Clinical implications of a mathematical-geometrical model to predict changes in the anterior arch dimension.

PURPOSE: Anterior arch length (AL) and the alterations in its dimension following incisor movements were shown to be predictable for an individual patient using a mathematical-geometrical model based on a third-degree parabola. Although the model has been validated previously, it is hard to apply in daily orthodontic routine. Thus, the aim of this study was to modify the model using different approaches to allow its establishment in daily routine. METHODS: This retrospective study was based on a study collective, which was described previously and consisted of 50 randomly chosen dental casts and lateral cephalograms taken before (T0) and after (T1) orthodontic treatment with fixed appliances. A JAVA computer program (Oracle, Austin, TX, USA) was developed to predict AL changes following therapeutic changes of arch width, depth or incisor inclination/position, taking the type of tooth movement into account. Performing exemplary AL calculations with the computer program, general rules and nomograms were set up, followed by multiple linear regression analyses to establish easy-to-use regression equations. RESULTS: The JAVA computer program is available for download. Sagittal changes showed more effect on AL than transverse modifications. Protruding incisors increased AL, but also reduced overbite. The extent of alteration in AL depended on the initial depth, width, incisor inclination, tooth movement type and distance between the incisal edge and the centre of rotation. CONCLUSIONS: The computer program precisely predicts individual changes in AL but is time-consuming. The presented regression equations and nomograms, considering metric variables, are easier to apply clinically and the differences compared to the AL calculated by the computer program are negligible.

INSIGHT: in situ heuristic tool for the efficient reduction of grazing-incidence X-ray scattering data.

INSIGHT is a Python-based software tool for processing and reducing 2D grazing-incidence wide- and small-angle X-ray scattering (GIWAXS/GISAXS) data. It offers the geometric transformation of the 2D GIWAXS/GISAXS detector image to reciprocal space, including vectorized and parallelized pixel-wise intensity correction calculations. An explicit focus on efficient data management and batch processing enables full control of large time-resolved synchrotron and laboratory data sets for a detailed analysis of kinetic GIWAXS/GISAXS studies of thin films. It processes data acquired with arbitrarily rotated detectors and performs vertical, horizontal, azimuthal and radial cuts in reciprocal space. It further allows crystallographic indexing and GIWAXS pattern simulation, and provides various plotting and export functionalities. Customized scripting offers a one-step solution to reduce, process, analyze and export findings of large in situ and operando data sets.

Bioinformatics and bioactive peptides from foods: Do they work together?

We live in the Big Data Era which affects many aspects of science, including research on bioactive peptides derived from foods, which during the last few decades have been a focus of interest for scientists. These two issues, i.e., the development of computer technologies and progress in the discovery of novel peptides with health-beneficial properties, are closely interrelated. This Chapter presents the example applications of bioinformatics for studying biopeptides, focusing on main aspects of peptide analysis as the starting point, including: (i) the role of peptide databases; (ii) aspects of bioactivity prediction; (iii) simulation of peptide release from proteins. Bioinformatics can also be used for predicting other features of peptides, including ADMET, QSAR, structure, and taste. To answer the question asked "bioinformatics and bioactive peptides from foods: do they work together?", currently it is almost impossible to find examples of peptide research with no bioinformatics involved. However, theoretical predictions are not equivalent to experimental work and always require critical scrutiny. The aspects of compatibility of in silico and in vitro results are also summarized herein.

ProLEED Studio: software for modeling low-energy electron diffraction patterns.

Low-energy electron diffraction patterns contain precise information about the structure of the surface studied. However, retrieving the real space lattice periodicity from complex diffraction patterns is challenging, especially when the modeled patterns originate from superlattices with large unit cells composed of several symmetry-equivalent domains without a simple relation to the substrate. This work presents ProLEED Studio software, built to provide simple, intuitive and precise modeling of low-energy electron diffraction patterns. The interactive graphical user interface allows real-time modeling of experimental diffraction patterns, change of depicted diffraction spot intensities, visualization of different diffraction domains, and manipulation of any lattice points or diffraction spots. The visualization of unit cells, lattice vectors, grids and scale bars as well as the possibility of exporting ready-to-publish models in bitmap and vector formats significantly simplifies the modeling process and publishing of results.

BioXTAS RAW 2: new developments for a free open-source program for small-angle scattering data reduction and analysis.

