Implementation of triple-scan protocol to evaluate the fit of complete-arch implant-supported fixed prostheses.

Passive fit is essential for multiple-unit implant-supported prostheses. Conventional methods to assess the passivity of complete-arch implant-supported prostheses do not allow 3-dimensional (3D) visualization and quantification of misfit. This report describes the marginal and internal fit evaluation of a complete-arch implant-supported prosthesis by using the triple-scan protocol involving a scanner and a 3D analysis freeware. This technique allows researchers, clinicians, or dental technicians to detect and quantify 3D prosthetic misfit, which may facilitate the preparation for dental appointments and objective measurement of misfit for research studies.

Single-cell spatial explorer: easy exploration of spatial and multimodal transcriptomics.

BACKGROUND: The development of single-cell technologies yields large datasets of information as diverse and multimodal as transcriptomes, immunophenotypes, and spatial position from tissue sections in the so-called 'spatial transcriptomics'. Currently however, user-friendly, powerful, and free algorithmic tools for straightforward analysis of spatial transcriptomic datasets are scarce. RESULTS: Here, we introduce Single-Cell Spatial Explorer, an open-source software for multimodal exploration of spatial transcriptomics, examplified with 9 human and murine tissues datasets from 4 different technologies. CONCLUSIONS: Single-Cell Spatial Explorer is a very powerful, versatile, and interoperable tool for spatial transcriptomics analysis.

Quantitative Muscle Fascicle Tractography Using Brightness-Mode Ultrasound.

A muscle's architecture, defined as the geometric arrangement of its fibers with respect to its mechanical line of action, impacts its abilities to produce force and shorten or lengthen under load. Ultrasound and other noninvasive imaging methods have contributed significantly to our understanding of these structure-function relationships. The goal of this work was to develop a MATLAB toolbox for tracking and mathematically representing muscle architecture at the fascicle scale, based on brightness-mode ultrasound imaging data. The MuscleUS_Toolbox allows user-performed segmentation of a region of interest and automated modeling of local fascicle orientation; calculation of streamlines between aponeuroses of origin and insertion; and quantification of fascicle length, pennation angle, and curvature. A method is described for optimizing the fascicle orientation modeling process, and the capabilities of the toolbox for quantifying and visualizing fascicle architecture are illustrated in the human tibialis anterior muscle. The toolbox is freely available.

Excel Methods to Design and Validate in Microelectronics (Complementary Metal-Oxide-Semiconductor, CMOS) for Biomedical Instrumentation Application.

CMOS microelectronics design has evolved tremendously during the last two decades. The evolution of CMOS devices to short channel designs where the feature size is below 1000 nm brings a great deal of uncertainty in the way the microelectronics design cycle is completed. After the conceptual idea, developing a thinking model to understand the operation of the device requires a good "ballpark" evaluation of transistor sizes, decision making, and assumptions to fulfill the specifications. This design process has iterations to meet specifications that exceed in number of the available degrees of freedom to maneuver the design. Once the thinking model is developed, the simulation validation follows to test if the design has a good possibility of delivering a successful prototype. If the simulation provides a good match between specifications and results, then the layout is developed. This paper shows a useful open science strategy, using the Excel software, to develop CMOS microelectronics hand calculations to verify a design, before performing the computer simulation and layout of CMOS analog integrated circuits. The full methodology is described to develop designs of passive components, as well as CMOS amplifiers. The methods are used in teaching CMOS microelectronics to students of electronic engineering with industrial partner participation. This paper describes an exhaustive example of a low-voltage operational transconductance amplifier (OTA) design which is used to design an instrumentation amplifier. Finally, a test is performed using this instrumentation amplifier to implement a front-end signal conditioning device for CMOS-MEMS biomedical applications.

Propagation of Oscillating Chemical Signals through Reaction Networks.

Akin to electronic systems that can tune to and process signals of select frequencies, systems/networks of chemical reactions also "propagate" time-varying concentration inputs in a frequency-dependent manner. Whereas signals of low frequencies are transmitted, higher frequency inputs are dampened and converted into steady-concentration outputs. Such behavior is observed in both idealized reaction chains as well as realistic signaling cascades, in the latter case explaining the experimentally observed responses of such cascades to input calcium oscillations. These and other results are supported by numerical simulations within the freely available Kinetix web application we developed to study chemical systems of arbitrary architectures, reaction kinetics, and boundary conditions.

