Multifractal approach for a biological porous media: Human dentin case.

A multifractal characterization to human dentin porosity is made. Micrographs of human dentin samples gotten from scanning electron microscopy (SEM) were studied in order to characterize porosity. We got the generalized dimensions (multifractal moments) D q for pore space and matrix skeleton on gray scale and binary images for samples of both gender. For the case, we found that superficial porosity η s is linked to mass fractal dimension D 0 in an approximately linear relationship as D 0 ≈ η s + d ¯ for binary images. In addition, probability density distribution (PDD) for pore diameters is found a normal PDD type. Other quantities of interest like mean, standard deviation, maximum and minimum pore diameters, voit ratios, and percentage of chemical composition are reported. RESEARCH HIGHLIGHTS: SEM sample, images and procedure for multifractal analysis are detailed. Micro patterns in grayscale are multifractal and in binary scale are monofractals. Superficial porosity is relate to mass fractal dimension approximately linearly. From the porosity values, voit ratios are determined. Pores diameters obey a normal PDD.

Self-perception of dual career barriers and athletic identity in student-athletes with disabilities according to disability type and level of professionalization.

The objective of this study was to analyze the perceived barriers to dual career success and athletic identity of student-athletes according to disability type and level of professionalization. The final sample consisted of 203 student-athletes with disabilities from five European countries. The questionnaires used were ESTPORT, EBBS and AIMS. Depending on disability type, it was found that student-athletes with hearing and physical impairment showed the highest difficulty in reconciling sports and studies (p = 0.001); that student-athletes with a hearing impairment showed the highest score in the barrier 'the cost of education is high' (p = 0.023); that student-athletes with a physical impairment had the highest scores in the barrier 'Exercise tires me' (p = 0.013); that student-athletes with cerebral palsy showed the highest scores in the barrier 'I do not have enough university/educational institution support' (p = 0.014) and 'Exercise facilities do not have convenient timetables for me' (p = 0.001). Depending on sports professionalization level, semi-professional student-athletes showed the highest values in the barrier 'the university/educational institution is far from my training center' (p = 0.040); while professional student-athletes had the highest score in the barrier 'exercise takes too much time from family responsibilities' (p = 0.034). In most of the variables related to identity as athletes, professional student-athletes showed the highest values, followed by semi-professional athletes (p = 0.043- < 0.001). In conclusion, the self-perception of barriers is quite relevant, with differences arising from disability type and level of professionalization, whereas the identity as an athlete is only different according to the level of professionalization.

An efficient removal approach for degradation of metformin from aqueous solutions with sulfate radicals.

Metformin consumption for diabetes treatment is increasing, leading to its presence in wastewater treatment plants where conventional methods cannot remove it. Therefore, this work aims to analyze the performance of advanced oxidation processes using sulfate radicals in the degradation of metformin from water. Experiments were performed in a photoreactor provided with a low-pressure Hg lamp, using K2S2O8 as oxidant and varying the initial metformin concentration (CA0), oxidant concentration (Cox), temperature (T), and pH in a response surface experimental design. The degradation percentages ranged from 26.1 to 87.3%, while the mineralization percentages varied between 15.1 and 64%. Analysis of variance (ANOVA) showed that the output variables were more significantly affected by CA0, Cox, and T. Besides, a reduction of CA0 and an increase of Cox up to 5000 µM maximizes the metformin degradation since the generation of radicals and their interaction with metformin molecules are favored. For the greatest degradation percentage, the first order apparent rate constant achieved was 0.084 min-1. Furthermore, while in acidic pH, temperature benefits metformin degradation, an opposite behavior is obtained in a basic medium because of recombination and inhibition reactions. Moreover, three degradation pathways were suggested based on the six products detected by HPLC-MS: N-cyanoguanidine m/z = 85; N,N-dimethylurea m/z = 89; N,N-dimethyl-cyanamide m/z = 71 N,N-dimethyl-formamide m/z = 74; glicolonitrilo m/z = 58; and guanidine m/z = 60. Finally, it was shown that in general the toxicity of the degradation byproducts was lower than the toxicity of metformin toward Chlamydomonas reinhardtii.

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.

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.

Improvements in the radiochemical method for separating 226Ra in solid samples through coprecipitation with BaSO4.

