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Background: The HHUS market is very complex due to a multitude of equipment variants and several different device manufacturers. Only a few studies have compared different HHUS devices under clinical conditions. We conducted a comprehensive prospective observer study with a direct comparison of nine different HHUS devices in terms of B-scan quality, device handling, and software features under abdominal imaging conditions. Methods: Nine different HHUS devices (Butterfly iQ+, Clarius C3HD3, D5CL Microvue, Philips Lumify, SonoEye Chison, SonoSite iViz, Mindray TE Air, GE Vscan Air, and Youkey Q7) were used in a prospective setting by a total of 12 experienced examiners on the same subjects in each case and then assessed using a detailed questionnaire regarding B-scan quality, handling, and usability of the software. The evaluation was carried out using a point scale (5 points: very good; 1 point: insufficient). Results: In the overall evaluation, Vscan Air and SonoEye Chison achieved the best ratings. They achieved nominal ratings between "good" (4 points) and "very good" (5 points). Both devices differed significantly (p < 0.01) from the other seven devices tested. Among the HHUS devices, Clarius C3HD3 and Vscan Air achieved the best results for B-mode quality, D5CL Microvue achieved the best results for device handling, and SonoEye Chison and Vscan Air achieved the best results for software. Conclusions: This is the first comprehensive study to directly compare different HHUS devices in a head-to-head manner. While the majority of the tested devices demonstrated satisfactory performance, notable discrepancies were observed between them. In particular, the B-scan quality exhibited considerable variation, which may have implications for the clinical application of HHUS. The findings of this study can assist in the selection of an appropriate HHUS device for specific applications, considering the clinical objectives and acknowledging the inherent limitations. [ABSTRACT FROM AUTHOR]

As part of the research carried out in the field of processing systems and the production process of oil-hydraulic cylinders of large dimensions and power, the specifics of fluid power transmission, in the functioning of hydropower facilities, were analyzed. The research also includes the optimization of the physical–mathematical model of non-stationary processes, which take place inside the chamber of a large hydrocylinder. In parallel with the definition of the optimization model, the work parameters that affect the process of fluid flow and piston movement were determined. The operating and technological construction parameters of the hydraulic cylinder, which most significantly affect the operation of the hydraulic cylinder, were defined, and the observed parameters were optimized, based on which a prototype with improved characteristics compared to existing solutions was realized. [ABSTRACT FROM AUTHOR]

In Internal Radiotherapy, radiopharmaceutical dosimetry provides an accurate estimation of absorbed radiation doses to organs at risk and tumours. In this paper Velocity Theranostics (Varian Medical Systems), is investigated. Its performances are compared to OLINDA 2.0 in both an anthropomorphic phantom and a group of patients. Velocity Theranostics was evaluated with a cohort of patients (15) treated with 177Lu radiolabelled peptides. The absorbed doses were calculated for the liver, spleen and kidneys, separately with OLINDA 2.0 and Velocity Theranostics using the same set of images. To reduce the contribution of Time-integrated activities (TIAs) on the results and to merely compare the dose calculation algorithms, the OLINDA 2.0 absorbed doses were calculated using the TIA values calculated in Velocity Theranostics. The absorbed doses from Velocity Theranostics were found to be correlated with the doses from OLINDA 2.0 with the TIAs from Theranostics (Lin's coefficient = 0.894 and R2 = 0.9531). Absorbed doses from Velocity Theranostics are reliable at least as reliable as those for OLINDA 2.0, with many advantages regarding accuracy of calculations and robustness. In conclusion, the personalisation of dosimetry may be totally fulfilled by computational systems for absorbed dose in internal radiotherapy, equipped with a complete workflow and borrowed from external radiotherapy. [ABSTRACT FROM AUTHOR]

Calcium imaging, especially two-photon imaging, has become essential in neuroscience for studying neuronal and astrocytic activity under in vivo and in vitro conditions. Current advances in the development of calcium sensors as well as imaging hardware enable high-frequency measurements of calcium signals in hundreds of cells simultaneously. The analysis of these large datasets requires special tools and usually a certain level of programming experience. Despite advancements in calcium imaging analysis software development, significant gaps remain, particularly for data acquired at a high sampling rate that would allow for the spectral analysis of calcium signals. The FluoAnalysis MATLAB toolbox addresses these gaps by offering a comprehensive solution for analyzing simultaneously measured calcium imaging and electrophysiological data. It features both GUI-based and command-line approaches, emphasizing frequency domain analysis to reveal network-level oscillatory signals linked to single-cell activity. In addition, the toolbox puts special emphasis on differentiating between astrocytes and neurons, revealing the interactions between the network activity of the two major cell types of the brain. It facilitates a streamlined workflow for data loading, ROI identification, cell classification, fluorescence intensity calculation, spectral analysis, and report generation, supporting both manual and automated high-throughput analysis. This versatile platform enables the comprehensive analysis of large imaging datasets. In conclusion, the FluoAnalysis MATLAB toolbox provides a robust and versatile platform for the integrated analysis of calcium imaging and electrophysiological data, supporting diverse neuroscience research applications. [ABSTRACT FROM AUTHOR]

Soft condensed matter is challenging to study due to the vast time and length scales that are necessary to accurately represent complex systems and capture their underlying physics. Multiscale simulations are necessary to study processes that have disparate time and/or length scales, which abound throughout biology and other complex systems. Herein we present ezAlign, an open-source software for converting coarse-grained molecular dynamics structures to atomistic representation, allowing multiscale modeling of biomolecular systems. The ezAlign v1.1 software package is publicly available for download at github.com/LLNL/ezAlign. Its underlying methodology is based on a simple alignment of an atomistic template molecule, followed by position-restraint energy minimization, which forces the atomistic molecule to adopt a conformation consistent with the coarse-grained molecule. The molecules are then combined, solvated, minimized, and equilibrated with position restraints. Validation of the process was conducted on a pure POPC membrane and compared with other popular methods to construct atomistic membranes. Additional examples, including surfactant self-assembly, membrane proteins, and more complex bacterial and human plasma membrane models, are also presented. By providing these examples, parameter files, code, and an easy-to-follow recipe to add new molecules, this work will aid future multiscale modeling efforts. [ABSTRACT FROM AUTHOR]

In the current digital landscape, artificial intelligence-driven automation has revolutionized efficiency in various areas, enabling significant time and resource savings. However, the reliability and efficiency of software systems remain crucial challenges. To address this issue, a generation of self-adaptive software has emerged with the ability to rectify errors and autonomously optimize performance. This study focuses on the development of self-adaptive software designed for pre-programmed tasks on the Internet. The software stands out for its self-adaptation, automation, fault tolerance, efficiency, and robustness. Various technologies such as Python, MySQL, Firebase, and others were employed to enhance the adaptability of the software. The results demonstrate the effectiveness of the software, with a continuously growing self-adaptation rate and improvements in response times. Probability models were applied to analyze the software's effectiveness in fault situations. The implementation of virtual cables and multiprocessing significantly improved performance, achieving higher execution speed and scalability. In summary, this study presents self-adaptive software that rectifies errors, optimizes performance, and maintains functionality in the presence of faults, contributing to efficiency in Internet task automation. [ABSTRACT FROM AUTHOR]