Free DICOM de-identification tools in clinical research: functioning and safety of patient privacy.

PURPOSE: To compare non-commercial DICOM toolkits for their de-identification ability in removing a patient's personal health information (PHI) from a DICOM header. MATERIALS AND METHODS: Ten DICOM toolkits were selected for de-identification tests. Tests were performed by using the system's default de-identification profile and, subsequently, the tools' best adjusted settings. We aimed to eliminate fifty elements considered to contain identifying patient information. The tools were also examined for their respective methods of customization. RESULTS: Only one tool was able to de-identify all required elements with the default setting. Not all of the toolkits provide a customizable de-identification profile. Six tools allowed changes by selecting the provided profiles, giving input through a graphical user interface (GUI) or configuration text file, or providing the appropriate command-line arguments. Using adjusted settings, four of those six toolkits were able to perform full de-identification. CONCLUSION: Only five tools could properly de-identify the defined DICOM elements, and in four cases, only after careful customization. Therefore, free DICOM toolkits should be used with extreme care to prevent the risk of disclosing PHI, especially when using the default configuration. In case optimal security is required, one of the five toolkits is proposed. KEY POINTS: • Free DICOM toolkits should be carefully used to prevent patient identity disclosure. • Each DICOM tool produces its own specific outcomes from the de-identification process. • In case optimal security is required, using one DICOM toolkit is proposed.

Proteomics made more accessible.

MS-based proteomics is a bioinformatic-intensive field. Additionally, the instruments and instrument-related and analytic software are expensive. Some free Internet-based proteomics tools have gained wide usage, but there have not been any single bioinformatic framework that in an easy and intuitive way guided the user through the whole process from analyses to submission. Together, these factors may have limited the expansion of proteomics analyses, and also the secondary use (reanalyses) of proteomic data. Vaudel et al. (Proteomics 2014, 14, 1001-1005) are now describing their Compomics framework that guides the user through all the main steps, from the database generation, via the analyses and validation, and through the submission process to PRIDE, a proteomic data bank. Vaudel et al. partly base the framework on tools that they have developed themselves, and partly they are integrating other freeware tools into the workflow. One of the most interesting aspects with the Compomics framework is the possibility of extending MS-based proteomics outside the MS laboratory itself. With the Compomics framework, any laboratory can handle large amounts of proteomic data, thereby facilitating collaboration and in-depth data analyses. The described software also opens the potential for any laboratory to reanalyze data deposited in PRIDE.

NeuroLab: A Set of Graphical Computer Simulations to Support Neuroscience Instruction at the High School and Undergraduate Level.

Young students struggle with concepts that involve the parallel activity of large numbers of similar entities, precisely the kind of concepts that abound in neuroscience. While a direct experience to laboratory work cannot be replaced, such activities include a steep learning curve and may be impractical in certain course settings. This article describes a set of computer simulations of a number of neural processes using NetLogo (Wilensky, 1999), a software environment for the design and implementation of multi-agent simulations that has an intuitive graphical interface and minimal learning curve. NeuroLab is a group of graphical simulations that portray ions, molecules, synapses or cells as individual recognizable agents with particular behaviors, depending on the level at which the particular process is simulated. On a typical assignment, students run the simulation a few times manipulating specific variables by means of buttons, switches and sliders and observe the results of their manipulations on the main window. Many simulations include one or more plots that help visualize statistical data in real time and allow for the testing of experimental hypotheses. Students may repeat the simulation as many times as they wish and collect data or answer questions based on their observations. Assignments may take just a few minutes to perform, but could conceivably be part of more involved activities as designed by the instructor.

A Comparison of Skeletal Muscle Diffusion Tensor Imaging Tractography Seeding Methods.

