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The steep increase in carbon dioxide (CO 2 ) emissions has created great concern due to its role in the greenhouse effect and global warming. One approach to mitigate CO 2 levels involves its application in specific technologies. In this context, CO 2 can be used for a more sustainable synthesis of polycarbonates (CO 2 -PCs). In this research, CO 2 -PC films and composites with multiwalled carbon nanotubes (MWCNTs, ranging from 0.2 to 7.0 wt.%) have been prepared to achieve more sustainable multifunctional sensing devices. The inclusion of the carbonaceous fillers allows for the electrical conductivity to be enhanced, reaching the percolation threshold (P c ) at 0.1 wt.% MWCNTs and a maximum electrical conductivity of 0.107 S·m -1 for the composite containing 1.5 wt.% MWCNTs. The composite containing 3.0 wt.% MWCNTs was also studied, showing a stable and linear response under temperature variations from 40 to 100 °C and from 30 to 45 °C, with a sensitivity of 1.3 × 10 -4 °C -1 . Thus, this investigation demonstrates the possibility of employing CO 2 -derived PC/MWCNT composites as thermoresistive sensing materials, allowing for the transition towards sustainable polymer-based electronics.

Electron tomography is an imaging technique that allows for the elucidation of three-dimensional structural information of biological specimens in a very general context, including cellular in situ observations. The approach starts by collecting a set of images at different projection directions by tilting the specimen stage inside the microscope. Therefore, a crucial preliminary step is to precisely define the acquisition geometry by aligning all the tilt images to a common reference. Errors introduced in this step will lead to the appearance of artifacts in the tomographic reconstruction, rendering them unsuitable for the sample study. Focusing on fiducial-based acquisition strategies, this work proposes a deep-learning algorithm to detect misalignment artifacts in tomographic reconstructions by analyzing the characteristics of these fiducial markers in the tomogram. In addition, we propose an algorithm designed to detect fiducial markers in the tomogram with which to feed the classification algorithm in case the alignment algorithm does not provide the location of the markers. This open-source software is available as part of the Xmipp software package inside of the Scipion framework, and also through the command-line in the standalone version of Xmipp., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)

We propose two new measures of resolution anisotropy for cryogenic electron microscopy maps: Fourier shell occupancy (FSO), and the Bingham test (BT). FSO varies from 1 to 0, with 1 representing perfect isotropy, and lower values indicating increasing anisotropy. The threshold FSO = 0.5 occurs at Fourier shell correlation resolution. BT is a hypothesis test that complements the FSO to ensure the existence of anisotropy. FSO and BT allow visualization of resolution anisotropy. We illustrate their use with different experimental cryogenic electron microscopy maps., (© 2023. The Author(s), under exclusive licence to Springer Nature America, Inc.)

Image-processing pipelines require the design of complex workflows combining many different steps that bring the raw acquired data to a final result with biological meaning. In the image-processing domain of cryo-electron microscopy single-particle analysis (cryo-EM SPA), hundreds of steps must be performed to obtain the three-dimensional structure of a biological macromolecule by integrating data spread over thousands of micrographs containing millions of copies of allegedly the same macromolecule. The execution of such complicated workflows demands a specific tool to keep track of all these steps performed. Additionally, due to the extremely low signal-to-noise ratio (SNR), the estimation of any image parameter is heavily affected by noise resulting in a significant fraction of incorrect estimates. Although low SNR and processing millions of images by hundreds of sequential steps requiring substantial computational resources are specific to cryo-EM, these characteristics may be shared by other biological imaging domains. Here, we present Scipion, a Python generic open-source workflow engine specifically adapted for image processing. Its main characteristics are: (a) interoperability, (b) smart object model, (c) gluing operations, (d) comparison operations, (e) wide set of domain-specific operations, (f) execution in streaming, (g) smooth integration in high-performance computing environments, (h) execution with and without graphical capabilities, (i) flexible visualization, (j) user authentication and private access to private data, (k) scripting capabilities, (l) high performance, (m) traceability, (n) reproducibility, (o) self-reporting, (p) reusability, (q) extensibility, (r) software updates, and (s) non-restrictive software licensing., Competing Interests: The authors declare no competing interests exist., (© The Author(s) 2023.)

Objective: The first-order absorption is a common model used in Pharmacokinetics. The absorption of some drugs follows carrier mediated transport. It has been proposed that the amount of drug available may saturate the transport mechanism resulting in an absorption slower than the one predicted by the first-order model. Saturable absorption has been modeled at the differential equation level by substituting the constant rate absorption by a Hill kinetics absorption. However, its exact solution is so far unknown. The goal of this is to know the exact solution of different Hill kinetic absorption models., Methods: We start defining different absorption models and increasing then their complexity. The simplest case is the first-order absorption model and the most complex will be a generalized Hill kinetic absorption model. The differential equation of each model is integrated., Results: The complexity of the models their solutions may be not expressed in a close-form, or in term of elementary functions. We obtain and discuss the exact solutions of the different Hill kinetics absorption models. To do that, the solutions are studied according to the possible values of the free parameters of the models. We show the differences between models through simulations., Conclusions: The knowledge of closed-form solutions allows to illustrate the differences between the different absorption models and minimizes the errors of numerical integration., (© 2022. The Author(s).)

