Misannotated domains in plant databases: lessons from 'PIPLC Y-box-containing' proteins.

Variation in Results of Three Biology‐Focused Search Engines: A Case Study Using North American Tree Species

Most tools used during the forensic examination process emphasize data and metadata extraction without a formal definition of the concepts used in their outputs. These vary not only in the terminology used, but also in the way values are represented. These differences hinder the adoption of computer-assisted analysis, since the elements to be analyzed are not well-defined, requiring ad hoc parsers to process and interpret the output of each tool. A framework for semantic annotation of digital evidence is presented in this work. Semantic annotations use concepts that are defined in an ontology to describe the annotated object. They can replace raw metadata, user-defined labels and tool-specific analysis results with computer-readable, formally defined terms that can be used in semantically advanced queries. The framework's components provide means to extract, analyze and index the contents of the digital evidence. The framework allows the augmentation of a base ontology, by adding domain and case-specific concepts to it. A prototype implementation is described and a case study is conducted to illustrate its potential uses and improvements to the forensic examination process.

The U.S Department of Energy Light Water Reactor Sustainability (LWRS) Program initiated research in to what is needed in order to provide a roadmap or model for Nuclear Power Plants to reference when building an architecture that can support the growing data supply and demand flowing through their networks. The Digital Architecture project published report Digital Architecture Planning Model (Oxstrand et. al, 2016) discusses things to consider when building an architecture to support the increasing needs and demands of data throughout the plant. Once the plant is able to support the data demands it still needs to be able to provide the data in an easy, quick and reliable method. A common method is to create a “one stop shop” application that a user can go to get all the data they need. The creation of this leads to the need of creating a Seamless Digital Environment (SDE) to integrate all the “siloed” data. An SDE is the desired perception that should be presented to users by gathering the data from any data source (e.g., legacy applications and work management systems) without effort by the user. The goal for FY16 was to complete a feasibility study for data mining and analytics for employing information from computer-based procedures enabled technologies for use in developing improved business analytics. The research team collaborated with multiple organizations to identify use cases or scenarios, which could be beneficial to investigate in a feasibility study. Many interesting potential use cases were identified throughout the FY16 activity. Unfortunately, due to factors out of the research team’s control, none of the studies were initiated this year. However, the insights gained and the relationships built with both PVNGS and NextAxiom will be valuable when moving forward with future research. During the 2016 annual Nuclear Information Technology Strategic Leadership (NITSL) group meeting it was identified would be very beneficial to the industry to support a research effort focused on data analytics. It was suggested that the effort would develop and evaluate use cases for data mining and analytics for employing information from plant sensors and database for use in developing improved business analytics.

Probiotics are microorganisms that confer beneficial effects on the host; nevertheless, before being allowed for human consumption, their safety must be verified with accurate protocols. In the genomic era, such procedures should take into account the genomic-based approaches. This study aims at assessing the safety traits of Bacillus coagulans GBI-30, 6086 integrating the most updated genomics-based procedures and conventional phenotypic assays. Special attention was paid to putative virulence factors (VF), antibiotic resistance (AR) genes and genes encoding enzymes responsible for harmful metabolites (i.e. biogenic amines, BAs). This probiotic strain was phenotypically resistant to streptomycin and kanamycin, although the genome analysis suggested that the AR-related genes were not easily transferrable to other bacteria, and no other genes with potential safety risks, such as those related to VF or BA production, were retrieved. Furthermore, no unstable elements that could potentially lead to genomic rearrangements were detected. Moreover, a workflow is proposed to allow the proper taxonomic identification of a microbial strain and the accurate evaluation of risk-related gene traits, combining whole genome sequencing analysis with updated bioinformatics tools and standard phenotypic assays. The workflow presented can be generalized as a guideline for the safety investigation of novel probiotic strains to help stakeholders (from scientists to manufacturers and consumers) to meet regulatory requirements and avoid misleading information.

