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The rapid advancements in sequencing technologies and bioinformatics have enabled metagenomic research of complex microbial systems, but reliable results depend on consistent laboratory and bioinformatics approaches. Current efforts to identify best practices often focus on optimizing specific steps, making it challenging to understand the influence of each stage on microbial population analysis and compare data across studies. This study evaluated DNA extraction, library construction methodologies, sequencing platforms, and computational approaches using a dog stool sample, two synthetic microbial community mixtures, and various sequencing data sources. Our work, the most comprehensive evaluation of metagenomic methods to date. We developed a software tool, termed minitax, which provides consistent results across the range of platforms and methodologies. Our findings showed that the Zymo Research Quick-DNA HMW MagBead Kit, Illumina DNA Prep library preparation method, and the minitax bioinformatics tool were the most effective for high-quality microbial diversity analysis. However, the effectiveness of pipelines or method combinations is sample-specific, making it difficult to identify a universally optimal approach. Therefore, employing multiple approaches is crucial for obtaining reliable outcomes in microbial systems. Evaluation of metagenomic methods for gut microbiome profiling using dog stool and microbial standards, leading to the development of minitax tool. Optimal wetlab and analysis pipelines are recommended for reliable crossplatform microbiome studies. [ABSTRACT FROM AUTHOR]

Background: Clostridium botulinum and Clostridium perfringens, 2 major foodborne pathogenic fusobacteria, have a variety of virulent protein types with nervous and enterotoxic pathogenic potential, respectively. Objective: The relationship between the molecular evolution of the 2 Clostridium genomes and virulence proteins was studied via a bioinformatics prediction method. The genetic stability, main features of gene coding and structural characteristics of virulence proteins were compared and analyzed to reveal the phylogenetic characteristics, diversity, and distribution of virulence factors of foodborne Clostridium strains. Methods: The phylogenetic analysis was performed via composition vector and average nucleotide identity based methods. Evolutionary distances of virulence genes relative to those of housekeeping genes were calculated via multilocus sequence analysis. Bioinformatics software and tools were used to predict and compare the main functional features of genes encoding virulence proteins, and the structures of virulence proteins were predicted and analyzed through homology modeling and a deep learning algorithm. Results: According to the diversity of toxins, genome evolution tended to cluster based on the protein-coding virulence genes. The evolutionary transfer distances of virulence genes relative to those of housekeeping genes in C. botulinum strains were greater than those in C. perfringens strains, and BoNTs and alpha toxin proteins were located extracellularly. The BoNTs have highly similar structures, but BoNT/A/B and BoNT/E/F have significantly different conformations. The beta2 toxin monomer structure is similar to but simpler than the alpha toxin monomer structure, which has 2 mobile loops in the N-terminal domain. The C-terminal domain of the CPE trimer forms a "claudin-binding pocket" shape, which suggests biological relevance, such as in pore formation. Conclusions: According to the genotype of protein-coding virulence genes, the evolution of Clostridium showed a clustering trend. The genetic stability, functional and structural characteristics of foodborne Clostridium virulence proteins reveal the taxonomy and diverse distribution of virulence factors. [ABSTRACT FROM AUTHOR]

Upgrades to advanced scientific user facilities such as next-generation x-ray light sources, nanoscience centers, and neutron facilities are revolutionizing our understanding of materials across the spectrum of the physical sciences, from life sciences to microelectronics. However, these facility and instrument upgrades come with a significant increase in complexity. Driven by more exacting scientific needs, instruments and experiments become more intricate each year. This increased operational complexity makes it ever more challenging for domain scientists to design experiments that effectively leverage the capabilities of and operate on these advanced instruments. Large language models (LLMs) can perform complex information retrieval, assist in knowledge-intensive tasks across applications, and provide guidance on tool usage. Using x-ray light sources, leadership computing, and nanoscience centers as representative examples, we describe preliminary experiments with a Context-Aware Language Model for Science (CALMS) to assist scientists with instrument operations and complex experimentation. With the ability to retrieve relevant information from facility documentation, CALMS can answer simple questions on scientific capabilities and other operational procedures. With the ability to interface with software tools and experimental hardware, CALMS can conversationally operate scientific instruments. By making information more accessible and acting on user needs, LLMs could expand and diversify scientific facilities' users and accelerate scientific output. [ABSTRACT FROM AUTHOR]

Amplicon sequencing has long served as a robust method for characterising microbial communities, and despite inherent resolution limitations, it remains a preferred technique, offering cost‐ and time‐effective insights into bacterial compositions. Here, we introduce ONT‐AmpSeq, a user‐friendly pipeline designed for processing amplicon sequencing data generated from Oxford Nanopore Technology (ONT) devices. Our pipeline enables efficient creation of taxonomically annotated operational taxonomic unit (OTU) tables from ONT sequencing data, with the flexibility to multiplex amplicons on the same barcode. The pipeline encompasses six main steps—statistics, quality filtering, alignment, clustering, polishing, and taxonomic classification—integrating various state‐of‐the‐art software tools. We provide a detailed description of each step, along with performance tests and robustness evaluations using both test data and a ZymoBIOMICS® Microbial Community Standard mock community dataset. Our results demonstrate the ability of ONT‐AmpSeq to effectively process ONT amplicon data, offering valuable insights into microbial community composition. Additionally, we discuss the influence of polishing tools on taxonomic insight and the impact of taxonomic annotation methods on the derived microbial composition. Overall, ONT‐AmpSeq represents a comprehensive solution for analysing ONT amplicon sequencing data, facilitating streamlined and reliable microbial community analysis. The pipeline, along with test data, is freely available for public use. [ABSTRACT FROM AUTHOR]

In recent years, crowd behavior detection has posed significant challenges in the realm of public safety and security, even with the advancements in surveillance technologies. The ability to perform real-time surveillance and accurately identify crowd behavior by considering factors such as crowd size and violence levels can avert potential crowd-related disasters and hazards to a considerable extent. However, most existing approaches are not viable to deal with the complexities of crowd dynamics and fail to distinguish different violence levels within crowds. Moreover, the prevailing approach to crowd behavior recognition, which solely relies on the analysis of closed-circuit television (CCTV) footage and overlooks the integration of online social media video content, leads to a primarily reactive methodology. This paper proposes a crowd behavior detection framework based on the swin transformer architecture, which leverages crowd counting maps and optical flow maps to detect crowd behavior across various sizes and violence levels. To support this framework, we created a dataset comprising videos capable of recognizing crowd behaviors based on size and violence levels sourced from CCTV camera footage and online videos. Experimental analysis conducted on benchmark datasets and our proposed dataset substantiates the superiority of our proposed approach over existing state-of-the-art methods, showcasing its ability to effectively distinguish crowd behaviors concerning size and violence level. Our method's validation through Nvidia's DeepStream Software Development Kit (SDK) highlights its competitive performance and potential for real-time intelligent surveillance applications. [ABSTRACT FROM AUTHOR]