Resurrection plants are able to deal with complete dehydration of their leaves and then recover normal metabolic activity after rehydration. Only a few resurrection species are exposed to freezing temperatures in their natural environments, making them interesting models to study the key metabolic adjustments of freezing tolerances. Here, we investigate the effect of cold and freezing temperatures on physiological and biochemical changes in the leaves of Haberlea rhodopensis under natural and controlled environmental conditions. Our data shows that leaf water content affects its thermodynamical properties during vitrification under low temperatures. The changes in membrane lipid composition, accumulation of sugars, and synthesis of stress-induced proteins were significantly activated during the adaptation of H. rhodopensis to both cold and freezing temperatures. In particular, the freezing tolerance of H. rhodopensis relies on a sucrose/hexoses ratio in favor of hexoses during cold acclimation, while there is a shift in favor of sucrose upon exposure to freezing temperatures, especially evident when leaf desiccation is relevant. This pattern was paralleled by an elevated ratio of unsaturated/saturated fatty acids and significant quantitative and compositional changes in stress-induced proteins, namely dehydrins and early light-induced proteins (ELIPs). Taken together, our data indicate that common responses of H. rhodopensis plants to low temperature and desiccation involve the accumulation of sugars and upregulation of dehydrins/ELIP protein expression. Further studies on the molecular mechanisms underlying freezing tolerance (genes and genetic regulatory mechanisms) may help breeders to improve the resistance of crop plants.

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.

Cryo-electron microscopy (CryoEM) has become a vital technique in structural biology. It is an interdisciplinary field that takes advantage of advances in biochemistry, physics, and image processing, among other disciplines. Innovations in these three basic pillars have contributed to the boosting of CryoEM in the past decade. This work reviews the main contributions in image processing to the current reconstruction workflow of single particle analysis (SPA) by CryoEM. Our review emphasizes the time evolution of the algorithms across the different steps of the workflow differentiating between two groups of approaches: analytical methods and deep learning algorithms. We present an analysis of the current state of the art. Finally, we discuss the emerging problems and challenges still to be addressed in the evolution of CryoEM image processing methods in SPA.

Phase control is a critical parameter in polarization measurements. It is well known that a proper combination of wave plates allows to obtain achromatic phase shift, i.e., a constant retardation in certain spectral ranges. This paper is focused on a different, but more useful, goal, as it is to achieve customized variable retarders in broad spectral ranges. To do that, a merit function was used to measure the similarity between the overall phase shift of the wave plate combinations and the desired target. The control variables are the thicknesses and orientations of the wave plates. All possible combinations with four and five wave plates of quartz and M g F 2 were analyzed, but our approach can be perfectly extended to deal with more wave plates. The result of an optimization process determines the thicknesses and orientations of the wave plates, which results in the closest retarder to the desired one. Numerical results show deviations below 10% between the target and the obtained retardation. These systems are of special interest in those fields and instruments in which polarization control plays a fundamental role.

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., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022. Published by Elsevier Inc.)

The well-known compound tetrakis(tert-butylammonium)-cyclo-tetrametavanadate (V), [(CH 3 ) 3 CNH 3 ] 4 [V 4 O 12 ] (1h_RT), which crystallizes in the tetragonal I4/m space group, undergoes an irreversible solid state transformation upon heating, constituting one of the few examples in which the initial and the final stages are structurally characterized by sc-XRD. Now, we observed the ability of the same compound to undergo an additional single-crystal-to-single-crystal (SCSC) transformation upon thermal stimuli, but this time at low temperatures (153 K). Compound 1h_RT contains a discrete unprotonated [V 4 O 12 ] 4- tetrahedral anion in which V and O bridging atoms are coplanar. In both phases, these tetrameric anions are linked through tert-butylammonium cations in an extensive network of hydrogen bonds, but at low temperatures, this phase loses its characteristic O-V-O coplanarity, with the resulting rearrangement of the crystal packing and hydrogen-bond network which provide its reversibility at low temperatures. Again, the initial and final stages have been characterized structurally by sc-XRD.

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., (open access.)

Xmipp is an open-source software package consisting of multiple programs for processing data originating from electron microscopy and electron tomography, designed and managed by the Biocomputing Unit of the Spanish National Center for Biotechnology, although with contributions from many other developers over the world. During its 25 years of existence, Xmipp underwent multiple changes and updates. While there were many publications related to new programs and functionality added to Xmipp, there is no single publication on the Xmipp as a package since 2013. In this article, we give an overview of the changes and new work since 2013, describe technologies and techniques used during the development, and take a peek at the future of the package.