BioXTAS RAW is a free open-source program for reduction, analysis and modelling of biological small-angle scattering data. Here, the new developments in RAW version 2 are described. These include improved data reduction using pyFAI; updated automated Guinier fitting and D max finding algorithms; automated series (e.g. size-exclusion chromatography coupled small-angle X-ray scattering or SEC-SAXS) buffer- and sample-region finding algorithms; linear and integral baseline correction for series; deconvolution of series data using regularized alternating least squares (REGALS); creation of electron-density reconstructions using electron density via solution scattering (DENSS); a comparison window showing residuals, ratios and statistical comparisons between profiles; and generation of PDF reports with summary plots and tables for all analysis. Furthermore, there is now a RAW API, which can be used without the graphical user interface (GUI), providing full access to all of the functionality found in the GUI. In addition to these new capabilities, RAW has undergone significant technical updates, such as adding Python 3 compatibility, and has entirely new documentation available both online and in the program.

TEMGYM Basic: transmission electron microscopy simulation software for teaching and training of microscope operation.

An interactive simulation of a transmission electron microscope (TEM) called TEMGYM Basic is developed here, which enables users to understand how to operate and control an electron beam without the need to access an instrument. TEMGYM Basic allows users to familiarize themselves with alignment procedures offline, reducing the time and money required to become a proficient TEM operator. In addition to teaching the basics of electron beam alignments, the software enables users to create bespoke microscope configurations and develop an understanding of how to operate the configurations without sitting at a microscope. TEMGYM Basic also creates static ray diagram figures for a given lens configuration. The available components include apertures, lenses, quadrupoles, deflectors and biprisms. The software design uses first-order ray transfer matrices to calculate ray paths through each electron microscope component, and the program is developed entirely in Python to facilitate compatibility with machine-learning packages for future exploration of automated control.

EDP2PDF: a computer program for extracting a pair distribution function from an electron diffraction pattern for the structural analysis of materials.

Pair distribution function (PDF) analysis is a powerful technique to understand atomic scale structure in materials science. Unlike X-ray diffraction (XRD)-based PDF analysis, the PDF calculated from electron diffraction patterns (EDPs) using transmission electron microscopy can provide structural information from specific locations with high spatial resolution. The present work describes a new software tool for both periodic and amorphous structures that addresses several practical challenges in calculating the PDF from EDPs. The key features of this program include accurate background subtraction using a nonlinear iterative peak-clipping algorithm and automatic conversion of various types of diffraction intensity profiles into a PDF without requiring external software. The present study also evaluates the effect of background subtraction and the elliptical distortion of EDPs on PDF profiles. The EDP2PDF software is offered as a reliable tool to analyse the atomic structure of crystalline and non-crystalline materials.

CX-ASAP: a high-throughput tool for the serial refinement and analysis of crystallographic data collected under varying conditions.

CX-ASAP is a new open-source software project designed to greatly reduce the time required to analyse crystallographic data collected under varying conditions. Scripted in Python3, CX-ASAP can automatically refine, finalize and analyse data collections with wide-ranging temperatures, pressures etc. This is achieved using a reference structure, allowing for quick identification of problems, phase changes and even model comparison. The modular design means that new features and customized scripts can be easily added, tailoring the capabilities to the specific needs of the user. It is envisioned that CX-ASAP will help to close the growing gap between fast collection times and slow data finalization.

Proposal of a Method for Transferring High-Quality Scientific Literature Data to Virtual Patient Cases Using Categorical Data Generated by Bernoulli-Distributed Random Values: Development and Prototypical Implementation.