Multi-heme cytochromes (MHCs), together with accessory proteins like porins and periplasmic cytochromes, enable microbes to transport electrons between the cytoplasmic membrane and extracellular substrates (e.g., minerals, electrodes, other cells). Extracellular electron transfer (EET) has been described in multiple systems; yet, the broad phylogenetic and mechanistic diversity of these pathways is less clear. One commonality in EET-capable systems is the involvement of MHCs, in the form of porin-cytochrome complexes, pililike cytochrome polymers, and lipid-anchored extracellular cytochromes. Here, we put forth MHCscan—a software tool for identifying MHCs and identifying potential EET capability. Using MHCscan, we scanned ∼60,000 bacterial and 2,000 archaeal assemblies, and identify a diversity of MHCs, many of which represent enzymes with no known function, and many found within organisms not previously known to be electroactive. In total, our scan identified ∼1,400 unique enzymes, each encoding more than 10 heme-binding motifs. In our analysis, we also find evidence for modularity and flexibility in MHC-dependent EET pathways, and suggest that MHCs may be far more common than previously recognized, with many facets yet to be discovered. [ABSTRACT FROM AUTHOR]

Establishing suitable in vitro culture conditions for microorganisms is crucial for dissecting their biology and empowering potential applications. However, a significant number of bacterial and fungal species, including Pneumocystis jirovecii, remain unculturable, hampering research efforts. P. jirovecii is a deadly pathogen of humans that causes life-threatening pneumonia in immunocompromised individuals and transplant patients. Despite the major impact of Pneumocystis on human health, limited progress has been made in dissecting the pathobiology of this fungus. This is largely due to the fact that its experimental dissection has been constrained by the inability to culture the organism in vitro. We present a comprehensive in silico genome-scale metabolic model of Pneumocystis growth and metabolism, to identify metabolic requirements and imbalances that hinder growth in vitro. We utilise recently published genome data and available information in the literature as well as bioinformatics and software tools to develop and validate the model. In addition, we employ relaxed Flux Balance Analysis and Reinforcement Learning approaches to make predictions regarding metabolic fluxes and to identify critical components of the Pneumocystis growth medium. Our findings offer insights into the biology of Pneumocystis and provide a novel strategy to overcome the longstanding challenge of culturing this pathogen in vitro. Author summary: Pneumocystis jirovecii is a human pathogen that causes life-threatening pneumonia in hundreds of thousands of immunocompromised individuals each year. Neither this fungus nor its close relative, the mouse pathogen Pneumocystis murina, can be cultured in vitro, and this is significantly hindering scientific progress. Therefore, we developed a comprehensive genome-scale metabolic model for P. murina using bioinformatics, software tools, and recently published genome data, and we used this metabolic model to predict critical components required for growth of the fungus. Our findings suggest that a subset of amino acids and specific lipids are essential for Pneumocystis survival. Additionally, we employed non-classical Flux Balance Analysis and Reinforcement Learning approaches to optimise ingredients for a Pneumocystis growth medium. This novel methodology has provided new insights into Pneumocystis metabolism and offers a potential approach to overcoming the challenge of culturing this pathogen in vitro, which would accelerate progress towards the development of improved diagnostics and therapies. [ABSTRACT FROM AUTHOR]

The educational landscape of toxicology is increasingly integrating computational methodologies due to ethical concerns about animal testing and advancements in biotechnological and data analysis tools. This paper examines the evolution and significance of the Toxicology in the 21st century (Tox21) initiative and its impact on computational toxicology education. It contrasts computational toxicology with traditional methods, highlighting the limitations of conventional approaches and the new perspectives offered by computational techniques. The study emphasizes the importance of incorporating computational toxicology into curricula, including case studies that demonstrate how this integration enhances students' problem-solving abilities, real-time data analysis skills, and innovation capabilities. Furthermore, it outlines effective teaching content and methods, including software tools, online resources, and academic literature. The paper also addresses the challenges and limitations faced in this educational shift and explores prospects for advancing computational toxicology education. By documenting these developments, the study aims to clarify the current advancements in toxicology education and the preparedness of students to address global chemical safety challenges with innovative solutions. [ABSTRACT FROM AUTHOR]

Over the past two decades, extensive studies, particularly in cancer analysis through large datasets like The Cancer Genome Atlas (TCGA), have aimed at improving patient therapies and precision medicine. However, limited overlap and inconsistencies among gene signatures across different cohorts pose challenges. The dynamic nature of the transcriptome, encompassing diverse RNA species and functional complexities at gene and isoform levels, introduces intricacies, and current gene signatures face reproducibility issues due to the unique transcriptomic landscape of each patient. In this context, discrepancies arising from diverse sequencing technologies, data analysis algorithms, and software tools further hinder consistency. While careful experimental design, analytical strategies, and standardized protocols could enhance reproducibility, future prospects lie in multiomics data integration, machine learning techniques, open science practices, and collaborative efforts. Standardized metrics, quality control measures, and advancements in single-cell RNA-seq will contribute to unbiased gene signature identification. In this perspective article, we outline some thoughts and insights addressing challenges, standardized practices, and advanced methodologies enhancing the reliability of gene signatures in disease transcriptomic research. [ABSTRACT FROM AUTHOR]

Background: Cardiovascular diseases (CVDs) remain the leading cause of mortality, especially in low‐ and middle‐income countries, many of which are in the Arab region. We aimed to conduct a bibliometric analysis to assess the scientific output concerning CVDs in the Arab region and the Middle East over the past decade. Methods: A bibliometric search was conducted on PubMed and Scopus between 2012 and 2022. The study analyzed the number of publications, countries, institutional sources, authors, journals, and keywords. Visualization analysis was executed using various software tools, including R, VOSviewer, and CiteSpace. Results: PubMed and Scopus yielded 5340 documents related to CVDs at the time of data collection. A total of 1263 documents were retrieved after screening based on specific inclusion criteria that guarantee the inclusion only for Arab region studies and authors. There has been a consistent increase in annual publications in recent years. The countries that contributed the most to research in this field were Egypt, Saudi Arabia, and the UAE. Although Egypt stood out as the most productive country, the institute with the highest number of documents was in Qatar. In addition, the Top 3 authors hailed from Qatar. Saudi Medical Journal leads the field as the most productive journal, followed closely by PLoS One and Angiology. Research topics of significant interest in the realm of CVDs include specific diseases such as heart failure, risk factors related to CVDs, genetic aspects of CVDs, and congenital disorders in infant's cardiac health. Conclusion: This study provides a comprehensive overview of the current status of CVD research in the Arab region. It includes research hotspots that can guide authors in determining the necessary future investigations within this field. There is a clear call for further exploration of various aspects of CVDs in the Arab world. Strengthening cooperation between countries and institutes is needed. [ABSTRACT FROM AUTHOR]