The aim of this work was to improve the commonly used method for 226Ra determination in water and to establish its application in solid samples. This method is based on the coprecipitation of Ra with BaSO4 and gross alpha counting of the precipitate. An exhaustive study of the coprecipitation behaviour of the most abundant cations present in solid samples was performed to avoid incorrect radiochemical yields. As a result, it was considered necessary to introduce two new purification steps into the conventional method. Likewise, two nuclides, 241Am and 226Ra, were compared to obtain the mass efficiency curve given their different behaviour in the coprecipitation process. While Ra behaves similarly to Ba, Am coprecipitates, forming mixed crystals that may behave differently in the self-absorption process. The influence of the cations on the chemical yield with no precipitate purification was: Sr2+≫Fe3+>Mg2+≈Ca2+>K+≈Na+. The method was successfully applied to soil, sediment, and plant ash samples.

[Update on prosthesis for partial hand and finger amputations]. / Actualización en prótesis para amputaciones parciales de mano y dedos.

Partial hand and finger amputations are relatively rare but devastating due to the consequences they provoque. In addition, they are more likely than lower limb amputations in car accidents, work accidents and by certain weapons of war. Men are going to have a much higher risk of traumatic amputation than women, with a rate 6.6 times higher. Fitting can be a complex process and a challenge for professionals. For this reason, it is important to know all the options available on the market that can meet the needs of patients, from cosmetic to myoelectric prostheses. Fitting requires the coordinated activity of a multiassistant clinical work team, the center of the team being the person who has suffered the amputation, who must have all the information possible to be able to actively participate in decision-making.

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.

SARS-CoV-2 contact tracing among disadvantaged populations during epidemic intervals should be a priority strategy: results from a pilot experiment in Barcelona.

OBJECTIVES: The aim of this study was to trace contacts of coronavirus disease 2019 (COVID-19) hospitalised patients and determine the risk factors of infection in urban areas. STUDY DESIGN: Longitudinal analysis of contacts identified from index cases. METHODS: A contact tracing study was carried out in the Northern Metropolitan area of Barcelona, Spain, during the inter-epidemic lapse of May to July 2020, a period of low SARS-CoV-2 incidence. Index cases were notified from the referral hospital. Contacts were traced and followed up for 14 days. Reverse transcription polymerase chain reaction was performed on day 0 and day 14 for contacts. RESULTS: In total, 368 contacts were identified from 81 index cases (median of seven contacts per index case), from which 308 were traced successfully. The median age of contacts was 28 years, 62% (223 of 368) were men. During the follow-up period, 100 contacts tested positive for COVID-19 (32.5% [95% confidence interval {CI} = 27.3-38.0]), with a secondary infection rate of 48.3% (95% CI = 40.8-55.9) among housemates. Clusters of index and respective contacts tended to aggregate within disadvantaged neighbourhoods (P < 0.001), and non-national index cases (N = 28, 34.1%) resulted in higher secondary infection rates compared with nationals (51.0% [95% CI = 41.0-60.9] vs 22.3% [95% CI = 16.8-28.8]; P < 0.001). CONCLUSIONS: Disadvantaged communities experience a disproportionate burden of COVID-19 and may act as infection reservoirs. Contact tracing with a cross-cutting approach among these communities is required, especially during inter-epidemic periods.

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.

Effect of organic and conventional farming on soil bacterial diversity of pecan tree (Carya illinoensis K. Kosh) orchard across two phenological stages.

We described the bacterial diversity of walnut grove soils under organic and conventional farming. The bacterial communities of rhizospheric and nonrhizospheric soils of pecan tree (Carya illinoensis K. Koch) were compared considering two phenological stages (sprouting and ripening). Sixteen operational taxonomic units (OTUs) were identified significantly more abundant according to the plant development, only one according to the farming condition, and none according to the soil origin. The OTUs specificaly abundant according to plant development included Actinobateria (2) and Betaproteobacteria (1) related OTUs more abundant at the sprouting stage, while at the fruit ripening (FR) stage the more abundant OTUs were related to Actinobacteria (6), Alphaproteobacteria (6), and unclassified Bacteria (1). The Gaiellaceae OTU18 (Actinobacteria) was more abundant under conventional farming. Thus, our study revealed that the plant development stage was the main factor shaping the bacterial community structure, while less influence was noticed for the farming condition. The bacterial communities exhibited specific metabolic capacities, a large range of carbon sources being used at the FR stage. The identified OTUs specifically more abundant represent indicators providing useful information on soil condition, potential tools for the management of soil bacterial communities.

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.