BACKGROUND: Teaching medicine is a complex task because medical teachers are also involved in clinical practice and research and the availability of cases with rare diseases is very restricted. Automatic creation of virtual patient cases would be a great benefit, saving time and providing a wider choice of virtual patient cases for student training. OBJECTIVE: This study explored whether the medical literature provides usable quantifiable information on rare diseases. The study implemented a computerized method that simulates basic clinical patient cases utilizing probabilities of symptom occurrence for a disease. METHODS: Medical literature was searched for suitable rare diseases and the required information on the respective probabilities of specific symptoms. We developed a statistical script that delivers basic virtual patient cases with random symptom complexes generated by Bernoulli experiments, according to probabilities reported in the literature. The number of runs and thus the number of patient cases generated are arbitrary. RESULTS: We illustrated the function of our generator with the exemplary diagnosis "brain abscess" with the related symptoms "headache, mental status change, focal neurologic deficit, fever, seizure, nausea and vomiting, nuchal rigidity, and papilledema" and the respective probabilities from the literature. With a growing number of repetitions of the Bernoulli experiment, the relative frequencies of occurrence increasingly converged with the probabilities from the literature. For example, the relative frequency for headache after 10.000 repetitions was 0.7267 and, after rounding, equaled the mean value of the probability range of 0.73 reported in the literature. The same applied to the other symptoms. CONCLUSIONS: The medical literature provides specific information on characteristics of rare diseases that can be transferred to probabilities. The results of our computerized method suggest that automated creation of virtual patient cases based on these probabilities is possible. With additional information provided in the literature, an extension of the generator can be implemented in further research.

xrd_simulator: 3D X-ray diffraction simulation software supporting 3D polycrystalline microstructure morphology descriptions.

An open source Python package named xrd_simulator, capable of simulating geometrical interactions between a monochromatic X-ray beam and a polycrystalline microstructure, is described and demonstrated. The software can simulate arbitrary intragranular lattice variations of single crystals embedded within a multiphase 3D aggregate by making use of a tetrahedral mesh representation where each element holds an independent lattice. By approximating the X-ray beam as an arbitrary convex polyhedral region in space and letting the sample be moved continuously through arbitrary rigid motions, data from standard and non-standard measurement sequences can be simulated. This implementation is made possible through analytical solutions to a modified, time-dependent version of the Laue equations. The software, which primarily targets three-dimensional X-ray diffraction microscopy (high-energy X-ray diffraction microscopy) type experiments, enables the numerical exploration of which sample quantities can and cannot be reconstructed for a given acquisition scheme. Similarly, xrd_simulator targets investigations of different measurement sequences in relation to optimizing both experimental run times and sampling.

Very large-scale diffraction investigations enabled by a matrix-multiplication facilitated radial and azimuthal integration algorithm: MatFRAIA.

As synchrotron facilities continue to generate increasingly brilliant X-rays and detector speeds increase, swift data reduction from the collected area detector images to more workable 1D diffractograms becomes of increasing importance. This work reports an integration algorithm that can integrate diffractograms in real time on modern laptops and can reach 10 kHz integration speeds on modern workstations using an efficient pixel-splitting and parallelization scheme. This algorithm is limited not by the computation of the integration itself but is rather bottlenecked by the speed of the data transfer to the processor, the data decompression and/or the saving of results. The algorithm and its implementation is described while the performance is investigated on 2D scanning X-ray diffraction/fluorescence data collected at the interface between an implant and forming bone.

Dental arch definition in computed tomographs using two semi-automatic methods.

Computed tomography is a widely used image examination in dental imaging that provides an accurate location of oral structures and features, including the dental arch, which is an important anatomical feature. This study proposes two new semi-automatic methods for arch definition in CTs, with minimal user effort. This study includes 25 CT examinations. The first method is based on the teeth pulps, and the second one is based on the whole mandible. The methods use thresholding and morphological operations to obtain the arches. The evaluation process includes two different metrics DTW and IoU. For both metrics, the initial results of M1 were very low, but the average performance of M2 can be considered high. The analysis showed that changing the input improves the M1 results substantially. The promising results presented here suggest that these methods can be used as auxiliary tools for the proposed task.

MoloVol: an easy-to-use program for analyzing cavities, volumes and surface areas of chemical structures.

Cavities are a ubiquitous feature of chemical structures encountered in various fields ranging from supramolecular chemistry to molecular biology. They are involved in the encapsulation, transport and transformation of guest molecules, thus necessitating a precise and accessible tool for estimating and visualizing their size and shape. MoloVol, a free user-parametrizable open-source software, developed for calculating a range of geometric features for both unit-cell and isolated structures, is presented here. MoloVol utilizes up to two spherical probes to define cavities, surfaces and volumes. The program was optimized by combining an octree data structure with voxel-partitioned space, allowing for even high-resolution protein structure calculations on reasonable timescales. MoloVol comes with a user-friendly graphic interface along with a command-line interface for high-throughput calculations. It was written in C++ and is available on Windows, macOS and Linux distributions.