This work presents the development of an embedded platform using Field Programmable Gate Arrays (FPGAs) for real-time simulation of dynamic systems in industrial plants. The platform, Real-Time Simulator for Dynamic Systems in FPGA (RTSDS-FPGA), is designed for industrial and academic applications. In industrial contexts, the RTSDS-FPGA facilitates the optimization and tuning of embedded control algorithms, while in academia, it supports research on new embedded solutions in automation and control. It is also an educational tool for undergraduate and postgraduate students developing embedded control system projects. Additionally, the simulator accelerates the simulation of slow dynamic systems, significantly reducing overall simulation time. Experimental results demonstrate the platform's capability to perform real-time simulations effectively, validating its accuracy and performance through comparative analyses with established software tools such as Matlab/Simulink. [ABSTRACT FROM AUTHOR]

This article discusses the software tool (Simscape—Multibody program of MATLAB) primarily intended for dynamic and kinematic processes with practical applications in static calculations. Currently, there are few published scientific works utilizing this tool for tasks like basic static calculations of truss systems. We were interested in comparing the calculation using the tools we use in our work and research activities for theoretical calculation; the potential reliance on simulations in the future could help to avoid the necessity of complex theoretical calculations, which can be time-consuming and prone to errors. Despite the fact that the structure may appear simple, in practice, there may not always be time for a verification calculation in the theoretical field (proper model creation, inclusion of all conditions, etc.). The beam system is intentionally both externally and internally statically indeterminate. For this reason, it is logically necessary to also consider deformation conditions. The achieved results were interesting in terms of accuracy compared to SOLIDWORKS, which was used for computation verification. Through very simple optimization, we were able to further increase the calculation accuracy without complicating other parameters. [ABSTRACT FROM AUTHOR]

Motivation Single cell profiling by cytometry has emerged as a key technology in biology, immunology and clinical-translational medicine. The correct annotation, which refers to the identification of clusters as specific cell populations based on their marker expression, of clustered high-dimensional cytometry data, is a critical step of the analysis. Its accuracy determines the correct interpretation of the biological data. Despite the progress in various clustering algorithms, the annotation of clustered data still remains a manual, time consuming and error-prone task. We developed a user-friendly cluster annotation and differential abundance detection tool that can be applied on data generated with Self Organizing Map clustering algorithms, thus simplifying the annotation process of datasets that consist of hundreds or thousands of clusters. Results We present Cytometry Cluster Annotation and Differential Abundance Suite (CyCadas), a semi-automated software tool that facilitates cluster annotation in cytometry data by offering both visual and computational guidance. CyCadas addresses the critical need for efficient and accurate annotation of high-resolution clustered cytometry data, significantly reducing the time needed to perform the analysis compared to both manual gating approaches and manual annotation of clustered data. The tool features a user-friendly interface, visual tools enabling data exploration and automated threshold estimation to separate negative and positive marker expression. It facilitates the definition and annotation of cell phenotypes among multiple clusters in a tree-based data structure. Finally, it calculates the abundance of various cell populations across the conditions with statistical interpretation. It is an ideal resource for researchers aiming to streamline their cytometry workflow. Availability and implementation CyCadas is available as open source at: https://github.com/DII-LIH-Luxembourg/cycadas. [ABSTRACT FROM AUTHOR]

This paper deals with the study of torsional energy (total squared torsion) at infinitesimal bending of curves and knots in three dimensional Euclidean space. During bending, the curve is subject to change, and its properties are changed. The effect that deformation has on the curve is measured by variations. Here, we observe the infinitesimal bending of the second order and variations of the first and the second order that occur in this occasion. The subjects of study are curves and knots, in particular torus knots. We analyze various examples both analytically and graphically, using our own calculation and visualization software tool. [ABSTRACT FROM AUTHOR]

Background: Genomic medicine has transformed clinical genetics by utilizing high‐throughput sequencing technologies to analyze genetic variants associated with diseases. Accurate variant classification is crucial for diagnosis and treatment decisions, and various tools and software such as the Ion Reporter Software and the Illumina Nirvana Software often used in a clinical setting utilize information from the ClinVar database/archive to aid in variant interpretation. However, these existing annotation tools may lack access to the latest ClinVar data, necessitating manual variant inspection. Aims: To address this gap in developing a tool providing the latest ClinVar data for variant annotation in clinical and research settings. Materials and Methods: We introduce CANVAR, a Python‐based script that efficiently annotates variants identified from next‐generation sequencing in a clinical or research context, offering comprehensive information from the latest ClinVar database. Results: CANVAR provides accurate, up‐to‐date variant annotations, streamlining variant analysis. Discussion: The rise in genomic data requires accurate variant annotation for clinical decision‐making. Misclassification poses risks, and current tools may not always access the latest data, challenging variant interpretation. Conclusion: CANVAR contributes to enhancing variant annotation by offering comprehensive information from the latest ClinVar database for genetic variants identified through next‐generation sequencing. [ABSTRACT FROM AUTHOR]

Simple Summary: Spatial epidemiology, integrating traditional epidemiology, geography, statistics, environmental science, and ecology, provides a comprehensive framework for analyzing the spatial dimensions of health and disease. This interdisciplinary approach enhances the development of effective public health strategies and interventions. However, its multifaceted nature can bring complexities in practical application. Using the case of spatial epidemiology in swine viral diseases (SVDs), we illustrate the objectives, methodologies, and essential considerations for the application of spatial epidemiology, which we hope to offer as a comprehensive reference for researchers in this field. Spatial epidemiology offers a comprehensive framework for analyzing the spatial distribution and transmission of diseases, leveraging advanced technical tools and software, including Geographic Information Systems (GISs), remote sensing technology, statistical and mathematical software, and spatial analysis tools. Despite its increasing application to swine viral diseases (SVDs), certain challenges arise from its interdisciplinary nature. To support novices, frontline veterinarians, and public health policymakers in navigating its complexities, we provide a comprehensive overview of the common applications of spatial epidemiology in SVD. These applications are classified into four categories based on their objectives: visualizing and elucidating spatiotemporal distribution patterns, identifying risk factors, risk mapping, and tracing the spatiotemporal evolution of pathogens. We further elucidate the technical methods, software, and considerations necessary to accomplish these objectives. Additionally, we address critical issues such as the ecological fallacy and hypothesis generation in geographic correlation analysis. Finally, we explore the future prospects of spatial epidemiology in SVD within the One Health framework, offering a valuable reference for researchers engaged in the spatial analysis of SVD and other epidemics. [ABSTRACT FROM AUTHOR]