The internal arrangement of a muscle's fibers with respect to its mechanical line of action (muscle architecture) is a major determinant of muscle function. Muscle architecture can be quantified using diffusion tensor magnetic resonance imaging-based tractography, which propagates streamlines from a set of seed points by integrating vectors that represent the direction of greatest water diffusion (and by inference, the local fiber orientation). Previous work has demonstrated that tractography outcomes are sensitive to the method for defining seed points, but this sensitivity has not been fully examined. To do so, we developed a realistic simulated muscle architecture and implemented four novel methods for tract seeding: seeding along the muscle-aponeurosis boundary with an updated procedure for rounding seed points prior to lookup in the muscle boundary mask and diffusion tensor matrix (APO-3); voxel-based seeding throughout the muscle volume at a user-specified spatial frequency (VXL-1); voxel-based seeding throughout the muscle volume at a variable spatial frequency (VXL-2), and seeding near external and internal muscle boundaries (VXL-3). We then implemented these methods in an example human dataset. The updated aponeurosis seeding procedures allow more accurate and robust tract propagation from seed points. The voxel-based seeding methods had quantification outcomes that closely matched the updated aponeurosis seeding method. Further, the voxel-based methods can accelerate the overall workflow and may be beneficial in high throughput analysis of multi-muscle datasets. Continued evaluation of these methods in a wider range of muscle architectures is warranted.

Early Challenges in the Implementation of Automated CranialRebuild Freeware for Generation of Patient-Specific Cranial Implant Using Additive Manufacturing: A Pilot Project in Review.

Traumatic Brain Injury (TBI) is a significant global health concern, particularly in low- and middle-income countries (LMICs) where access to medical resources is limited. Decompressive craniectomy (DHC) is a common procedure to alleviate elevated intracranial pressure (ICP) following TBI, but the cost of subsequent cranioplasty can be prohibitive, especially in resource-constrained settings. We describe challenges encountered during the beta-testing phase of CranialRebuild 1.0, an automated software program tasked with creating patient-specific cranial implants (PSCIs) from CT images. Two pilot clinical teams in the Philippines and Ukraine tested the software, providing feedback on its functionality and challenges encountered. The constructive feedback from the Philippine and Ukrainian teams highlighted challenges related to CT scan parameters, DICOM file arrays, software limitations, and the need for further software improvements. CranialRebuild 1.0 shows promise in addressing the need for affordable PSCIs in LMICs. Challenges and improvement suggestions identified throughout the beta-testing phase will shape the development of CranialRebuild 2.0, with the aim of enhancing its functionality and usability. Further research is needed to validate the software's efficacy in a clinical setting and assess its cost-effectiveness.

Wind and mini-hydraulic energy potential in the lower basins of the rivers of the mountain ranges, given their topology.

This document intends to auscultate the potential wind and mini-hydraulic energy in the lower basins of the rivers of the mountain ranges; given its topology, taking as an example the lower basin of the Ocoña river in Arequipa Peru, characterized by the canyoning of the mountain range, from the coast (0 masl) to the highlands (4,500 masl), and by the important flow hydraulic when descending from the highlands to the Pacific Ocean, in an area of 16,045 km2. For this, the wind speed has been recorded in anemometers placed at 6, 12, and 18 m above the surface. The section of the river and its speed have also been determined, the height of the river's water level has been recorded; all with an hourly periodicity. With this information we have determined the potential for wind and mini-hydro energy in this characteristic place. Wind speeds in the order of 10 m/s have been obtained, with a persistence of 8 h a day. As for the mini-hydraulic, with a minimum flow of 50 m3/s there is a persistence greater than 90 %. In conclusion, the potential of wind, mini-hydro, and combined energy of the place is sufficient to satisfy various energy demands, from very small to very large.

Technical note: A freeware, equitable approach to dental topographic analysis.

Dental topographic analysis has proved a valuable tool for quantifying dental morphology. Established workflows often use proprietary software for pre-processing dental surfaces, rendering the method expensive and inaccessible to many. This study explores the use of freeware pre-processing alternatives. We tested 4 decimation tools and 13 smoothing tools across 7 different freeware packages. Surfaces generated via proprietary software could not be replicated, but it was possible to obtain statistically similar measurements using freeware. Based on this investigation, we propose a freeware workflow for researchers to conduct dental topographic analysis, with the expectation that their results will be comparable to that obtained through proprietary methods.

A Software Suite for Limb Volume Analysis Applicable in Clinical Settings: Upper Limb Quantification.