Hiperentorno educativo para el aprendizaje de la asignatura Metodología de la Investigación e introducción a la Inferencia Estadística / Educative hyper-environment for learning the subject Methodology of the Investigation and the introduction to Inferencial Statistics for the nursing career

Se elaboró un hiperentorno educativo sobre el programa de estudio de Metodología de la Investigación e introducción a la Inferencia Estadística para la carrera de Enfermería, lo que permitió organizar el acceso a información actualizada y, con ello, favorecer el proceso de enseñanza-aprendizaje. A tal efecto, fueron entrevistados 10 profesores y 57 estudiantes de cuarto año de la Licenciatura en Enfermería de la Facultad de Enfermería-Tecnología de la Salud de Santiago de Cuba; asimismo, se valoró el nivel de efectividad de las acciones realizadas junto con los estudiantes -bajo la orientación de docentes y tutores-, con vistas a beneficiar la formación científico-profesional, lo cual se evidenció en los cambios de actitud y motivación al valorar la significatividad de los resultados, así como en el aumento del número de participantes a los eventos científicos y la mayor calidad del contenido de las investigaciones. Los docentes, tutores y estudiantes evaluaron de adecuado el hiperentorno y se demostró que su aplicación puede contribuir al proceso de enseñanza-aprendizaje del programa de Metodología de la Investigación e introducción a la Inferencia Estadística.

An educative hyper-environment on the study program of the subjects Methodology of Investigation and Introduction to the Inferencial Statistics was implemented, which allowed to organize the access to updated information, and, with this, to improve the teaching-learning process. For this purpose, 10 professors and 57 students belonging to the fourth year of the nursing degree from the Health Technology-Nursing Faculty in Santiago de Cuba city were interviewed, likewise, the effectiveness level of the actions carried out with the students -under the guide of professors and tutors- aimed at improving the scientific and professional training, which was evidenced in the changes in attitude and motivation when evaluating the significance of the results, as well as in the increase in the number of participants in the scientific events and in the higher quality in the contents of the investigations. Teachers, tutors and students evaluated the hyper-environment as adequate and it was shown that its implementation may contribute to the teaching-learning process of the Methodology of Investigations and of the introduction to Inferencial Statistics.

Scipion-ED: a graphical user interface for batch processing and analysis of 3D ED/MicroED data.

Three-dimensional electron diffraction (3D ED)/microcrystal electron diffraction (MicroED) techniques are gaining in popularity. However, the data processing often does not fit existing graphical user interface software, instead requiring the use of the terminal or scripting. Scipion-ED, described in this article, provides a graphical user interface and extendable framework for processing of 3D ED/MicroED data. An illustrative project is described, in which multiple 3D ED/MicroED data sets collected on tetragonal lysozyme were processed with DIALS through the Scipion-ED interface. The ability to resolve unmodelled features in the electrostatic potential map was compared between three strategies for merging data sets.

SAXSDOG: open software for real-time azimuthal integration of 2D scattering images.

In situ small- and wide-angle scattering experiments at synchrotrons often result in massive quantities of data within just seconds. Especially during such beamtimes, processing of the acquired data online, without appreciable delay, is key to obtaining feedback on the failure or success of the experiment. This had led to the development of SAXSDOG, a Python-based environment for real-time azimuthal integration of large-area scattering images. The software is primarily designed for dedicated data pipelines: once a scattering image is transferred from the detector onto the storage unit, it is automatically integrated and pre-evaluated using integral parameters within milliseconds. The control and configuration of the underlying server-based processes is achieved via a graphical user interface, SAXSLEASH, which visualizes the resulting 1D data together with integral classifiers in real time. SAXSDOG further includes a portable 'take-home' version for users that runs on standalone computers, enabling its use in laboratories or at the preferred workspace.

TXM-Sandbox: an open-source software for transmission X-ray microscopy data analysis.

A transmission X-ray microscope (TXM) can investigate morphological and chemical information of a tens to hundred micrometre-thick specimen on a length scale of tens to hundreds of nanometres. It has broad applications in material sciences and battery research. TXM data processing is composed of multiple steps. A workflow software has been developed that integrates all the tools required for general TXM data processing and visualization. The software is written in Python and has a graphic user interface in Jupyter Notebook. Users have access to the intermediate analysis results within Jupyter Notebook and have options to insert extra data processing steps in addition to those that are integrated in the software. The software seamlessly integrates ImageJ as its primary image viewer, providing rich image visualization and processing routines. As a guide for users, several TXM specific data analysis issues and examples are also presented.