SoCs with analog‐circuit‐based unsigned weight‐accumulating spiking neural networks (UWA‐SNNs) are a highly promising solution for achieving low‐power AI‐SoCs. This paper addresses the challenges that must be overcome to realize the potential of UWA‐SNNs in low‐power AI‐SoCs: (i) the absence of UWA‐SNN learning methods and the lack of an environment for developing applications based on trained SNN models and (ii) the inherent issue of testing and validating applications on the system being nearly impractical until the final chip is fabricated owing to the mixed‐signal circuit implementation of UWA‐SNN‐based SoCs. This paper argues that, by integrating the proposed solutions, the development of an EDA tool that enables the easy and rapid development of UWA‐SNN‐based SoCs is feasible, and demonstrates this through the development of the SNN eXpress (SNX) tool. The developed SNX automates the generation of RTL code, FPGA prototypes, and a software development kit tailored for UWA‐SNN‐based application development. Comprehensive details of SNX development and the performance evaluation and verification results of two AI‐SoCs developed using SNX are also presented. [ABSTRACT FROM AUTHOR]

As one of the two most ancient groups of extant vertebrates, lamprey has become an important model organism in various fields of biology. In this paper, we present a comprehensive tissue-wide spatial metabolomics dataset for lampreys, where 14 distinct tissues were analyzed using liquid chromatography-mass spectrometry (LC-MS) in both positive and negative ion modes. The dataset has been fully validated using internal standard and pooled quality control samples and is readily accessible at the UCSD Metabolomics Workbench. This dataset serves as a valuable resource for researchers using lampreys as a model organism. Additionally, it acts as a benchmark metabolomics dataset for evaluating new algorithms and software tools and comparing them with previously published results. A lamprey spatial metabolomics database is also provided to support studies utilizing lampreys as an animal model, and to complement and validate other spatial metabolomics studies on lampreys conducted with mass spectrometry imaging or other techniques. [ABSTRACT FROM AUTHOR]

Copyright of Environmental & Social Management Journal / Revista de Gestão Social e Ambiental is the property of Environmental & Social Management Journal and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

RNA viruses exhibit vast phylogenetic diversity and can significantly impact public health and agriculture. However, current bioinformatics tools for viral discovery from metagenomic data frequently generate false positive virus results, overestimate viral diversity, and misclassify virus sequences. Additionally, current tools often fail to determine virus–host associations, which hampers investigation of the potential threat posed by a newly detected virus. To address these issues we developed VirID, a software tool specifically designed for the discovery and characterization of RNA viruses from metagenomic data. The basis of VirID is a comprehensive RNA-dependent RNA polymerase database to enhance a workflow that includes RNA virus discovery, phylogenetic analysis, and phylogeny-based virus characterization. Benchmark tests on a simulated data set demonstrated that VirID had high accuracy in profiling viruses and estimating viral richness. In evaluations with real-world samples, VirID was able to identify RNA viruses of all types, but also provided accurate estimations of viral genetic diversity and virus classification, as well as comprehensive insights into virus associations with humans, animals, and plants. VirID therefore offers a robust tool for virus discovery and serves as a valuable resource in basic virological studies, pathogen surveillance, and early warning systems for infectious disease outbreaks. [ABSTRACT FROM AUTHOR]

Copyright of European Journal of Management & Business Economics is the property of Emerald Publishing Limited and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Retos: Nuevas Perspectivas de Educación Física, Deporte y Recreación is the property of Federacion Espanola de Asociaciones de Docentes de Educacion Fisica and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Accurate information of the fine-scale spatial patterns of trees and their interactions within a stand is critical for explaining the competition, health and vigor status, and future development of a stand. There are a number of indices which can show such patterns, but the stand spatial structure index is the most important. This index can be quantified based on the spatial information of trees (tree positions) within a stand and has paramount importance in identifying candidate trees to be thinned. This study develops a software tool (algorithm), which can conveniently and accurately estimate the stand spatial structure index. Our proposed algorithm considers the spatial relationships between a reference tree and its four adjacent trees, and computes the three most important stand structure indices (neighborhood comparison, uniform angle index and species mingling) using GIS (ArcEngine) and the C# programming language. The implementation of the developed algorithm (stand spatial structure index) shows that, for any reference tree assumed, its four adjacent trees identified by each of the three stand spatial structure indices (uniform angle index—UAI, mingling—M and neighborhood comparison—NC) are the same, indicating the consistency and accuracy between the three-stand spatial structural indices. For the same tree species in a forest stand, the computational results from each of the spatial structure indices used (UAI, M, NC) are also the same. Thus, the results of this algorithm developed in this study are consistent with that of the Winkelmass1.0 software (a type of software used to simulate stand spatial structure). As this article is based on the GIS technique, the computational results can be visually displayed and implemented on actual maps, making it more convenient and intuitive for forest management. The proposed approach will be useful for accurately identifying the trees to be thinned and helpful for maintaining the vigor stand structure. This study also demonstrates the implementation of the algorithm to the real-world data and proves that the computational process is simple and efficient. The application of this algorithm for the identification of trees to be thinned may help the stakeholders to focus their attention towards multi-functional forest management. The algorithm will also provide an important basis for optimizing thinning and maintaining well-structured forest stands. [ABSTRACT FROM AUTHOR]

This editorial introduces a special issue of Large-Scale Assessments in Education (LSAE) that addresses key challenges in analyzing longitudinal data from large-scale studies. These challenges include ensuring fair measurement across time, developing common metrics, and correcting for measurement errors. The special issue highlights recent methodological innovations, particularly for studies like the National Education Panel Study (NEPS), providing approaches for improving the accuracy and robustness of longitudinal educational research. The papers in this issue present advances in methods for estimating trends, incorporating background information, and analyzing longitudinal relationships between constructs. Innovative approaches such as Bayesian modeling for borrowing historical information, continuous-time models for capturing developmental trends, and plausible value estimation provide practical solutions for researchers working with complex longitudinal data. In addition, the issue presents new software tools that facilitate the implementation of these advanced methodologies. Together, these papers contribute to both the theory and practice of educational assessment and provide valuable insights for those working with longitudinal data in national and international panel studies. [ABSTRACT FROM AUTHOR]