In medicine, tridimensional scanning devices produce digital surfaces that replicate the bodies of patients, facilitating anthropometric measurement and limb volume quantification in pathological conditions. Free programs that address this task are not commonly found, with doctors mainly relying on proprietary software. This aspect brings reduced reproducibility of studies and evaluation of alternative measures. A software package made up of three programs has been developed and released together with supporting materials to enhance reproducibility and comparisons between medical centers. In this article, the functions of the programs and steps for volume assessment were introduced together with a pilot study for upper limb volume quantification. This initial experiment aimed to also verify the performance of digital volumes derived from the convex-hull gift-wrapping algorithm and the alternative analysis methods enclosed in the software. Few of these digital volumes are parameter-dependent, requiring a value selection. The experiment was conducted on a small mixed-gender group of young adults without correction for factors like arm dominance or specific physical training. In the sample under investigation, the analysis confirmed the substantial agreement between the clinical and current configurations of digital volumes produced by the package (R 2 interval from 0.93 to 0.97, r ranged from 0.965 to 0.984); in addition, as a general consideration, gender appears as a variable that could influence upper limb volume quantification if a single model is built.

RACINE2.2: A Software Application for Processing and Mapping Spatial Distribution of Root Length Density and Potential Root Extraction Ratio from Root Counts on Trench Profiles.

A method has been developed to measure root intersection density (RID) on a trench-profile in field conditions. Here we describe how 2D spatial distribution mapping of RID can be processed and converted into root length density (RLD) and root distances (ARD) using a new freeware named RACINE2.2. The software also allows a simple modeling of potential root extraction ratio in the soil (PRER). The software contains models calculating RLD, ARD, and PRER from RID for several crops (maize, sorghum, sugarcane, rice, pearl millet, pineapple, eucalyptus). Models may be changed or added into RACINE2.2. RLD, ARD, and PRER are calculated for each spatial unit and can be used to generate 2D maps using RACINE2.2. Data can be exported to a spreadsheet or a surface mapping software for further analysis. It is also possible to import data into RACINE2.2 from a spreadsheet. This application thus makes studies about root-soil interactions, root growth, and root uptake easier. It opens new avenues to characterize root systems to improve root water and nutrient uptake in field conditions.

A non-conformational QSAR study for plant-derived larvicides against Zika Aedes aegypti L. vector.

A set of 263 plant-derived compounds with larvicidal activity against Aedes aegypti L. (Diptera: Culicidae) vector is collected from the literature, and is studied by means of a non-conformational quantitative structure-activity relationships (QSAR) approach. The balanced subsets method (BSM) is employed to split the complete dataset into training, validation and test sets. From 26,775 freely available molecular descriptors, the most relevant structural features of compounds affecting the bioactivity are taken. The molecular descriptors are calculated through four different freewares, such as PaDEL, Mold2, EPI Suite and QuBiLs-MAS. The replacement method (RM) variable subset selection technique leads to the best linear regression models. A successful QSAR equation involves 7-conformation-independent molecular descriptors, fulfiling the evaluated internal (loo, l30%o, VIF and Y-randomization) and external (test set with Ntest = 65 compounds) validation criteria. The practical application of this QSAR model reveals promising predicted values for some natural compounds with unknown experimental larvicidal activity. Therefore, the present model constitutes the first one based on a large molecular set, being a useful computational tool for identifying and guiding the synthesis of new active molecules inspired by natural products.

Available videoconferencing freeware and medical education.

BACKGROUND: Traditionally medical education involves classroom teaching, small group discussions and bed-side clinics. These have become difficult to conduct in times of the COVID-19 pandemic. Video-conferencing software and apps provide pragmatic alternatives for medical education in this scenario. However, the apps are not designed specifically for medical education. In this background, we aimed to review available video-conferencing freeware (platforms/apps) for their suitability in imparting post-graduate medical education. METHODOLOGY: Software and apps were searched on Android and iOS platforms. Freeware were selected based on pre-defined criteria. They were evaluated for features supporting post-graduate medical education like participant numbers, time limit, user comfort and security features. RESULTS: Our search yielded 118 video conferencing software and apps. Of these, 07 free apps met the initial inclusion and exclusion criteria. 'Say Namaste' was included post-hoc. Most apps allowed adequate numbers of participants and were comfortable for users. Only two apps had end-to-end encryption. CONCLUSION: Video-conferencing freeware can serve as a viable alternative for some aspects of medical teaching. Provision of certain additional features would make these apps more effective for post-graduate medical education.

Introduction, comparison, and validation of Meta-Essentials: A free and simple tool for meta-analysis.