The traditional manual recording of vaccination records in Germany faced challenges during the COVID-19 pandemic, prompting the introduction of a COVID smartphone app with QR codes. However, this solution brought new challenges, emphasizing the need for a centrally managed European digital vaccination record for efficiency and validity. This study assesses the feasibility of using the HL7 FHIR standard in the healthcare industry for implementing a digital vaccination pass management and monitoring system. The system aims to offer convenience and improved efficiency for both patients and healthcare providers while promoting interoperability with other healthcare systems. To this end, we developed a prototype using modern technologies, such as React, Quarkus, and Keycloak. Results indicate potential benefits for patients and healthcare providers, offering access to immunization records, personalized recommendations, and streamlined management. However, integrating nuanced vaccination processes into the standardized FHIR system requires custom extensions, which might hinder interoperability. Manual data entry and the integration of an identity provider present further obstacles in industry scenarios. Despite these challenges, this study suggests that implementing HL7 FHIR can enhance efficiency, data accessibility, and accuracy in the vaccination process, supporting broader digitization efforts in the German healthcare system and beyond. [ABSTRACT FROM AUTHOR]

We aimed to obtain the optimal formula for human milk fat substitute (HMFS) through a combination of software and an evaluation model and further verify its practicability through an animal experiment. The results showed that a total of 33 fatty acid (FA) and 63 triglyceride (TAG) molecular species were detected in vegetable oils. Palmitic acid, oleic acid, linoleic acid, 18:1/16:0/18:1, 18:2/16:0/18:2, 18:1/18:1/18:1 and 18:1/18:2/18:1, were the main molecular species among the FAs and TAGs in the vegetable oils. Based on the HMFS evaluation model, the optimal mixed vegetable oil formula was blended with 21.3% palm oil, 2.8% linseed oil, 2.6% soybean oil, 29.9% rapeseed oil and 43.4% maize oil, with the highest score of 83.146. Moreover, there was no difference in the weight, blood routine indices or calcium and magnesium concentrations in the feces of the mice between the homemade mixed vegetable oil (HMVO) group and the commercial mixed vegetable oil (CMVO) group, while nervonic acid (C24:1) and octanoic acid (C8:0) were absorbed easily in the HMVO group. Therefore, these results demonstrate that the mixing of the different vegetable oils was feasible via a combination of computer software and an evaluation model and provided a new way to produce HMFS. [ABSTRACT FROM AUTHOR]

The study of evolutionary algorithms (EAs) has witnessed an impressive increase during the last decades. The need to explore this area is determined by the growing request for design and the optimization of more and more engineering problems in society, such as highway construction processes, food and agri-technologies processes, resource allocation problems, logistics and transportation systems, microarchitectures, suspension systems optimal design, etc. All of these matters refer to specific highly computational problems with a huge design space, hence the obvious need for evolutionary algorithms and frameworks, or platforms that allow for the implementing and testing of such algorithms and methods. This paper aims to comparatively analyze the existing software platforms and state-of-the-art multi-objective optimization algorithms and make a review of what features exist and what features might be included next as further developments in such tools, from a researcher's perspective. Additionally, it is essential for a framework to be easily extendable with new types of problems and optimization algorithms, metrics and quality indicators, genetic operators or specific solution representations and results analysis and comparison features. After presenting the most relevant existing features in these types of platforms, we suggest some future steps and the developments we have been working on. [ABSTRACT FROM AUTHOR]

This is a scoping review on mapping the use of digital tools to assess food consumption in Brazil. Searches were carried out in nine electronic databases (Medline, Lilacs, Scopus, Embase, Web of Science, Science Direct, Ovid, Free Medical Journal and Crossref) to select studies published from October 2020 to December 2023. This review identified forty-eight digital tools in the 94 publications analyzed, the most frequent being web-based technologies (60%) and mobile devices (40%). Among these studies, 55% (n = 52) adopted a population-based approach, while 45% (n = 42) focused on specific regions. The predominant study design observed was cross-sectional (n = 63). A notable trend observed was the increasing frequency of validation studies in recent years. Although the use of digital tools in the assessment of food consumption in Brazil has grown in recent years, studies did not describe the process of creating and validating the tools, which would contribute to the improvement of data quality. Investments that allow the expansion of the use of the internet and mobile devices; the improvement of digital literacy; and the development of open-access tools, especially in the North and Northeast regions, are challenges that require a concerted effort towards providing equal opportunities, fostering encouragement, and delving deeper into the potential of digital tools within studies pertaining to food consumption in Brazil. [ABSTRACT FROM AUTHOR]

Simple Summary: Quantitative assessment of the therapy response in oncological patients undergoing chemo- or immunotherapy is becoming increasingly important not only in the context of clinical studies but also in clinical routine. To facilitate the sometimes complex and time-consuming oncological response assessment, dedicated software solutions, e.g., according to (i)RECIST, have been developed. Considering the higher degree of complexity of iRECIST, we investigated the benefits of software-assisted assessments compared to manual approaches with respect to reader agreement, error rate, and reading time. iRECIST assessments were more feasible and reliable when supported by dedicated software. We conclude that oncologic response assessment in clinical trials should be performed software-assisted rather than manually. Objectives: To compare the feasibility and reliability of manual versus software-assisted assessments of computed tomography scans according to iRECIST in patients undergoing immune-based cancer treatment. Methods: Computed tomography scans of 30 tumor patients undergoing cancer treatment were evaluated by four independent radiologists at baseline (BL) and two follow-ups (FU), resulting in a total of 360 tumor assessments (120 each at BL/FU1/FU2). After image interpretation, tumor burden and response status were either calculated manually or semi-automatically as defined by software, respectively. The reading time, calculated sum of longest diameter (SLD), and tumor response (e.g., "iStable Disease") were determined for each assessment. After complete data collection, a consensus reading among the four readers was performed to establish a reference standard for the correct response assignments. The reading times, error rates, and inter-reader agreement on SLDs were statistically compared between the manual versus software-assisted approaches. Results: The reading time was significantly longer for the manual versus software-assisted assessments at both follow-ups (median [interquartile range] FU1: 4.00 min [2.17 min] vs. 2.50 min [1.00 min]; FU2: 3.75 min [1.88 min] vs. 2.00 min [1.50 min]; both p < 0.001). Regarding reliability, 2.5% of all the response assessments were incorrect at FU1 (3.3% manual; 0% software-assisted), which increased to 5.8% at FU2 (10% manual; 1.7% software-assisted), demonstrating higher error rates for manual readings. Quantitative SLD inter-reader agreement was inferior for the manual compared to the software-assisted assessments at both FUs (FU1: ICC = 0.91 vs. 0.93; FU2: ICC = 0.75 vs. 0.86). Conclusions: Software-assisted assessments may facilitate the iRECIST response evaluation of cancer patients in clinical routine by decreasing the reading time and reducing response misclassifications. [ABSTRACT FROM AUTHOR]

Accurate visualization of bubbles in multiphase flow is a crucial aspect of modeling heat transfer, mixing, and turbulence processes. It has many applications, including chemical processes, wastewater treatment, and aquaculture. A new software, Flow_Vis, based on experimental data visualization, has been developed to visualize the movement and size distribution of bubbles within multiphase flow. Images and videos recorded from an experimental rig designed to generate microbubbles were analyzed using the new software. The bubbles in the fluid were examined and found to move with different velocities due to their varying sizes. The software was used to measure bubble size distributions, and the obtained results were compared with experimental measurements, showing reasonable accuracy. The velocity measurements were also compared with literature values and found to be equally accurate. [ABSTRACT FROM AUTHOR]