[Use of the Myo Plus system in transradial amputation patients]. / Utilidad del sistema Myo Plus en pacientes amputados transradiales.

Upper limb amputations are uncommon but cause severe disability. It is usually of traumatic origin and in young males less than 40 years-old, and active. The frequency of amputation at transradial level is around 35% of cases, with the myoelectric prosthesis achieving greater functionality. Around 25% of the patients give up using of the prosthesis, due to its complexity of use by means of 2 conventional electrodes, one of the most common causes for giving up. The Myo Plus system with an 8-channel electromyograph helps the patient to control the prosthesis using the phantom limb and achieving the closing, opening, and pronation-supination patterns of the hand in a time less than the conventional one and more easily. It also leads to less rehabilitation time, decreasing costs and unnecessary travel, without increasing the time for the manufacture of the socket.

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.

Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy.

Single-particle analysis by electron microscopy is a well established technique for analyzing the three-dimensional structures of biological macromolecules. Besides its ability to produce high-resolution structures, it also provides insights into the dynamic behavior of the structures by elucidating their conformational variability. Here, the different image-processing methods currently available to study continuous conformational changes are reviewed.

Using Scipion for stream image processing at Cryo-EM facilities.

Three dimensional electron microscopy is becoming a very data-intensive field in which vast amounts of experimental images are acquired at high speed. To manage such large-scale projects, we had previously developed a modular workflow system called Scipion (de la Rosa-Trevín et al., 2016). We present here a major extension of Scipion that allows processing of EM images while the data is being acquired. This approach helps to detect problems at early stages, saves computing time and provides users with a detailed evaluation of the data quality before the acquisition is finished. At present, Scipion has been deployed and is in production mode in seven Cryo-EM facilities throughout the world.

Blind estimation of DED camera gain in Electron Microscopy.

The introduction of Direct Electron Detector (DED) videos in the Electron Microscope field has boosted Single Particle Analysis to a point in which it is currently considered to be a key technique in Structural Biology. In this article we introduce an approach to estimate the DED camera gain at each pixel from the movies themselves. This gain is needed to have the set of recorded frames into a coherent gray level range, homogeneous over the whole image. The algorithm does not need any other input than the DED movie itself, being capable of providing an estimate of the camera gain image, helping to identify dead pixels and cases of incorrectly calibrated cameras. We propose the algorithm to be used either to validate the experimentally acquired gain image (for instance, to follow its possible change over time) or to verify that there is no residual gain image after experimentally correcting for the camera gain. We show results for a number of DED camera models currently in use (DE, Falcon II, Falcon 3, and K2).

Tumor infiltrating lymphocytes in acral lentiginous melanoma: a study of a large cohort of cases from Latin America.

PURPOSE: Acral lentiginous melanoma (ALM) is a poor prognosis subtype and is the most prevalent in non-Caucasian populations. The presence of tumor infiltrating lymphocytes (TILs) has been associated with poor prognosis in melanoma. A large cohort of ALM cases was studied to determine status of TIL and its association with outcome. METHODS: All patients with cutaneous melanoma presenting from 2005 to 2012 at Instituto Nacional de Enfermedades Neoplasicas in Peru were retrospectively identified. Clinicopathological information was obtained from the medical charts. A prospective evaluation of TIL was performed. Analysis of association between ALM and clinicopathological features including TIL as well as survival analysis compared the outcome of ALM to whole group and extremity NALM was performed. RESULTS: 537 ALM from a total of 824 cutaneous melanoma cases were studied. Older age (p = 0.022), higher Breslow (p = 0.008) and ulceration (p < 0.001) were found to be more frequent in ALM. Acral had worse overall survival (OS) compared with the whole group (p = 0.04). Clinical stage (CS) I-II patients had a median OS of 5.3 (95% CI 4.3-6.2) for ALM and 9.2 (95% CI 5.0-7.0) for extremity NALM (p = 0.016). Grade 0 (absence of TIL), I, II and III were found in 7.5, 34.5, 32.1, and 25.9%, respectively. Lower TIL grade was associated with larger tumor size (p = 0.003), higher Breslow (p = 0.001), higher Clark level (p = 0.007), higher CS (p = 0.002), extremity location (p = 0.048), histological subtype ALM (p = 0.024) and better OS (p = 0.001). CONCLUSIONS: ALM is highly prevalent in Peru and carries poor outcome. Lower TIL levels were associated with poor outcome and ALM.