We assess the UK Biobank (UKB) Polygenic Risk Score (PRS) Release, a set of PRSs for 28 diseases and 25 quantitative traits that has been made available on the individuals in UKB, using a unified pipeline for PRS evaluation. We also release a benchmarking software tool to enable like-for-like performance evaluation for different PRSs for the same disease or trait. Extensive benchmarking shows the PRSs in the UKB Release to outperform a broad set of 76 published PRSs. For many of the diseases and traits we also validate the PRS algorithms in a separate cohort (100,000 Genomes Project). The availability of PRSs for 53 traits on the same set of individuals also allows a systematic assessment of their properties, and the increased power of these PRSs increases the evidence for their potential clinical benefit. [ABSTRACT FROM AUTHOR]

Simple Summary: This study investigated the genetic attributes of the Jiangshan black pig conservation population, with a specific focus on genetic diversity, family structure, and levels of inbreeding. The results provide significant insights for the management and conservation of a pig population with limited numbers. The study proposes the use of genomic data by breeders to improve breeding practices, especially by taking into account familial relationships. Suggestions include maintaining an equitable distribution of male and female pigs within each family and choosing individuals with a kinship coefficient lower than 0.1 for breeding purposes. The Jiangshan black pig is an indigenous pig breed in China, renowned for its superior meat quality and adaptability to roughage. However, the population of Jiangshan black pigs has dwindled due to the introduction of cosmopolitan pig breeds and the outbreak of African swine fever, putting them at risk of extinction. To offer insights into the conservation and breeding of Jiangshan black pigs, this study involved 118 Jiangshan black pigs as the research subjects and employed the Zhongxin-1 Porcine Breeding Array PLUS chip to detect whole-genome SNPs. Additionally, various software tools were utilized to accurately analyze the genetic diversity, phylogenetic relationship, inbreeding coefficient, and pedigree structure of the Jiangshan black pig conservation population. The findings indicated that the effective population size (Ne) of the Jiangshan black pig was 4.9, with an average inbreeding coefficient of 0.253 within the population. A genetic relationship analysis identified that the 16 male pigs were clustered into four families, and the 100 female pigs were also assigned to these familial groups. Furthermore, two female pigs were classified as "other" due to their distant genetic relatedness to all the males. These results contribute to a better understanding of the current status of the conservation of the Jiangshan black pig population and offer a theoretical foundation for the development of conservation strategies. [ABSTRACT FROM AUTHOR]

Objective: Cardiovascular magnetic resonance enables the quantification of functional and morphological parameters with an impact on therapeutical decision making. While quantitative assessment is established in 2D, novel 3D techniques lack a standardized approach. Multi-planar-reformatting functionality in available software relies on visual matching location and often lacks necessary functionalities for further post-processing. Therefore, the easy-to-use Reslice3Dto2D software tool was developed as part of another research project to fill this gap and is now introduced with this work. Results: The Reslice3Dto2D reformats 3D data at the exact location of a reference slice with a two-step-based interpolation in order to reflect in-plane discretization and through-plane slice thickness including a slice profile selection. The tool was successfully validated on an artificial dataset and tested on 119 subjects with different underlying pathologies. The exported reformatted data could be imported into three different post-processing software tools. The quantified image sharpness by the Frequency Domain Image Blur Measure was significantly decreased by around 40% on rectangular slice profiles with 7 mm slice thickness compared to 0 mm due to partial volume effects. Consequently, Reslice3Dto2D enables the quantification of 3D data with conventional post-processing tools as well as the comparison of 3D acquisitions with their established 2D version. [ABSTRACT FROM AUTHOR]

Reproducibility of computational research is often challenging despite established guidelines and best practices. Translating these guidelines into practical applications remains difficult. Here, we present ENCORE, an approach to enhance transparency and reproducibility by guiding researchers in how to structure and document a computational project. ENCORE builds on previous efforts in computational reproducibility and integrates all project components into a standardized file system structure. It utilizes pre-defined files as documentation templates, leverages GitHub for software versioning, and includes an HTML-based navigator. ENCORE is designed to be agnostic to the type of computational project, data, programming language, and ICT infrastructure, and does not rely on specific software tools. We also share our group's experience using ENCORE, highlighting that the most significant challenge to the routine adoption of approaches like ours is the lack of incentives to motivate researchers to dedicate sufficient time and effort to ensure reproducibility. Reproducibility of computational research remains challenging. Here, authors present ENCORE, an approach to enhance reproducibility. The most significant challenge to the routine adoption of approaches like ENCORE is the lack of incentives for researchers to dedicate sufficient time and effort to ensure reproducibility. [ABSTRACT FROM AUTHOR]

This article emphasizes the importance of training scientists in software development skills, specifically in the field of computational biology. It highlights the need for open access and accurate implementation of software in scientific research. The article provides guidelines for teaching software engineering skills to researchers, including the emphasis on coding practices and the support for students to develop these practices. It also discusses the benefits of incorporating software engineering into scientific education and provides examples of successful software packages developed by students. The authors encourage graduate training programs to prioritize software development skills and promote sustainable software practices. [Extracted from the article]

Extensive research is currently underway to determine the security of existing ciphers in light of the advancements in quantum computing. Against symmetric key cryptography, Grover's search algorithm is a prominent attack, capable of reducing search costs to the square root. For using Grover's algorithm, it is imperative to embed the target cipher into a quantum circuit. Even so, this area of research is relatively new; it has garnered significant attention from the research community. In this study, we provide the first estimation of the cost of Grover's key search attack against the AES-based AEAD schemes Rocca-S, AEGIS-128, and Tiaoxin-346. Our analysis considers circuit depth restrictions specified in NIST's PQC standardization process. Considering NIST's maximum depth constraints, We present the overall cost of these attacks using gate count and depth-times-width metrics. We observed that for MAXDEPTH = 2 40 , Rocca-S, AEGIS-128, and Tiaoxin-346 can be retrieved using Grover's search algorithm with gate count of 1.09 × 2253, 1.14 × 2124, and 1.22 × 2124 respectively. Concerning the current updated values by NIST, these ciphers are secure in terms of the cost of implementing Grover's attack for key recovery. The quantum circuits of these ciphers are implemented using QISKIT, an open-source software development kit (SDK) designed for working with quantum computers running on the IBM Quantum Experience platform. [ABSTRACT FROM AUTHOR]