Uncrewed-Aerial Vehicles (UAVs) and hyperspectral sensors are emerging as effective alternatives for monitoring water quality on-demand. However, image mosaicking for largely featureless coastal water surfaces or open seas has shown to be challenging. Another pertinent issue observed is the systematic image misalignment between adjacent flight lines due to the time delay between the UAV-borne sensor and the GNSS system. To overcome these challenges, this study introduces a workflow that entails a GPS-based image mosaicking method for push-broom hyperspectral images, together with a correction method to address the aforementioned systematic image misalignment. An open-source toolkit, CoastalWQL, was developed to facilitate the workflow, which includes essential pre-processing procedures for improving the image mosaic's quality, such as radiometric correction, de-striping, sun glint correction, and object masking classification. For validation, UAV-based push-broom hyperspectral imaging surveys were conducted to monitor coastal turbidity in Singapore, and the implementation of CoastalWQL's pre-processing workflow was evaluated at each step via turbidity retrieval. Overall, the results confirm that the image mosaicking of the push-broom hyperspectral imagery over featureless water surface using CoastalWQL with time delay correction enabled better localisation of the turbidity plume. Radiometric correction and de-striping were also found to be the most important pre-processing procedures, which improved turbidity prediction by 46.5%. [ABSTRACT FROM AUTHOR]

Magnetic Particle Inspection (MPI) is one of the most used methods in Non-Destructive Testing (NDT), allowing precise and robust defect detection on industrial-grade manufactured parts. However, human controllers perform this task in full black environments under UV-A lighting only (with safety glasses) and use chemical products in a confined environment. Those constraints tends to lower control performance and increase stress and fatigue. As a solution, we propose an AI-based assistive machine (called "PARADES") inside the hazardous environment, remotely manipulated by a human operator, outside of the confined area, in cleaner and safer conditions. This paper focuses on the development of a complete industrial-grade AI machine, both in terms of hardware and software. The result is a standalone assistive AI-based vision system, plug-and-play and controller-friendly, which only needs the usual power supply 230 V plug that detects defects and measures defect length. In conclusion, the PARADES machines address for the first time the problem of occupational health in MPI with an industrial standalone machine which can work on several parts and be integrated into current production lines. Providing cleaner and healthier working conditions for operators will invariably lead to increased quality of detection. These results suggest that it would be beneficial to spread this kind of AI-based assistive technology in NDT, in particular MPI, but also in Fluorescent Penetrant Testing (FPT) or in visual inspection. [ABSTRACT FROM AUTHOR]

Achieving the UN Sustainable Development Goals is impossible without sustainable oil and gas production, both in terms of ensuring equal access to cheap energy and preserving the environment, as well as caring for non-renewable fossil energy sources. This actualizes the need for the digital 3D modeling of wells, which allows one to assess their current condition and predict their future condition as well as determine the feasibility of investing in their reconstruction and the expansion of the well network. This is possible due to the fact that the visualization of a well, reflecting its physical and technical parameters, gives engineers, designers and ecologists the opportunity to recognize the defects of the well (cracks, cavities, behind casing and interlayer leaks, etc.) and predict their appearance and proliferation on which the service life, hydrocarbon flow rate, pollution, operating and capital costs directly depend. The software required for this must be versatile enough to cover different types of logging and fit different operating systems. The goal of the study is to develop a software for creating visual 3D models of wells based on acoustic and various types of radioactive logging data, capable of integrating drilling rig parameters and geophysical survey data with modern 3D modeling and programming methods. The developed software meets the requirements of various operating systems and the specifics of different types of logging, which is designed to help in increasing the productivity of oil and gas wells, save energy consumption and reduce groundwater pollution from chemicals used in hydrocarbon production. This is achievable by ensuring trouble-free execution and the operation of well systems, minimizing the risks of collapses and the destruction of well walls through accurate monitoring and forecasting their dynamic condition in real time using 3D models, which is not available for static 2D models. [ABSTRACT FROM AUTHOR]

Liquid chromatography–high-resolution mass spectrometry (LC-HRMS), as applied to untargeted metabolomics, enables the simultaneous detection of thousands of small molecules, generating complex datasets. Alignment is a crucial step in data processing pipelines, whereby LC-MS features derived from common ions are assembled into a unified matrix amenable to further analysis. Variability in the analytical factors that influence liquid chromatography separations complicates data alignment. This is prominent when aligning data acquired in different laboratories, generated using non-identical instruments, or between batches from large-scale studies. Previously, we developed metabCombiner for aligning disparately acquired LC-MS metabolomics datasets. Here, we report significant upgrades to metabCombiner that enable the stepwise alignment of multiple untargeted LC-MS metabolomics datasets, facilitating inter-laboratory reproducibility studies. To accomplish this, a "primary" feature list is used as a template for matching compounds in "target" feature lists. We demonstrate this workflow by aligning four lipidomics datasets from core laboratories generated using each institution's in-house LC-MS instrumentation and methods. We also introduce batchCombine, an application of the metabCombiner framework for aligning experiments composed of multiple batches. metabCombiner is available as an R package on Github and Bioconductor, along with a new online version implemented as an R Shiny App. [ABSTRACT FROM AUTHOR]

The disruptive effect of radio frequency interference (RFI) on global navigation satellite system (GNSS) signals is well known, and in the last four decades, many have been investigated as countermeasures. Recently, low-Earth orbit (LEO) satellites have been looked at as a good opportunity for GNSS RFI monitoring, and the last five years have seen the proliferation of many commercial and academic initiatives. In this context, this paper proposes a new spaceborne system to detect, classify, and localize terrestrial GNSS RFI signals, particularly jamming and spoofing, for civil use. This paper presents the implementation of the RFI detection software module to be hosted on a nanosatellite. The whole development work is described, including the selection of both the target platform and the algorithms, the implementation, the detection performance evaluation, and the computational load analysis. Two are the implemented RFI detectors: the chi-square goodness-of-fit (GoF) algorithm for non-GNSS-like interference, e.g., chirp jamming, and the snapshot acquisition for GNSS-like interference, e.g., spoofing. Preliminary testing results in the presence of jamming and spoofing signals reveal promising detection capability in terms of sensitivity and highlight room to optimize the computational load, particularly for the snapshot-acquisition-based RFI detector. [ABSTRACT FROM AUTHOR]

Simple Summary: This scientific study focuses on glioblastoma, a highly aggressive cancer with a poor prognosis. Despite various treatment modalities, including immune checkpoint inhibitors (ICBs), the efficacy of ICBs remains limited, prompting the need for a proactive approach to understand treatment response and resistance. This study involves a thorough analysis of two glioblastoma patient cohorts treated with the Programmed Cell Death Protein 1 (PD-1) blockade. Notably, 60% of the patients exhibited persistent disease progression despite the ICBs. We characterized the immune profiles of these patients with continued cancer progression, revealing multiple defects such as compromised macrophage, monocyte, and T follicular helper responses, impaired antigen presentation, abnormal regulatory T cell (Tregs) responses, and increased expression of immunosuppressive molecules. Using machine learning algorithms, we developed predictive models and software. This computational tool achieved significant success, accurately predicting the progression status of 82.82% of the glioblastoma patients in this study following ICBs based on their unique immune characteristics. In conclusion, this study proposes a personalized approach to immunotherapy in glioblastoma patients. By utilizing patient-specific attributes and computational predictions, we advocate for a paradigm shift towards tailored therapies. This approach has the potential to improve glioblastoma management, offering new possibilities for improved patient care following immunotherapy. Glioblastoma is a highly aggressive cancer associated with a dismal prognosis, with a mere 5% of patients surviving beyond five years post diagnosis. Current therapeutic modalities encompass surgical intervention, radiotherapy, chemotherapy, and immune checkpoint inhibitors (ICBs). However, the efficacy of ICBs remains limited in glioblastoma patients, necessitating a proactive approach to anticipate treatment response and resistance. In this comprehensive study, we conducted a rigorous analysis involving two distinct glioblastoma patient cohorts subjected to PD-1 blockade treatments. Our investigation revealed that a significant portion (60%) of patients exhibit persistent disease progression despite ICB intervention. To elucidate the underpinnings of resistance, we characterized the immune profiles of glioblastoma patients with continued cancer progression following anti-PD1 therapy. These profiles revealed multifaceted defects, encompassing compromised macrophage, monocyte, and T follicular helper responses, impaired antigen presentation, aberrant regulatory T cell (Tregs) responses, and heightened expression of immunosuppressive molecules (TGFB, IL2RA, and CD276). Building upon these resistance profiles, we leveraged cutting-edge machine learning algorithms to develop predictive models and accompanying software. This innovative computational tool achieved remarkable success, accurately forecasting the progression status of 82.82% of the glioblastoma patients in our study following ICBs, based on their unique immune characteristics. In conclusion, our pioneering approach advocates for the personalization of immunotherapy in glioblastoma patients. By harnessing patient-specific attributes and computational predictions, we offer a promising avenue for the enhancement of clinical outcomes in the realm of immunotherapy. This paradigm shift towards tailored therapies underscores the potential to revolutionize the management of glioblastoma, opening new horizons for improved patient care. [ABSTRACT FROM AUTHOR]