Mobile application for couple relationships: Results of a pilot effectiveness study.

Mobile apps in mental health have seen a significant growth in recent years. Most of them are aimed at treating depression, anxiety, and stress disorders using cognitive behavioural therapy methods and relatively few apps are being developed to address interpersonal issues. This study tested the effectiveness of the iCognito Relationship Program, a self-help application for couple relationships based on the chatbot technology. A between-group experimental study was conducted in Russia using the bibliotherapy as a control condition (N = 58, female sample), with results showing that, after 2 weeks, iCognito's users had increased satisfaction, tenderness, constructive communication, as well as commitment to the relationship. Also, indicators for relationship self-efficacy, communicative skills in relationships, and self-esteem regarding relationship skills had significantly increased, while level of conflicts had decreased. A medium effect size was reported for most indicators. The participants of an experimental group expressed a high level of satisfaction with the technology and a generally positive attitude towards the idea of working with a "virtual psychologist"-chatbot on their personal issues. Despite the need to reproduce the research results, iCognito program demonstrates that both mobile application and chatbot technologies can be useful for training individuals' relationship satisfaction and communication skills, and that they can be more efficient in increasing satisfaction and reducing conflict in relationships than self-help books.

En los últimos años, las aplicaciones móviles en la salud mental han crecido considerablemente. La mayoría están orientadas a tratar trastornos de depresión, ansiedad y estrés usando métodos de la terapia cognitivo-conductual, pero se están desarrollando relativamente pocas aplicaciones para abordar problemas interpersonales. En este estudio se evaluó la eficacia de la iCognito Relationship Program, una aplicación de autoayuda para las relaciones de pareja basada en la tecnología de bots de charla. Se realizó un estudio experimental intergrupal en Rusia usando la biblioterapia como condición de control (N = 58, muestra femenina), cuyos resultados demostraron que, después de 2 semanas, los usuarios de iCognito habían aumentado la satisfacción, la amabilidad, la comunicación constructiva y el compromiso con la relación. Además, los indicadores de la autoeficacia de la relación, las habilidades comunicativas en las relaciones y la autoestima con respecto a las habilidades relacionales habían aumentado significativamente, mientras que el nivel de conflictos había disminuido. Se informó un tamaño del efecto mediano para la mayoría de los indicadores. Los participantes de un grupo experimental expresaron un alto nivel de satisfacción con la tecnología y una actitud generalmente positiva hacia la idea de trabajar con un "psicólogo virtual" en un bot de charla sobre sus problemas personales. A pesar de la necesidad de reproducir los resultados de la investigación, el programa iCognito demuestra que tanto la aplicación móvil como las tecnologías de bot de charla pueden ser útiles para formar las habilidades de satisfacción con la relación y de comunicación de las personas, y que pueden ser más eficaces que los libros de autoayuda a la hora de aumentar la satisfacción y reducir el conflicto en las relaciones.

Ventilator Mode Finder: An Android application to find equivalent of a mode on different ventilators.

There are hundreds of ventilator modes on different ventilators. Despite different names, many are similar in functions and options. Educational institutions only teach a limited collection of ventilator modes of a few numbers of models; therefore, graduates may have substantial difficulties encountering new ventilator models with unfamiliar mode names on them. In this article, an Android application for finding similar modes on different ventilators is presented. The aim is to help an intensive care practitioner to easily find a familiar mode on a new ventilator.

CrystalExplorer: a program for Hirshfeld surface analysis, visualization and quantitative analysis of molecular crystals.

CrystalExplorer is a native cross-platform program supported on Windows, MacOS and Linux with the primary function of visualization and investigation of molecular crystal structures, especially through the decorated Hirshfeld surface and its corresponding two-dimensional fingerprint, and through the visualization of void spaces in the crystal via isosurfaces of the promolecule electron density. Over the past decade, significant changes and enhancements have been incorporated into the program, such as the capacity to accurately and quickly calculate and visualize quantitative intermolecular interactions and, perhaps most importantly, the ability to interface with the Gaussian and NWChem programs to calculate quantum-mechanical properties of molecules. The current version, CrystalExplorer21, incorporates these and other changes, and the software can be downloaded and used free of charge for academic research.