We present a new tool for meta-analysis, Meta-Essentials, which is free of charge and easy to use. In this paper, we introduce the tool and compare its features to other tools for meta-analysis. We also provide detailed information on the validation of the tool. Although free of charge and simple, Meta-Essentials automatically calculates effect sizes from a wide range of statistics and can be used for a wide range of meta-analysis applications, including subgroup analysis, moderator analysis, and publication bias analyses. The confidence interval of the overall effect is automatically based on the Knapp-Hartung adjustment of the DerSimonian-Laird estimator. However, more advanced meta-analysis methods such as meta-analytical structural equation modelling and meta-regression with multiple covariates are not available. In summary, Meta-Essentials may prove a valuable resource for meta-analysts, including researchers, teachers, and students.

Bioinactivation: Software for modelling dynamic microbial inactivation.

This contribution presents the bioinactivation software, which implements functions for the modelling of isothermal and non-isothermal microbial inactivation. This software offers features such as user-friendliness, modelling of dynamic conditions, possibility to choose the fitting algorithm and generation of prediction intervals. The software is offered in two different formats: Bioinactivation core and Bioinactivation SE. Bioinactivation core is a package for the R programming language, which includes features for the generation of predictions and for the fitting of models to inactivation experiments using non-linear regression or a Markov Chain Monte Carlo algorithm (MCMC). The calculations are based on inactivation models common in academia and industry (Bigelow, Peleg, Mafart and Geeraerd). Bioinactivation SE supplies a user-friendly interface to selected functions of Bioinactivation core, namely the model fitting of non-isothermal experiments and the generation of prediction intervals. The capabilities of bioinactivation are presented in this paper through a case study, modelling the non-isothermal inactivation of Bacillus sporothermodurans. This study has provided a full characterization of the response of the bacteria to dynamic temperature conditions, including confidence intervals for the model parameters and a prediction interval of the survivor curve. We conclude that the MCMC algorithm produces a better characterization of the biological uncertainty and variability than non-linear regression. The bioinactivation software can be relevant to the food and pharmaceutical industry, as well as to regulatory agencies, as part of a (quantitative) microbial risk assessment.

nmsBuilder: Freeware to create subject-specific musculoskeletal models for OpenSim.

BACKGROUND AND OBJECTIVE: Musculoskeletal modeling and simulations of movement have been increasingly used in orthopedic and neurological scenarios, with increased attention to subject-specific applications. In general, musculoskeletal modeling applications have been facilitated by the development of dedicated software tools; however, subject-specific studies have been limited also by time-consuming modeling workflows and high skilled expertise required. In addition, no reference tools exist to standardize the process of musculoskeletal model creation and make it more efficient. Here we present a freely available software application, nmsBuilder 2.0, to create musculoskeletal models in the file format of OpenSim, a widely-used open-source platform for musculoskeletal modeling and simulation. nmsBuilder 2.0 is the result of a major refactoring of a previous implementation that moved a first step toward an efficient workflow for subject-specific model creation. METHODS: nmsBuilder includes a graphical user interface that provides access to all functionalities, based on a framework for computer-aided medicine written in C++. The operations implemented can be used in a workflow to create OpenSim musculoskeletal models from 3D surfaces. A first step includes data processing to create supporting objects necessary to create models, e.g. surfaces, anatomical landmarks, reference systems; and a second step includes the creation of OpenSim objects, e.g. bodies, joints, muscles, and the corresponding model. RESULTS: We present a case study using nmsBuilder 2.0: the creation of an MRI-based musculoskeletal model of the lower limb. The model included four rigid bodies, five degrees of freedom and 43 musculotendon actuators, and was created from 3D surfaces of the segmented images of a healthy subject through the modeling workflow implemented in the software application. CONCLUSIONS: We have presented nmsBuilder 2.0 for the creation of musculoskeletal OpenSim models from image-based data, and made it freely available via nmsbuilder.org. This application provides an efficient workflow for model creation and helps standardize the process. We hope this would help promote personalized applications in musculoskeletal biomechanics, including larger sample size studies, and might also represent a basis for future developments for specific applications.

Four Models to Guide AT Projects Intending Innovative Technology Development Outcomes.

Generating innovations - including Assistive Technology products or services - requires expertise in project planning and management. University faculty and small businesses ventures often lack such expertise for development and production tasks, yet governments allocate most funding to these sectors. They need help to achieve results. Four evidence-based models now exist to guide investigators intending to generate AT innovations in: 1) standards/guidelines; 2) tools/ instruments; 3) freeware or 4) commercial products.