Software specifications are of great importance to improve the quality of software. To automatically mine specifications from software systems, some specification mining approaches based on finite-state automatons have been proposed. However, these approaches are inaccurate when dealing with large-scale systems. In order to improve the accuracy of mined specifications, we propose a specification mining approach based on the ordering points to identify the clustering structure clustering algorithm and model checking. In the approach, the neural network model is first used to produce the feature values of states in the traces of the program. Then, according to the feature values, finite-state automatons are generated based on the ordering points to identify the clustering structure clustering algorithm. Further, the finite-state automaton with the highest F-measure is selected. To improve the quality of the finite-state automatons, we refine it based on model checking. The proposed approach was implemented in a tool named MCLSM and experiments, including 13 target classes, were conducted to evaluate its effectiveness. The experimental results show that the average F-measure of finite-state automatons generated by our method reaches 92.19%, which is higher than most related tools. [ABSTRACT FROM AUTHOR]

Cryo electron microscopy (cryo-EM) instrumentation allows obtaining 3D reconstruction of the structure of biomolecular complexes in vitro (purified complexes studied by single particle analysis) and in situ (complexes studied in cells by cryo electron tomography). Standard cryo-EM approaches allow high-resolution reconstruction of only a few conformational states of a molecular complex, as they rely on data classification into a given number of classes to increase the resolution of the reconstruction from the most populated classes while discarding all other classes. Such discrete classification approaches result in a partial picture of the full conformational variability of the complex, due to continuous conformational transitions with many, uncountable intermediate states. In this article, we present the software with a user-friendly graphical interface for running two recently introduced methods, namely, MDSPACE and MDTOMO, to obtain continuous conformational landscapes of biomolecules by analyzing in vitro and in situ cryo-EM data (single particle images and subtomograms) based on molecular dynamics simulations of an available atomic model of one of the conformations. The MDSPACE and MDTOMO software is part of the open-source ContinuousFlex software package (starting from version 3.4.2 of ContinuousFlex), which can be run as a plugin of the Scipion software package (version 3.1 and later), broadly used in the cryo-EM field. [ABSTRACT FROM AUTHOR]

The use of electroencephalography (EEG) techniques has many advantages in the study of human performance in air traffic control (ATC). At present, these are non-intrusive techniques that allow large volumes of data to be recorded on a continuous basis using wireless equipment. To achieve the most with these techniques, it is essential to establish appropriate EEG parameters with a clear understanding of the process followed to obtain them and their practical application. This study explains, step by step, the approach adopted to obtain six EEG parameters: excitement, stress, boredom, relaxation, engagement, and attention. It then explains all the steps involved in analysing the relationship between these parameters and two other parameters that characterise the state of the air traffic control sector during the development of real-time simulations (RTS): taskload and number of simultaneous aircraft. For this case study, the results showed the highest relationships for the engagement and attention parameters. In general, the results confirmed the potential of using these EEG parameters. [ABSTRACT FROM AUTHOR]

Background and Objectives: Significant progress has been made in skin cancer diagnosis, with a surge in available technologies in recent years. Despite this, the practical application and integration of these technologies in dermatology and plastic surgery remain uneven. Materials and Methods: A comprehensive 20-question survey was designed and distributed using online survey administration software (Google Forms, 2018, Google, Mountain View, CA, USA) from June 2023 to September 2023. The survey aimed to assess the knowledge and utilization of dermatologic diagnostic advancements among plastic surgeons in various European countries. Results: Data were obtained from 29 plastic surgeons across nine European countries, revealing a notable gap between diagnostic technologies and their routine use in surgical practice. The gap for some technologies was both cognitive and applicative; for electrical impedance spectroscopy (EIS) and multispectral imaging, only 6.9% of the sample knew of the technologies and no surgeons in the sample used them. In the case of other technologies, such as high-frequency ultrasound (HFUS), 72.4% of the sample knew about them but only 34.5% used them, highlighting a more significant application problem. Conclusions: Spotlighting this discrepancy provides a valuable foundation for initiating collaborative efforts between units and facilitating knowledge exchange among diverse specialists. This, in turn, contributes to advancing clinical practice by integrating the innovative opportunities presented by ongoing research. [ABSTRACT FROM AUTHOR]

The inherent complexity of the Raman spectra of biomedical samples reflects the intricate molecular composition and intermolecular interactions of these diverse systems. Unraveling the complexities of biological Raman spectra is essential for bioscience and bioengineering research because it provides insight into cellular processes, disease states, and drug interactions. For the effective analysis of such complex data, robust and cutting-edge software is required that provides sophisticated algorithms for data preprocessing, thereby enhancing the signal-to-noise ratio and revealing hidden spectral information. In addition, novel applications of this type may include machine learning algorithms for automated clustering analysis, enabling the identification of biomolecules and their conformational changes in diverse biological specimens. We present a Python 3 package built around popular scientific Python libraries that aims to provide Raman spectroscopists with user-friendly programming tools for the analysis of complex biomedical Raman data. [ABSTRACT FROM AUTHOR]

Protein variation that occurs during alternative splicing has been shown to play a major role in disease onset and oncogenesis. Due to this, we have developed OutSplice, a user-friendly algorithm to classify splicing outliers in tumor samples compared to a distribution of normal samples. Several tools have previously been developed to help uncover splicing events, each coming with varying methodologies, complexities, and features that can make it difficult for a new researcher to use or to determine which tool they should be using. Therefore, we benchmarked several algorithms to determine which may be best for a particular user's needs and demonstrate how OutSplice differs from these methodologies. We find that despite detecting a lower number of genes with significant aberrant events, OutSplice is able to identify those that are biologically impactful. Additionally, we identify 17 genes that contain significant splicing alterations in tumor tissue that were discovered across at least 5 of the tested algorithms, making them good candidates for future studies. Overall, researchers should consider a combined use of OutSplice with other splicing software to help provide additional validation for aberrant splicing events and to narrow down biologically relevant events. [ABSTRACT FROM AUTHOR]

Urbanization and climate change have increased the need for stormwater management and nature-based solutions. Decisions made at the project level impact the emergence of the systemic traits of the stormwater network and the functionality of the catchment areas in urban planning. To that end, it is vital to introduce the decision-making tools for analysing both the utilities and amenities of nature-based solutions (NBS) to increase their adoption to reduce the peak loads in the stormwater system and, to that end, mitigate the impacts of climate change. There is a deficiency in employing a software-based approach to analyse the qualitative and quantitative aspects of NBSs to back up design decisions. This paper demonstrates a workflow using drone-based photogrammetry, 3D modelling, and simulation software to generate visual and functional models assisting in informed decision-making in the design of stormwater systems as functional landscape architecture. Using aerial data from drones and modelled design solutions, the proposed workflow simulates rain events, infiltration, evaporation, water flow, and the accumulation of stormwater in a way that allows the visual and quantified analysis of detailed landscape architecture designs. The paper provides an example of a rooftop site simulation demonstrating the infiltration and flow of water to the drainage. The visual decision-making method provided can aid in investment decisions for functional landscape design in support of stormwater management. [ABSTRACT FROM AUTHOR]