An underexplored question in evolutionary genetics concerns the extent to which mutational bias in the production of genetic variation influences outcomes and pathways of adaptive molecular evolution. In the genomes of at least some vertebrate taxa, an important form of mutation bias involves changes at CpG dinucleotides: if the DNA nucleotide cytosine (C) is immediately 5' to guanine (G) on the same coding strand, then-depending on methylation status-point mutations at both sites occur at an elevated rate relative to mutations at non-CpG sites. Here, we examine experimental data from case studies in which it has been possible to identify the causative substitutions that are responsible for adaptive changes in the functional properties of vertebrate haemoglobin (Hb). Specifically, we examine the molecular basis of convergent increases in Hb-O2 affinity in high-altitude birds. Using a dataset of experimentally verified, affinity-enhancing mutations in the Hbs of highland avian taxa, we tested whether causative changes are enriched for mutations at CpG dinucleotides relative to the frequency of CpG mutations among all possible missense mutations. The tests revealed that a disproportionate number of causative amino acid replacements were attributable to CpG mutations, suggesting that mutation bias can influence outcomes of molecular adaptation. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.

A new trend for data analysis in the life sciences is Cloud computing, enabling the analysis of large datasets in short time. This chapter introduces Big Data challenges in the genomic era and how Cloud computing can be one feasible approach for solving them. Technical and security issues are discussed and a case study where Clouds are successfully applied to resolve computational bottlenecks in the analysis of genomic data is presented. It is an intentional outcome of this chapter that Cloud computing is not essential for analyzing Big Data. Rather, it is argued that for the optimized utilization of IT, it is required to choose the best architecture for each use case, either by security requirements, financial goals, optimized runtime through parallelization, or the ability for easier collaboration and data sharing with business partners on shared resources.

A Semantic-enhanced Augmented Reality Tool for OpenStreetMap POI Discovery

Cysteine is a highly conserved amino acid with diverse roles in protein function. Whilst its role in the formation of disulfide bridges is well characterized, the contribution of isolated cysteines in protein folding is by and large unexplored. Here we investigate the impact of cysteine residues on the folding pathway of the MATH domain in the SPOP protein by comparing wild-type and serine mutants. Through kinetic analyses, we demonstrate that a buried cysteine residue stabilizes both an early folding intermediate and the main transition state. Most notably, such effects are disrupted upon substitution with serine but preserved with alanine. These findings suggest that, in certain structural contexts, cysteine behaves as a hydrophobic rather than a polar residue. Our results challenge the traditional classification of cysteine as a polar amino acid and highlight its unique contributions to protein folding, with implications for protein engineering and structural biology.

Protein domains can be viewed as building blocks, essential for understanding structure-function relationships in proteins. However, each domain database classifies protein domains using its own methodology. Thus, in many cases, boundaries between different domains or families differ from one domain database to the other, raising the question of domain definition and enumeration. The answer to this question cannot be found in a single database. Rather, expert integration and curation of various databases are required to refine the contours of a domain of interest, in a domain-centric approach. Here, we illustrate the role of 3-D structure in clarifying domain definition with the help of CroMaSt: “Cross-Mapper for Structural Domains”, a fully automated workflow that classifies all structural instances of a given domain into 3 different categories (core, true and domain-like). CroMaSt is developed in Common Workflow Language (CWL) and takes advantage of 2 well-known and widely used domain databases, Pfam (sequence-based) and CATH (structure-based). It uses the domain definitions from Pfam and CATH and SIFTS resource for cross-mapping of structural instances from the above-mentioned sources. Structural alignments generated by Kpax allow to identify the false positive instances from each domain database. We tested CroMaSt on the RNA Recognition Motif (RRM), the most prevalent and diverse RNA-binding domain. Starting from PF00076 and 3.30.70.330 domain families from Pfam and CATH respectively, our workflow identifies 882 core, 1120 true and 89 domain-like structural instances. The information generated by this method will play a crucial role in machine learning methods applied to domain-specific synthetic biology.