Genome-wide association studies (GWAS) have revolutionized our understanding of the genetic architecture of complex traits and diseases. GWAS summary statistics have become essential tools for various genetic analyses, including meta-analysis, fine-mapping, and risk prediction. However, the increasing number of GWAS summary statistics and the diversity of software tools available for their analysis can make it challenging for researchers to select the most appropriate tools for their specific needs. This systematic review aims to provide a comprehensive overview of the currently available software tools and databases for GWAS summary statistics analysis. We conducted a comprehensive literature search to identify relevant software tools and databases. We categorized the tools and databases by their functionality, including data management, quality control, single-trait analysis, and multiple-trait analysis. We also compared the tools and databases based on their features, limitations, and user-friendliness. Our review identified a total of 305 functioning software tools and databases dedicated to GWAS summary statistics, each with unique strengths and limitations. We provide descriptions of the key features of each tool and database, including their input/output formats, data types, and computational requirements. We also discuss the overall usability and applicability of each tool for different research scenarios. This comprehensive review will serve as a valuable resource for researchers who are interested in using GWAS summary statistics to investigate the genetic basis of complex traits and diseases. By providing a detailed overview of the available tools and databases, we aim to facilitate informed tool selection and maximize the effectiveness of GWAS summary statistics analysis. [ABSTRACT FROM AUTHOR]

Background: Advancements over the past decade in DNA sequencing technology and computing power have created the potential to revolutionize medicine. There has been a marked increase in genetic data available, allowing for the advancement of areas such as personalized medicine. A crucial type of data in this context is genetic variant data which is stored in variant call format (VCF) files. However, the rapid growth in genomics has presented challenges in analyzing and comparing VCF files. Results: In response to the limitations of existing tools, this paper introduces a novel web application that provides a user-friendly solution for VCF file analyses and comparisons. The software tool enables researchers and clinicians to perform high-level analysis with ease and enhances productivity. The application's interface allows users to conveniently upload, analyze, and visualize their VCF files using simple drag-and-drop and point-and-click operations. Essential visualizations such as Venn diagrams, clustergrams, and precision–recall plots are provided to users. A key feature of the application is its support for metadata-based file grouping, accomplished through flexible data matrix uploads, streamlining organization and analysis of user-defined categories. Additionally, the application facilitates standardized benchmarking of VCF files by integrating user-provided ground truth regions and variant lists. Conclusions: By providing a user-friendly interface and supporting essential visualizations, this software enhances the accessibility of VCF file analysis and assists researchers and clinicians in their scientific inquiries. [ABSTRACT FROM AUTHOR]

Summary MGI sequencing is reported to be an inexpensive solution to obtain genomics information. There is a growing need for software and tools to analyse MGI's outputs efficiently. mgikit is a tool collection to demultiplex MGI fastq data, reformat it effectively and produce visual quality reports. mgikit overcomes several limitations of the standard MGI demultiplexer. It is highly customizable to suit different kinds of datasets and is designed to achieve high performance and optimal memory utilization. Availability and implementation The tool and its documentation are available at: https://sagc-bioinformatics.github.io/mgikit/. [ABSTRACT FROM AUTHOR]

Abstract: The green analytical procedure index (GAPI) has been widely used to assess the greenness of different steps in analytical methodology. In the GAPI index, the different stages of the chemical analysis process are depicted using five pentagrams divided in subsections, labeled green, yellow, or red according to the degree of greenness. This GAPI tool provides a quick overview of the environmental impact and safety of the procedure. However, there is no total score that can be calculated from the GAPI metric to enable comparison between methods. In this work, a modified GAPI tool (MoGAPI) and software have been developed and applied to address the limitations of the current GAPI metric. The presented tool offers a more precise assessment of greenness, while the software simplifies and expedites its application. It also combines the advantages of the analytical Eco-Scale with the merits of the widely used GAPI metric. This tool was successfully applied to calculate the greenness of a few case studies and applications to show the applicability of this modified metric. The software for the MoGAPI tool is also freely available (open source) at bit.ly/MoGAPI to facilitate application and method comparison. The MoGAPI tool and its software represent a significant advancement in greenness assessment, providing researchers with a robust and user-friendly means to evaluate and compare analytical methods. [ABSTRACT FROM AUTHOR]

The aim of the present study was to develop and evaluate the performance of a methodology to estimate the population pharmacokinetic (PK) parameters along with the inter-individual variabilities (IIVs) from patients' reported aggregate concentration–time data, in particular, mean plasma concentrations and their standard deviations (SDs) versus time, such as those often found in published graphs. This method was applied to the published data of gevokizumab, a novel monoclonal anti-interleukin-1β antibody, in order to estimate the drug's population pharmacokinetic (PopPK) parameters of a second-generation minimal physiologically based pharmacokinetic (mPBPK) model. Assuming this mPBPK model, a mixed effects approach was utilized to allow accounting for the random inter-group variability (IGV) that was assumed among different dosage groups. The entire analysis was performed using R software (Rstudio) and the Bayesian software tool RStan was used for the application of Bayesian priors on the parameters. Conclusively, the proposed method could be applied to monoclonal antibodies for which the second-generation mPBPK model has been proposed as well as to other drugs with different PK models when only a published graph with aggregate concentration–time data is available. In addition, the method could be used when multiple aggregate datasets from different sources need to be combined in a meta-analysis approach in order to estimate the PopPK parameters of a drug. [ABSTRACT FROM AUTHOR]

The Exascale Computing Project (ECP) Software Technology and Co-Design teams addressed the growing complexities in high-performance computing (HPC) by developing scalable software libraries and tools that leverage exascale system capabilities. As we enter the exascale era, the need for reusable, optimized software solutions that can handle the unique challenges posed by these systems becomes increasingly important. The primary challenges the ECP teams faced were to create software libraries and tools that are performant on exascale architectures and portable and usable across diverse hardware platforms. Efforts addressed issues related to concurrent execution, memory management, and the integration of heterogeneous computing resources, such as GPUs from multiple vendors. The ECP's strategy involved a structured development process encompassing the creation, optimization, and deployment of software in collaboration with industry, academia, and national laboratories. The project was organized into several technical areas: co-design of domain-specific suites with target applications, programming models and runtimes, development tools, mathematical libraries, data and visualization tools, and software ecosystem and delivery mechanisms. ECP has successfully developed a large portfolio of software libraries and tools that demonstrate significant improvements in performance and scalability on exascale systems. These products have been integrated into the Department of Energy's computing facilities, supporting various scientific applications and ensuring robust performance across different hardware setups. ECP advancements in software development for exascale computing highlight the importance of a collaborative and adaptive approach to handling next-generation HPC systems complexities. The lessons learned emphasize the need for continuous engagement with end-users and vendors, and the importance of maintaining a balance between innovation and practical implementation. Future efforts will focus on ensuring scalability, keeping pace with rapid hardware advancements, and further enhancing the interoperability and usability of the software ecosystem. Subsequent articles in this special issue provide in-depth discussions and case studies into specific library and tool efforts. [ABSTRACT FROM AUTHOR]