OpenToolFlux 1.0 is an open-source software designed to estimate soil gas fluxes from gas concentration time-series data generated by automatic chamber systems. This paper describes the physical equipment used as well as the software design and workflow. The software is a command-line application that imports tabular time-series data from the analyzer following the instructions specified in a configuration file by the user, performs configurable data-cleaning operations, and outputs a data file with volumetric flux estimates as well as diagnostic plots. The software can be configured according to the specifics of the physical equipment and experimental setups, and it is, therefore, applicable to a wide range of studies. [ABSTRACT FROM AUTHOR]

The visualization of neuronal activity in vivo is an urgent task in modern neuroscience. It allows neurobiologists to obtain a large amount of information about neuronal network architecture and connections between neurons. The miniscope technique might help to determine changes that occurred in the network due to external stimuli and various conditions: processes of learning, stress, epileptic seizures and neurodegenerative diseases. Furthermore, using the miniscope method, functional changes in the early stages of such disorders could be detected. The miniscope has become a modern approach for recording hundreds to thousands of neurons simultaneously in a certain brain area of a freely behaving animal. Nevertheless, the analysis and interpretation of the large recorded data is still a nontrivial task. There are a few well-working algorithms for miniscope data preprocessing and calcium trace extraction. However, software for further high-level quantitative analysis of neuronal calcium signals is not publicly available. NeuroActivityToolkit is a toolbox that provides diverse statistical metrics calculation, reflecting the neuronal network properties such as the number of neuronal activations per minute, amount of simultaneously co-active neurons, etc. In addition, the module for analyzing neuronal pairwise correlations is implemented. Moreover, one can visualize and characterize neuronal network states and detect changes in 2D coordinates using PCA analysis. This toolbox, which is deposited in a public software repository, is accompanied by a detailed tutorial and is highly valuable for the statistical interpretation of miniscope data in a wide range of experimental tasks. [ABSTRACT FROM AUTHOR]

In recent years, the number of similar software products with many common parts has been increasing due to the reuse and plagiarism of source code in the software development process. Pattern matching, which is an existing method for detecting similarity, cannot detect the similarities between these software products and other programs. It is necessary, for example, to detect similarities based on commonalities in both functionality and control structures. At the same time, detailed software analysis requires manual reverse engineering. Therefore, technologies that automatically identify similarities among the arge amounts of code present in software products in advance can reduce these oads. In this paper, we propose a representation earning model to extract feature expressions from assembly code obtained by statically analyzing such code to determine the similarity between software products. We use assembly code to eliminate the dependence on the existence of source code or differences in development anguage. The proposed approach makes use of Asm2Vec, an existing method, that is capable of generating a vector representation that captures the semantics of assembly code. The proposed method also incorporates information on the program control structure. The control structure can be represented by graph data. Thus, we use graph embedding, a graph vector representation method, to generate a representation vector that reflects both the semantics and the control structure of the assembly code. In our experiments, we generated expression vectors from multiple programs and used clustering to verify the accuracy of the approach in classifying similar programs into the same cluster. The proposed method outperforms existing methods that only consider semantics in both accuracy and execution time. [ABSTRACT FROM AUTHOR]

Low-field time-domain proton Nuclear Magnetic Resonance (NMR) spectroscopy is an attractive and powerful tool for studying the structure and dynamics of elastomers. The existence of crosslinks and other topological constraints in rubber matrices (entanglements and filler–rubber interactions, among others) renders the fast segmental fluctuations of the polymeric chains non-isotropic, obtaining nonzero residual dipolar couplings, which is the main observable of MQ-NMR experiments. A new software, Multiple quantum nuclear magnetic resonance analyzer for Elastomeric Networks v2 (MEW2), provides a new tool to facilitate the study of the molecular structure of elastomeric materials. This program quantitatively analyzes two different sets of experimental data obtained in the same experiment, which are dominated by multiple-quantum coherence and polymer dynamics. The proper quantification of non-coupled network defects (dangling chain ends, loops, etc.) allows the analyzer to normalize the multiple quantum intensity, obtaining a build-up curve that contains the structural information without any influence from the rubber dynamics. Finally, it provides the spatial distribution of crosslinks using a fast Tikhonov regularization process based on a statistical criterion. As a general trend, this study provides an automatic solution to a tedious procedure of analysis, demonstrating a new tool that accelerates the calculations of network structure using 1H MQ-NMR low-field time-domain experiments for elastomeric compounds. [ABSTRACT FROM AUTHOR]

Genetic variants on non-recombining DNA and the hierarchical order in which they accumulate are commonly of interest. This variant hierarchy can be established and combined with information on the population and geographic origin of the individuals carrying the variants to find population structures and infer migration patterns. Further, individuals can be assigned to the characterized populations, which is relevant in forensic genetics, genetic genealogy, and epidemiologic studies. However, there is currently no straightforward method to obtain such a variant hierarchy. Here, we introduce the software SNPtotree v1.0, which uniquely determines the hierarchical order of variants on non-recombining DNA without error-prone manual sorting. The algorithm uses pairwise variant comparisons to infer their relationships and integrates the combined information into a phylogenetic tree. Variants that have contradictory pairwise relationships or ambiguous positions in the tree are removed by the software. When benchmarked using two human Y-chromosomal massively parallel sequencing datasets, SNPtotree outperforms traditional methods in the accuracy of phylogenetic trees for sequencing data with high amounts of missing information. The phylogenetic trees of variants created using SNPtotree can be used to establish and maintain publicly available phylogeny databases to further explore genetic epidemiology and genealogy, as well as population and forensic genetics. [ABSTRACT FROM AUTHOR]

The increasing popularity of mHealth presents an opportunity for collecting rich datasets using mobile phone applications (apps). Our health-monitoring mobile application uses motion detection to track an individual's physical activity and location. The data collected are used to improve health outcomes, such as reducing the risk of chronic diseases and promoting healthier lifestyles through analyzing physical activity patterns. Using smartphone motion detection sensors and GPS receivers, we implemented an energy-efficient tracking algorithm that captures user locations whenever they are in motion. To ensure security and efficiency in data collection and storage, encryption algorithms are used with serverless and scalable cloud storage design. The database schema is designed around Mobile Advertising ID (MAID) as a unique identifier for each device, allowing for accurate tracking and high data quality. Our application uses Google's Activity Recognition Application Programming Interface (API) on Android OS or geofencing and motion sensors on iOS to track most smartphones available. In addition, our app leverages blockchain and traditional payments to streamline the compensations and has an intuitive user interface to encourage participation in research. The mobile tracking app was tested for 20 days on an iPhone 14 Pro Max, finding that it accurately captured location during movement and promptly resumed tracking after inactivity periods, while consuming a low percentage of battery life while running in the background. [ABSTRACT FROM AUTHOR]

Today, land and ocean observations are crucial for monitoring climate change. The method of GNSS reflectometry is an opportunistic way to provide low-cost observations of many geophysical parameters. However, although this method has been the subject of numerous research studies, work is still in progress to improve its possibilities and fields of application. This paper focuses on GNSS reflectometry using carrier phase measurements for water altimetry measurements. The difficulties in implementing such a method lie in the need to collect a coherent signal and to solve the integer ambiguity value. In this context, the implementation of innovative signal processing is described, including the correlation of the reflected signals in dedicated software and the prolongation of the coherent integration time to enhance signal coherency. These processes were applied to data collected over Carcans-Hourtin Lake in France to compute the height of the reflection surface which was then compared to in situ GNSS buoy height measurements. The results show that at 300 ft (91.44 m), the differences between the lake heights measured with the buoy and with the reflectometry data can reach less than 1 cm for the L1, E1 and E5 GNSS signals. In addition, the slope of the geoid estimated with the reflectometry data is very consistent with that of the RAF20 geoid model, with a difference of up to less than 2 mm/km. [ABSTRACT FROM AUTHOR]