Looking to nature for inspiration has led to many diverse technological advances. The spiral valve intestine of sharks has provided the opportunity to observe the efficiency of different valve systems. It is supposed that the spiral intestine present in sharks, skates and rays slows the transit rate of digesta through the gut and provides increased surface area for the absorption of nutrients. In this investigation, we use a novel technique-creating three-dimensional reconstructions from CT scans of spiral intestines-to describe the morphology of the spiral intestine of at least one species from 22 different shark families. We discuss the morphological data in an evolutionary, dietary and functional context. The evolutionary analyses suggest that the columnar morphology is the ancestral form of the spiral intestine. Dietary analyses reveal no correlation between diet type and spiral intestine morphology. Flow rate was slowed significantly more when the two funnel-shaped spiral intestines were subjected to flow in the posterior to anterior direction, indicating their success at producing unidirectional flow, similar to a Tesla valve. These data are available to generate additional three-dimensional morphometrics, create computational models of the intestine, as well as to further explore the function of the gastrointestinal tract of sharks in structural and physiological contexts.

Chapter 13 Use of micro-porous affinity membranes for protein purification: a case study

Morphometrics are fundamental for the analysis of size and shape in fossils, particularly because soft parts or DNA are rarely preserved and hard parts such as shells are commonly the only source of information. Geometric morphometrics, that is, landmark analysis, is well established for the description of shape but it exhibits a couple of shortcomings resulting from subjective choices during landmarking (number and position of landmarks) and from difficulties in resolving shape at the level of micro‐sculpture.With the aid of high‐resolution 3D scanning technology and analyses of fractal dimensions, we test whether such shortcomings of linear and landmark morphometrics can be overcome. As a model group, we selected a clade of modern viviparid gastropods from Lake Lugu, with shells that show a high degree of sculptural variation. Linear and landmark analyses were applied to the same shells in order to establish the fractal dimensions. The genetic diversity of the gastropod clade was assessed.The genetic results suggest that the gastropod clade represents a single species. The results of all morphometric methods applied are in line with the genetic results, which is that no specific morphotype could be delimited. Apart from this overall agreement, landmark and fractal dimension analyses do not correspond to each other but represent data sets with different information. Generally, the fractal dimension values quantify the roughness of the shell surface, the resolution of the 3D scans determining the level. In our approach, we captured the micro‐sculpture but not the first‐order sculptural elements, which explains that fractal dimension and landmark data are not in phase.We can show that analyzing fractal dimensions of gastropod shells opens a window to more detailed information that can be considered in evolutionary and ecological contexts. We propose that using low‐resolution 3D scans may successfully substitute landmark analyses because it overcomes the subjective landmarking. Analyses of 3D scans with higher resolution than used in this study will provide surface roughness information at the mineralogical level. We suggest that fractal dimension analyses of a combination of differently resolved 3D models will significantly improve the quality of shell morphometrics.

Understanding the functional impact of genetic mutations on protein structures is essential for advancing cancer research and developing targeted therapies. The main challenge lies in accurately mapping these mutations to protein structures and analysing their effects on protein function. To address this, Mut-Map (https://genemutation.org/) is a comprehensive computational pipeline designed to integrate mutation data from the Catalogue Of Somatic Mutations In Cancer database with protein structural data from the Protein Data Bank and AlphaFold models. The pipeline begins by taking a UniProt ID and proceeds through mapping corresponding Protein Data Bank structures, renumbering residues, and assessing disorder percentages. It then overlays mutation data, categorizes mutations based on structural context, and visualizes them using advanced tools like MolStar. This approach allows for a detailed analysis of how mutations may disrupt protein function by affecting key regions such as DNA interfaces, ligand-binding sites, and dimer interactions. To validate the pipeline, a case study on the TP53 gene, a critical tumour suppressor often mutated in cancers, was conducted. The analysis highlighted the most frequent mutations occurring at the DNA-binding interface, providing insights into their potential role in cancer progression. Mut-Map offers a powerful resource for elucidating the structural implications of cancer-associated mutations, paving the way for more targeted therapeutic strategies and advancing our understanding of protein structure-function relationships.

The article deals with the formation of the social biographies of young people through the interplay of structure and agency. The aim is to provide a grounded typology of patterns of young people's agency within the process of shaping social biographies. The structural context addressed in the article consists of family resources and habitus. The evidence comes from a longitudinal qualitative study with young people from families of workers and families of professionals in two urban neighbourhoods in Belgrade. The narrative analysis of young people's agency that combines longitudinal biographical data and lifelines accounts comes from case studies from the last wave of research. Several patterns of young people's agency that have emerged are explored as related to structural opportunities/constraints, and family habitus. It is argued that family resources and support are mechanisms by which social inequality in Serbian society is reproduced during transition to adulthood. On the other hand, young people as strategic actors develop and exhibit different types of agency within the structural contexts of family resources and habitus.