An overwhelming majority of protein–protein interaction (PPI) studies are conducted in a select few model organisms largely due to constraints in time and cost of the associated 'wet lab' experiments. In silico PPI inference methods are ideal tools to overcome these limitations, but often struggle with cross-species predictions. We present INTREPPPID, a method that incorporates orthology data using a new 'quintuplet' neural network, which is constructed with five parallel encoders with shared parameters. INTREPPPID incorporates both a PPI classification task and an orthologous locality task. The latter learns embeddings of orthologues that have small Euclidean distances between them and large distances between embeddings of all other proteins. INTREPPPID outperforms all other leading PPI inference methods tested on both the intraspecies and cross-species tasks using strict evaluation datasets. We show that INTREPPPID's orthologous locality loss increases performance because of the biological relevance of the orthologue data and not due to some other specious aspect of the architecture. Finally, we introduce PPI.bio and PPI Origami, a web server interface for INTREPPPID and a software tool for creating strict evaluation datasets, respectively. Together, these two initiatives aim to make both the use and development of PPI inference tools more accessible to the community. [ABSTRACT FROM AUTHOR]

The analysis of utilising unmanned aerial vehicles (UAVs) to form flying networks in obstacle conditions and various algorithms for obstacle avoidance is conducted. A planning scheme for deploying a flying LiFi network based on UAVs in a production facility with obstacles is developed and described. Such networks are necessary to ensure reliable data transmission from sensors or other sources of information located in dangerous or hard-to-reach places to the crisis centre. Based on the planning scheme, the following stages are described: (1) laying the LiFi signal propagation route in conditions of interference, (2) placement of the UAV at the specified points of the laid route for the deployment of the LiFi network, and (3) ensuring the reliability of the deployed LiFi network. Strategies for deploying UAVs from a stationary depot to form a flying LiFi network in a room with obstacles are considered, namely the strategy of the first point for the route, the strategy of radial movement, and the strategy of the middle point for the route. Methods for ensuring the uninterrupted functioning of the flying LiFi network with the required level of reliability within a given time are developed and discussed. To implement the planning stages for deploying the UAV flying LiFi network in a production facility with obstacles, the "Simulation Way" and "Reliability Level" software tools are developed and described. Examples of utilising the proposed software tools are given. [ABSTRACT FROM AUTHOR]

The escalating demand for water, energy, and food, coupled with the imperative for sustainable development, necessitates innovative solutions to address the complex interdependencies within the water–energy–food nexus. In this context, agriculture and photovoltaics (Agri-PV or Agri–voltaics) systems have emerged as a promising approach to promoting sustainable agricultural practices while enhancing energy efficiency and food production. However, limited research, especially on the technical aspects of Agri-PV, has resulted in a knowledge gap regarding how to model and determine the suitability of Agri-PV for different crops based on local conditions. This study presents a novel approach to modeling and simulating Agri-PV systems for various major crops in developing countries, using Uzbekistan as a case study. It provides a blueprint for selecting suitable Agri-PV systems. The research investigates the technical feasibility of Agri-PV technology tailored to Uzbekistan's agricultural landscape, with broader implications for Central Asia. Employing a systematic methodology, the study begins by selecting appropriate sites and crops for Agri-PV system testing, ensuring the relevance and applicability of the research findings to the local context. Using advanced software tools such as PVSyst, the study accurately calculates photosynthetically active radiation (PAR) values specific to selected crops, bridging a significant knowledge gap and providing empirical data essential for informed decision making. The methodology further incorporates an in-depth analysis of economic and technical considerations in selecting PV modules and inverters, enhancing the scientific accuracy of the study. By strategically modeling Agri-PV systems based on parameters like row density, module distance, and tilt angle, this research aims to optimize the integration of photovoltaic technology with agricultural practices in Uzbekistan. Moreover, this study helps to understand the impact of Agri-PV systems on the water–energy–food nexus, providing valuable insights into the potential benefits and challenges specific to the region. The study identifies the positive impact of Agri-PV on major crops and provides a suitable design and modeling approach for sustainable farming practices. [ABSTRACT FROM AUTHOR]

High-throughput chromosome conformation capture (Hi-C) technology captures spatial interactions of DNA sequences into matrices, and software tools are developed to identify topologically associating domains (TADs) from the Hi-C matrices. With structural information theory, SuperTAD adopted a dynamic programming approach to find the TAD hierarchy with minimal structural entropy. However, the algorithm suffers from high time complexity. To accelerate this algorithm, we design and implement an approximation algorithm with a theoretical performance guarantee. We implemented a package, SuperTAD-Fast. Using Hi-C matrices and simulated data, we demonstrated that SuperTAD-Fast achieved great runtime improvement compared with SuperTAD. SuperTAD-Fast shows high consistency and significant enrichment of structural proteins from Hi-C data of human cell lines in comparison with the existing six hierarchical TADs detecting methods. [ABSTRACT FROM AUTHOR]

Multilayer gratings are increasingly popular optical elements at X‐ray beamlines, as they can provide much higher photon flux in the tender X‐ray range compared with traditional single‐layer coated gratings. While there are several proprietary software tools that provide the functionality to simulate the efficiencies of such gratings, until now the X‐ray community has lacked an open‐source alternative. Here MLgrating is presented, a program for simulating the efficiencies of both multilayer gratings and single‐layer coated gratings for X‐ray applications. MLgrating is benchmarked by comparing its output with that of other software tools and plans are discussed for how the program could be extended in the future. [ABSTRACT FROM AUTHOR]