As a subclass of nanosatellites, CubeSats have changed the game's rules in the scientific research industry and the development of new space technologies. The main success factors are their cost effectiveness, relative ease of production, and predictable life cycle. CubeSats are very important for training future engineers: bachelor's and master's students of universities. At the same time, using CubeSats is a cost-effective method of nearest space exploration and scientific work. However, many issues are related to efficient time-limited development, software and system-level quality assurance, maintenance, and software reuse. In order to increase the flexibility and reduce the complexity of CubeSat projects, this article proposes a "hybrid" development model that combines the strengths of two approaches: the agile-a-like model for software and the waterfall model for hardware. The paper proposes a new computing platform solution, "Falco SBC/CDHM", based on Microchip (Atmel) ATSAMV71Q21 with improved performance. This type of platform emphasizes low-cost space hardware that can compete with space-grade platforms. The paper substantiates the architecture of onboard software based on microservices and containerization to break down complex software into relatively simple components that undergraduates and graduates can handle within their Master's studies, and postgraduates can use for scientific space projects. The checking of the effectiveness of the microservice architecture and the new proposed platform was carried out experimentally, involving the time spent on executing three typical algorithms of different algorithmic complexities. Algorithms were implemented using native C (Bare-metal) and WASM3 on FreeRTOS containers on two platforms, and performance was measured on both "Falco" and "Pi Pico" by Raspberry. The experiment confirmed the feasibility of the complex application of the "hybrid" development model and microservices and container-based architecture. The proposed approach makes it possible to develop complex software in teams of inexperienced students, minimize risks, provide reusability, and thus increase the attractiveness of CubeSat student projects. [ABSTRACT FROM AUTHOR]

As the world's population continues to grow and the demand for energy increases, there is an urgent need for sustainable and efficient energy systems. Renewable energy sources, such as wind and solar power, have the potential to play a significant role in meeting this demand, but their intermittency can make integration into existing energy systems a challenge. Moreover, the development of sustainable energy systems has become even more critical in recent years, due to a confluence of events, including the decline in fuel prices, geopolitical conflicts, and the recent COVID-19 pandemic. The decrease in fuel prices has led to a decline in investment in renewable energy and has slowed the transition to sustainable energy systems. Additionally, geopolitical conflicts and pandemics have highlighted the need for resilient and self-sufficient energy systems that can operate independently of external factors. Also, energy storage technologies play a critical role in achieving this goal by providing reliable backup power and enabling microgrids to operate independently of the larger power grid. As such, developing efficient and effective energy storage technologies is essential for creating sustainable energy systems that can meet the demands of modern society while mitigating the impact of external factors. In this regard, this work provides an overview of microgrids' latest energy storage technologies, including their applications, types, integration strategies, optimization algorithms, software, and uncertainty analysis. Energy storage technologies have a wide range of applications in microgrids, including providing backup power and balancing the supply and demand of energy. Different energy storage techniques have been discussed, including batteries, flywheels, supercapacitors, pumped hydro energy storage, and others. Moreover, integration strategies of energy storage in microgrids, models, assessment indices, and optimization algorithms used in the design of energy storage systems are presented in detail. The capabilities of software used in energy storage sizing are explored. Further, uncertainty analysis in modeling energy storage devices is presented and discussed. This state-of-the-art technology has been prepared to demonstrate the effectiveness of energy storage technologies in microgrids, providing valuable insights for future developments in the field. [ABSTRACT FROM AUTHOR]

The appearance of genetic variants impacts vaccination efficiency and therapeutic options, generating a need to map and relate mutations observed in the proteome and the genome. We develop an user-friendly web service software (Viral Instant Mutation Viewer or VIMVer) which allows a direct identification of mutations in the genome and its counterpart in the viral proteome. Since its emergence in 2019, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), responsible for the COVID-19 pandemic, has generated an overwhelming amount of data while becoming one of the most studied viruses of the Nidovirales order. We originally developed this tool during the COVID pandemic; thus, for any SARS-CoV-2 nucleotide sequence, the web service gives a fast identification, mapping, and display of new mutations simultaneously at the nucleotide and amino acid level in comparison to a reference sequence (Wuhan-1). Furthermore, the lineage or the relative position to the known lineage of the variant of interest is available on the link to Phylogenetic Assignment of Named Global Outbreak LINeages (PANGOLIN COVID-19). The workflow presented here is available online. The source code is released under public license and can be easily adapted for further development to other viruses. [ABSTRACT FROM AUTHOR]

Color fading naturally occurs with time under light illumination. It is triggered by the high photon energy of light. The rate of color fading and darkening depends on the substance, lighting condition, and storage conditions. Color fading is only observed after some time has passed. The current color of objects of interest can only be compared with old photographs or the observer's perception at the time of reference. Color fading and color darkening rates between two or more points in time in the past can only be determined using photographic images from the past. For objective characterization of color difference between two or more different times, quantification of color in either digital or printed photographs is required. A newly developed image analysis and comparison software (PicMan) has been used for color quantification and pixel-by-pixel color difference mapping in this study. Images of two copies of Japanese wood-block prints with and without color fading have been selected for the exemplary study of quantitative characterization of color fading and color darkening. The fading occurred during a long period of exposure to light. Pixel-by-pixel, line-by-line, and area-by-area comparisons of color fading and darkening between two images were very effective in quantifying color change and visualization of the phenomena. RGB, HSV, CIE L*a*b* values between images and their differences of a single pixel to areas of interest in any shape can be quantified. Color fading and darkening analysis results were presented in numerical, graphical, and image formats for completeness. All formats have their own advantages and disadvantages over the other formats in terms of data size, complexity, readability, and communication among parties of interest. This paper demonstrates various display options for color analysis, a summary of color fading, or color difference among images of interest for practical artistic, cultural heritage conservation, and museum applications. Color simulation for various moments in time was proposed and demonstrated by interpolation or extrapolation of color change between images, with and without color fading, using PicMan. The degree of color fading and color darkening over the various moments in time (past and future) can be simulated and visualized for decision-making in public display, storage, and restoration planning. [ABSTRACT FROM AUTHOR]

Astrophysical sources show variability in their emissions over a range of timescales, with transients such as fast radio bursts (FRBs) and magnetar giant flares (MGFs) showing variability on timescales as short as a few milliseconds. Recent advances in gamma-ray astronomy such as telescopes' high temporal resolution and relatively high uptime, combined with follow-up programs between different facilities, should allow serendipitous observations of burst-like phenomena. Even so, no very-high-energy gamma-ray counterparts for FRBs have been detected so far, and there is a general lack of software tools suited to search for such phenomena. We present a tool capable of searching gamma-ray telescope data for transient phenomena over arbitrary timescales—it is based on the Gammapy package and recursively scans the given field of view for clusters of events within user-defined time and angular-separation intervals. The generalized implementation allows for its application in many other cases and multiple gamma-ray telescopes. The main features and methodology of the developed tool are presented here, along with an analysis of the open gamma ray telescope data performed using it. [ABSTRACT FROM AUTHOR]

