia fácil de usar y eficaz para el tratamiento de las crisis de dolor irruptivo oncológico, con amplia aceptación tanto por parte de pacientes y cuidadores como de los profesionales sanitarios.(AU)

Objective: To assess the degree of satisfaction of patients and/or caregivers with transmucosal fentanyl citrate treatment in the management of breakthrough cancer pain crises in terms of ease of use. Methods: An observational, prospective and multicenter study was carried out with 48 patients undergoing maintenance treatment with opioids for baseline chronic cancer pain and who, in addition, suffered breakthrough pain crises for those who were receiving treatment with fentanyl citrate. The main variable of the study was the degree of satisfaction of the patients and/or their caregivers with fentanyl citrate in the management of breakthrough cancer pain crises, evaluatedby means of Visual Analogue Scale (VAS) questionnaires. Results: 90.6 % of patients/caregivers show a high degree of satisfaction with the use of fentanyl citrate in terms of ease of use (mean VAS value of 8.2). For its part, both the general assessment by the patients/caregivers and by the healthcare professionals has been very positive (mean VAS value 7.7). Conclusions: Fentanyl citrate is an easy-to-use and effective therapy for the treatment of breakthrough cancer pain crises, widely accepted by both patients and caregivers as well as health professionals.(AU)

Adicción frente a seudoadicción / Addiction versus pseudoaddiction

El uso extendido de los opioides, sobre todo los fentanilos de acción rápida para el tratamiento del dolor oncológico, ha producido la aparición de conductas aberrantes asociadas a su administración prolongada y un resurgimiento de antiguos mitos de la morfina como la adicción; hoy día se manejan nuevos términos: seudoadicción, seudotolerancia y afrontamiento químico (chemical coping). En este artículo se analizan los distintos conceptos y comportamientos que deben hacer sospechar estos diagnósticos, los factores asociados al riesgo de mal uso de opioides, así como las recomendaciones terapéuticas para realizar una prescripción segura y eficiente. Para prevenir la aparición de adicción, seudoadicción y afrontamiento químico en un paciente con dolor asociado al cáncer, es necesario un abordaje multidisciplinar de cada una de sus dimensiones (física, psicológica, social y espiritual), con especial interés en el manejo de la ansiedad y la depresión

The widespread use of opioids, especially fast-acting fentanyl preparations for the treatment of cancer pain, has produced the development of aberrant behaviors during the chronic opioid therapy, and a resurgence of old myths about morphine addiction. Nowadays, new terms are used such as pseudoaddiction, pseudotolerance and chemical coping. In this article, we analyze the different concepts and behaviors that should lead clinicians to suspect these diagnoses, the factors associated with opioid misuse and the treatment recommendations for safe and efficient prescription. To prevent the development of addiction, pseudoaddiction and chemical coping in patients with cancer pain, a multidisciplinary approach is required for each of its factors (physical, psychological, social and spiritual), with special emphasis on the management of anxiety and depression