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This study introduces a mixed integer secondorder cone programming (MISOCP) model called the green Ellipsoid model for power saving in communication networks. The goal of this research is to optimize power consumption in communication networks by applying the conic optimization technique which is an emerging branch of research. The consumed power in communication networks is minimized considering network data variation using robust optimization. We apply the ellipsoidal uncertainty set to grant a variation in the network data and presented the model in the form of MISOCP. To scale down the total energy utilization in the network, the study proposes shutting down some unnecessary links throughout the entire network. By identifying and deactivating these redundant or unused links, the overall power consumption is reduced. Based on the numerical results obtained, the proposed green Ellipsoid model demonstrates the ability to save consumed power in comparison to the existing green Hose approach. The results indicate that the green Ellipsoid model exceeds the green Hose approach in terms of power savings. This suggests that the introduced model is more adequate in optimizing power utilization and achieving energy efficiency in the communication networks. An additional advantage of the green Ellipsoid model is its ability to accommodate data variation across the network through a single parameter. Acknowledging that MISOCP is a known NP-hard problem, the study also proposes an improved method to minimize computation time. This is achieved by leveraging optimization software tools that make the model tractable. By utilizing these tools, the presented model can be efficiently solved within an acceptable time. [ABSTRACT FROM AUTHOR]

In this paper we introduce a new class of software tools engaged in delivering successful explanations of complex processes on top of basic Explainable AI (XAI) software systems. These tools, that we call cumulatively Explanatory AI (YAI) systems, enhance the quality of the basic output of a XAI by adopting a user-centred approach to explanation that can cater to the individual needs of the explainees with measurable improvements in usability. Our approach is based on Achinstein's theory of explanations, where explaining is an illocutionary (i.e., broad yet pertinent and deliberate) act of pragmatically answering a question. Accordingly, user-centrality enters in the equation by considering that the overall amount of information generated by answering all questions can rapidly become overwhelming and that individual users may perceive the need to explore just a few of them. In this paper, we give the theoretical foundations of YAI, formally defining a user-centred explanatory tool and the space of all possible explanations, or explanatory space, generated by it. To this end, we frame the explanatory space as an hypergraph of knowledge and we identify a set of heuristics and properties that can help approximating a decomposition of it into a tree-like representation for efficient and user-centred explanation retrieval. Finally, we provide some old and new empirical results to support our theory, showing that explanations are more than textual or visual presentations of the sole information provided by a XAI. [ABSTRACT FROM AUTHOR]

Carbon storage estimates are essential for sustainable urban planning and development. This study examines the spatio-temporal effects of land use and land cover changes on the provision and monetary value of above- and below-ground carbon sequestration and storage during 2011, 2019, and the simulated year 2027 in Noida. The Google Earth Engine-Random Forests (GEE-RF) classifier, the Cellular Automata Artificial Neural Network (CA-ANN) model, and the InVEST-CCS model are some of the software tools applied for the analysis. The findings demonstrate that the above- and below-ground carbon storage for Noida is 23.95 t/ha. Carbon storage in the city increased between 2011 and 2019 by approximately 67%. For the predicted year 2027, a loss in carbon storage is recorded. The simulated land cover for the year 2027 indicates that if the current pattern continues for the next decade, the majority of the land will be transformed into either built-up or barren land. This predicted decline in agriculture and vegetation would further lead to a slump in the potential for terrestrial carbon sequestration. Urban carbon storage estimates provide past records to serve as a baseline and a precursor to study future changes, and therefore more such city-scale analyses are required for overall urban sustainability. [ABSTRACT FROM AUTHOR]

This study examines how ESG risks and opportunities can be systematically identified, assessed, and incorporated into the early-stage design and planning of natural resources projects. The focus for this study will be on the mining activities required to source the resources for the global decarbonization effort. The need for a framework to incorporate ESG risks and opportunities into the strategic mine planning process was first identified in the de Beers Sustainability Valuation Approach. The Social Value Capital Decision Model advanced by BHP represents an advance on the de Beers model. This is the first example of a structured methodology for systematically considering stakeholder values and incorporating these into the capital decision framework. To test the applicability of a new approach to mine design by using Quality Function Deployment (QFD), a case study involving a copper mine located in South America was developed. This case study demonstrates how QFD can provide clear line-of-sight to connect design decisions with priority stakeholder concerns. The framework provides a communications tool for aligning the ESG design process across functional silos within complex organizations. The development of appropriate software tools could assist in managing the inherent complexity associated with integrating stakeholder value concerns into early stage design decisions. [ABSTRACT FROM AUTHOR]

In this research work, a new software tool concept and its application for the rapid and flexible development of mechanistic digital twin core models for bioprocesses in various reactor designs are presented. The newly developed software tool concept automatically combines user-selected submodels into an overall digital twin core model. The main part is a biokinetic submodel, of which three were designed for enzymatic, microbial and biocatalytic processes, which can be adapted to specific processes. Furthermore, the digital twin core model contains a physico-chemical submodel (e.g., calculating pH or oxygen transfer) and a reactor submodel. The basis of the reactor submodel is an ideally mixed stirred tank reactor. The biokinetic submodel is decoupled from the reactor submodels and enables an independent parameterisation of submodels. Connecting ideally mixed stirred tank reactor models allows for the simulation of different reactor designs. The implementation of an executable digital twin core model was accelerated, creating a new software tool concept. When the concept was applied, the development time and the computing time of digital twin core models for the cultivation of Saccharomyces cerevisiae in two coupled stirred tank reactors as well as for enzymatic hydrolysis processes in a packed-bed reactor were reduced by 90%. [ABSTRACT FROM AUTHOR]

Due to the tool-less fabrication of parts and the high degree of geometric design freedom, additive manufacturing is experiencing increasing relevance for various industrial applications. In particular, the powder bed fusion of metals using a laser beam (PBF-LB/M) process allows for the metal-based manufacturing of complex parts with high mechanical properties. However, residual stresses form during PBF-LB/M due to high thermal gradients and a non-uniform cooling. These lead to a distortion of the parts, which reduces the dimensional accuracy and increases the amount of post-processing necessary to meet the defined requirements. To predict the resulting residual stress state and distortion prior to the actual PBF-LB/M process, this paper presents the finite-element-based simulation tool AscentAM with its core module and several sub-modules. The tool is based on open-source programs and utilizes a sequentially coupled thermo-mechanical simulation, in which the significant influences of the manufacturing process are considered by their physical relations. The simulation entirely emulates the PBF-LB/M process chain including the heat treatment. In addition, algorithms for the part pre-deformation and the export of a machine-specific file format were implemented. The simulation results were verified, and an experimental validation was performed for two benchmark geometries with regard to their distortion. The application of the optimization sub-module significantly minimized the form deviation from the nominal geometry. A high level of accuracy was observed for the prediction of the distortion at different manufacturing states. The process simulation provides an important contribution to the first-time-right manufacturing of parts fabricated by the PBF-LB/M process. [ABSTRACT FROM AUTHOR]