Background: Prevention plays a key role in ensuring health and safety and is particularly important in scenarios when life is threatened. Adverse thermal conditions are experienced by billions of people daily, affecting the human capacity for thermoregulation and increasing the risks of life-threatening accidents, diseases, and fatalities. The aim of this study was to develop and validate a new, freely accessible method that will ultimately allow health, as well as exercise and labour organizations, to predict and potentially mitigate the physiological strain experienced by people who exercise or work in thermally stressful environmental conditions. Methods: First, we used concurrent technological advances and thermophysiological modelling to (i) develop a mobile phone application that predicts the physiological heat strain experienced by individuals conducting physical activity in adverse environmental conditions, and (ii) provide them with individualized heat mitigation strategies. Second, to examine the construct validity of the newly developed mobile phone application, core body temperature was recorded using gastrointestinal thermometry in 37 healthy soldiers during different activities. These data were used to examine the predictive capacity of our application in pre-classifying individuals with an increased risk of experiencing elevated physiological heat strain during work based on the guidelines (core body temperature ≥ 38 °C) of the World Health Organization. Results: The core body temperature predictions made by the mobile phone application were positively related (r = 0.57, p < 0.05) with the actual physiological measurements taken by our participants (mean absolute error: 0.28 °C). More importantly, our application correctly predicted 93% of occurrences of elevated physiological heat strain and 90% of those that were not (overall accuracy: 92%). Conclusions: Mobile phone applications integrating thermophysiological models can predict the physiological heat strain experienced by an individual, but it remains to be studied whether the suggested heat mitigation strategies can reduce or prevent adverse impacts. [ABSTRACT FROM AUTHOR]

Simple Summary: Next-generation sequencing (NGS) is a cutting-edge technology that enables rapid, high-throughput sequencing of DNA and RNA. Researchers and clinicians can identify genetic mutations, gene fusions, and other alterations that may drive cancer growth. This is particularly important in precision oncology as it is applied in the context of Molecular Tumor Boards (MTBs). The latter are multidisciplinary teams of experts who use NGS and bioinformatics tools to analyze patients' genetic profiles and develop personalized treatment recommendations for cancer patients. Thus, a crucial process for MTB decision-making is the analysis, compilation, and presentation of high-dimensional sequencing data, which are used for both preparation of and case presentation to all stakeholders. MIRACUM-Pipe precisely addresses these requirements and offers an easy-to-use, one-prompt standardized solution to analyze NGS data, including quality control, variant calling, copy number estimation, annotation, visualization, and report generation. (1) Background: Next-generation sequencing (NGS) of patients with advanced tumors is becoming an established method in Molecular Tumor Boards. However, somatic variant detection, interpretation, and report generation, require in-depth knowledge of both bioinformatics and oncology. (2) Methods: MIRACUM-Pipe combines many individual tools into a seamless workflow for comprehensive analyses and annotation of NGS data including quality control, alignment, variant calling, copy number variation estimation, evaluation of complex biomarkers, and RNA fusion detection. (3) Results: MIRACUM-Pipe offers an easy-to-use, one-prompt standardized solution to analyze NGS data, including quality control, variant calling, copy number estimation, annotation, visualization, and report generation. (4) Conclusions: MIRACUM-Pipe, a versatile pipeline for NGS, can be customized according to bioinformatics and clinical needs and to support clinical decision-making with visual processing and interactive reporting. [ABSTRACT FROM AUTHOR]

Analysis and design of siphonic roof drainage systems are usually performed with specific software developed by the system's manufacturers. An experimental study was carried out to verify if a general software for the analysis of hydraulic pressurized pipe networks can be used to analyze a siphonic roof drainage system. A test model was built and tests were conducted to compare the prototype results with simulation runs in EPANET. A new EPANET data model was developed to overcome software limitations for the siphonic drainage systems analysis. Considering the results, less than 5% of average error was observed between the measures in the real test model and the simulation results, which can be attributed to measurement error. To validate the EPANET data model, it was compared with a specific software that analyzes siphonic roof drainage systems. It can be concluded that EPANET is a software that can be used to analyze and, therefore, to design, siphonic roof drainage systems in buildings. [ABSTRACT FROM AUTHOR]

At present, temporary anchorage devices (TADs) are continuously gaining importance because of their usability and their possibility to broaden clinical force applications; however, how difficult can their placement planning be? Aim: The aim is to evaluate the association between clinical experience, digital knowledge and the capability of virtual planning in palatal orthodontic miniscrew insertion in various types of clinicians, divided by different levels of experience. Methods: A total of 30 participants (10 dental students, 10 orthodontics students and 10 orthodontists) with different levels of clinical and digital experience were randomly recruited in this cross-sectional study. All participants performed a pre-test survey followed by two consecutive digital planning tests and, finally a post-test survey. The digital planning test was made using software BlueSkyBio-BlueSkyPlan, a surgical guide module. The differences in terms of planning execution time, miniscrew insertion and surgical guide realization were evaluated. The Kruskal–Wallis and Mann–Whitney U-tests were performed to determine the effects of independent variables and interactions between groups. Results: The relation between clinical experience and bicorticalism was statistically significant (p = 0.017); in the planning execution time, a significant difference was evident between the dental students and the orthodontics students (T1: p = 0.015 and T2: p = 0.019), who, having good digital knowledge, took an average of 4.58 min less in T1 (p = 0.025), while this difference was significantly reduced in T2 (p = 0.106). Conclusion: Clinical experience increased miniscrew placement accuracy and digital knowledge reduced execution planning time but both had a stronger impact in the first test than in the second. [ABSTRACT FROM AUTHOR]

This study aimed to investigate the clinical implications and prognostic value of artificial intelligence (AI)-based results for chest radiographs (CXR) in coronavirus disease 2019 (COVID-19) patients. Patients who were admitted due to COVID-19 from September 2021 to March 2022 were retrospectively included. A commercial AI-based software was used to assess CXR data for consolidation and pleural effusion scores. Clinical data, including laboratory results, were analyzed for possible prognostic factors. Total O2 supply period, the last SpO2 result, and deterioration were evaluated as prognostic indicators of treatment outcome. Generalized linear mixed model and regression tests were used to examine the prognostic value of CXR results. Among a total of 228 patients (mean 59.9 ± 18.8 years old), consolidation scores had a significant association with erythrocyte sedimentation rate and C-reactive protein changes, and initial consolidation scores were associated with the last SpO2 result (estimate −0.018, p = 0.024). All consolidation scores during admission showed significant association with the total O2 supply period and the last SpO2 result. Early changing degree of consolidation score showed an association with deterioration (odds ratio 1.017, 95% confidence interval 1.005–1.03). In conclusion, AI-based CXR results for consolidation have potential prognostic value for predicting treatment outcomes in COVID-19 patients. [ABSTRACT FROM AUTHOR]

Background: The outbreak of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) resulted in the global COVID-19 pandemic. The urgency for an effective SARS-CoV-2 vaccine has led to the development of the first series of vaccines at unprecedented speed. The discovery of SARS-CoV-2 spike-glycoprotein mutants, however, and consequentially the potential to escape vaccine-induced protection and increased infectivity, demonstrates the persisting importance of monitoring SARS-CoV-2 mutations to enable early detection and tracking of genomic variants of concern. Results: We developed the CoVigator tool with three components: (1) a knowledge base that collects new SARS-CoV-2 genomic data, processes it and stores its results; (2) a comprehensive variant calling pipeline; (3) an interactive dashboard highlighting the most relevant findings. The knowledge base routinely downloads and processes virus genome assemblies or raw sequencing data from the COVID-19 Data Portal (C19DP) and the European Nucleotide Archive (ENA), respectively. The results of variant calling are visualized through the dashboard in the form of tables and customizable graphs, making it a versatile tool for tracking SARS-CoV-2 variants. We put a special emphasis on the identification of intrahost mutations and make available to the community what is, to the best of our knowledge, the largest dataset on SARS-CoV-2 intrahost mutations. In the spirit of open data, all CoVigator results are available for download. The CoVigator dashboard is accessible via covigator.tron-mainz.de. Conclusions: With increasing demand worldwide in genome surveillance for tracking the spread of SARS-CoV-2, CoVigator will be a valuable resource of an up-to-date list of mutations, which can be incorporated into global efforts. [ABSTRACT FROM AUTHOR]

One developing approach for robotic control is the use of networks of dynamic neurons connected with conductance-based synapses, also known as Synthetic Nervous Systems (SNS). These networks are often developed using cyclic topologies and heterogeneous mixtures of spiking and non-spiking neurons, which is a difficult proposition for existing neural simulation software. Most solutions apply to either one of two extremes, the detailed multi-compartment neural models in small networks, and the large-scale networks of greatly simplified neural models. In this work, we present our open-source Python package SNS-Toolbox, which is capable of simulating hundreds to thousands of spiking and non-spiking neurons in real-time or faster on consumer-grade computer hardware. We describe the neural and synaptic models supported by SNS-Toolbox, and provide performance on multiple software and hardware backends, including GPUs and embedded computing platforms. We also showcase two examples using the software, one for controlling a simulated limb with muscles in the physics simulator Mujoco, and another for a mobile robot using ROS. We hope that the availability of this software will reduce the barrier to entry when designing SNS networks, and will increase the prevalence of SNS networks in the field of robotic control. [ABSTRACT FROM AUTHOR]

The article proposes a generalized algorithm for evaluating the shielding effectiveness (SE) of electronic equipment enclosures. The algorithm is based on a number of analytical models that use equivalent circuits to obtain SE values. The article begins with a brief review and interpretation of the mathematical formulation used in the algorithm. Then, we describe the proposed algorithm using flowcharts, and we perform its validation. The validation results show that the proposed algorithm has acceptable accuracy and gives SE values comparable to numerical methods or measurements, with much less time costs. The last part of the article presents the software developed to evaluate SE based on analytical models. [ABSTRACT FROM AUTHOR]

Drug combinations are increasingly studied in the field of anticancer agents. Mathematical models, such as Loewe, Bliss, and HSA, are used to interpret drug combinations, while informatics tools help cancer researchers identify the most effective combinations. However, the different algorithms each software uses lead to results that do not always correlate. This study compared the performance of Combenefit (Ver. 2.021) and SynergyFinder (Ver. 3.6) in analyzing drug synergy by studying combinations involving non-steroidal analgesics (celecoxib and indomethacin) and antitumor drugs (carboplatin, gemcitabine, and vinorelbine) on two canine mammary tumor cell lines. The drugs were characterized, their optimal concentration–response ranges were determined, and nine concentrations of each drug were used to make combination matrices. Viability data were analyzed under the HSA, Loewe, and Bliss models. Celecoxib-based combinations showed the most consistent synergistic effect among software and reference models. Combination heatmaps revealed that Combenefit gave stronger synergy signals, while SynergyFinder produced better concentration–response fitting. When the average values of the combination matrices were compared, some combinations shifted from synergistic to antagonistic due to differences in the curve fitting. We also used a simulated dataset to normalize each software's synergy scores, finding that Combenefit tends to increase the distance between synergistic and antagonistic combinations. We conclude that concentration–response data fitting biases the direction of the combination (synergistic or antagonistic). In contrast, the scoring from each software increases the differences among synergistic or antagonistic combinations in Combenefit when compared to SynergyFinder. We strongly recommend using multiple reference models and reporting complete data analysis for synergy claiming in combination studies. [ABSTRACT FROM AUTHOR]

Medical image segmentation, whether semi-automatically or manually, is labor-intensive, subjective, and needs specialized personnel. The fully automated segmentation process recently gained importance due to its better design and understanding of CNNs. Considering this, we decided to develop our in-house segmentation software and compare it to the systems of established companies, an inexperienced user, and an expert as ground truth. The companies included in the study have a cloud-based option that performs accurately in clinical routine (dice similarity coefficient of 0.912 to 0.949) with an average segmentation time ranging from 3′54″ to 85′54″. Our in-house model achieved an accuracy of 94.24% compared to the best-performing software and had the shortest mean segmentation time of 2′03″. During the study, developing in-house segmentation software gave us a glimpse into the strenuous work that companies face when offering clinically relevant solutions. All the problems encountered were discussed with the companies and solved, so both parties benefited from this experience. In doing so, we demonstrated that fully automated segmentation needs further research and collaboration between academics and the private sector to achieve full acceptance in clinical routines. [ABSTRACT FROM AUTHOR]

The unambiguous identification of lipids is a critical component of lipidomics studies and greatly impacts the interpretation and significance of analyses as well as the ultimate biological understandings derived from measurements. The level of structural detail that is available for lipid identifications is largely determined by the analytical platform being used. Mass spectrometry (MS) coupled with liquid chromatography (LC) is the predominant combination of analytical techniques used for lipidomics studies, and these methods can provide fairly detailed lipid identification. More recently, ion mobility spectrometry (IMS) has begun to see greater adoption in lipidomics studies thanks to the additional dimension of separation that it provides and the added structural information that can support lipid identification. At present, relatively few software tools are available for IMS-MS lipidomics data analysis, which reflects the still limited adoption of IMS as well as the limited software support. This fact is even more pronounced for isomer identifications, such as the determination of double bond positions or integration with MS-based imaging. In this review, we survey the landscape of software tools that are available for the analysis of IMS-MS-based lipidomics data and we evaluate lipid identifications produced by these tools using open-access data sourced from the peer-reviewed lipidomics literature. [ABSTRACT FROM AUTHOR]

The subjective analysis of conventional radiography represents the principal method for bone diagnostics in endoprosthetics. Alternative objective quantitative methods are described but not commonly used. Therefore, semi-quantitative methods are tested using digital computation and artificial intelligence to standardize, simplify, and ultimately improve the assessment. This study aimed to evaluate the correlation between relative density progressions and clinical outcomes. Radiographs and clinical examinations before and 24 and 48 weeks after surgery were obtained from sixty-eight patients with a modular hip stem. For the calculation of the relative bone density, the modal gray values of the Gruen zones were measured using ImageJ and were normalized by gray values of the highest and lowest ROI. The clinical outcomes were measured according to the Harris hip score before evaluating them for correlations. Analyses were performed separately for subgroups and bone regions. The Harris hip score increased from 44.15 ± 15.00 pre-operatively to 66.20 ± 13.87 at the latest follow-up. The relative bone density adjustment of Gruen zone 7 showed a significant correlation to its clinical outcome. Other bone adaptations could be realistically reproduced and differences by regional zones and patients' histories visualized. Next to the simplicity and that no additional examination is required, the method provides good semi-quantitative results and visualizes adaptations, which make it suitable for use. [ABSTRACT FROM AUTHOR]

Blockchain is currently a core technology for developing new types of decentralized applications. With the unique properties of blockchain, unique challenges and characteristics are introduced to the system. Among these characteristics, the infrastructure costs and benefits of the system are critical to evaluate the feasibility of any system and have yet to be addressed in the current literature. This work presents a framework for evaluating blockchain applications' infrastructure costs and benefits. The framework includes a taxonomy to classify the related transactions, a model to evaluate the infrastructure costs and benefits in applications using public or private blockchains, and a methodology to guide the use of the model. The model is based on simple parameters that describe the systems, and the methodology helps to identify and estimate these parameters at any stage of the application life cycle. We quantitatively analyze three real use cases to demonstrate the framework's merit. The analyses highlight the model's accuracy by achieving the same results presented in the use cases. Furthermore, the use-case analyses emphasize the framework's potential to evaluate different scenarios across the entire life cycle of blockchain-based applications. [ABSTRACT FROM AUTHOR]