STRUCTURED ABSTRACT Context: This research is embedded within the Academic Master's program in Administration at the Graduate Program in Administration (PPGAdm) – UFU/FAGEN, focusing on the importance of entrepreneurship in various contexts, including education and the public sector. It highlights the economic and social benefits of entrepreneurship, as well as the relevance of entrepreneurial education for student learning and skill development. The research proposal specifically focuses on the implementation of the entrepreneurial education project called the "Entrepreneurship Pathway," developed by the Center for Incubation of Entrepreneurial Activities at the Federal University of Uberlândia (CIAEM/UFU), involving students from the College of Application School of Basic Education at UFU (CAp/Eseba UFU). Objective: The general objective of this study is to analyze the activities developed by the Center for Incubation of Entrepreneurial Activities at the Federal University of Uberlândia (CIAEM/UFU), specifically through the project aimed at promoting entrepreneurial education among students of the College of Application School of Basic Education at the Federal University of Uberlândia (CAp/Eseba UFU). The specific objectives include: describing the conception and development of the entrepreneurial education project; analyzing its trajectory and execution over time; and evaluating the results and implications of implementing the entrepreneurial education project. Method: The classification of methodological procedures used in the research was based on their approaches to objectives, as descriptive research. As it was submitted on the 22/10/2023 and approved by the Ethics Committee CAAE: 74490723.7.0000.5152. Its epistemological anchor is based on the qualitative approach, while the method for the procedure adopted is a case study. Sources for the research include documentary analysis of the 'Entrepreneurship Pathway' project and data from CIAEM/UFU and CAp Eseba/UFU. Data analysis techniques involved participant observation, documentary analysis of the 'Entrepreneurship Pathway' project, and conducting semi-structured interviews with teachers and managers from CAp Eseba/UFU and CIAEM/UFU. Results: The research aims to provide an understanding of how entrepreneurship in basic education contributes to student formation, developing specific skills. It will monitor how students structure acquired knowledge into ideas and project proposals, potentially presented throughout the course. Alignment of the research with the concentration area of the PPGAdm (Regionality and Management) and with the research line: The research is part of the research line "Organizational Management and Regionality – General Themes," justified by the emphasis on managing educational institutions, exploring the dynamics between entrepreneurship, education, and the regional context. The analysis of entrepreneurial practices at the College of Application, associated with the incubator's activities and their impact on the local community, directly reflects the scope of the research line. The research seeks not only to understand organizational practices within the educational scope but also to investigate how these practices are related to promoting regional entrepreneurial vocation. It will explore how basic education of students can foster and guide entrepreneurial initiatives that impact local economic development. Impact and innovative character in intellectual production: The research promises to fill a gap in academic literature by addressing the intersection of entrepreneurship, education, and regional management. Its innovative character lies in the specific analysis of entrepreneurial practices in basic education and the evaluation of the role of an incubator in this process, offering new perspectives on promoting entrepreneurship in education. Economic, social, and regional impact: The research aims to contribute to understanding how entrepreneurship in basic education, driven by an incubator, can positively impact the local economy, generate jobs, and enhance community quality of life. By identifying effective practices, the research has the potential to guide policies and strategies that promote economic and social development through entrepreneurial education. Additionally, it seeks to comprehend how entrepreneurial practices in education can influence local community development and provide replicable insights for other regional contexts. To assess the effectiveness of these initiatives, given that impacts will become more evident in the future, qualitative indicators will be employed. These will include teachers' perceptions of students' entrepreneurial skill development, such as academic knowledge acquisition, socio-emotional skills enhancement, and stimulation of creativity, critical thinking, and problem-solving abilities. Sustainable Development Goals addressed in the research: The research contributes to several Sustainable Development Goals (SDGs), including SDG 4 (Quality Education), SDG 8 (Decent Work and Economic Growth), SDG 9 (Industry, Innovation and Infrastructure), SDG 10 (Reduced Inequalities), SDG 12 (Responsible Consumption and Production), and SDG 17 (Partnerships for the Goals). It promotes entrepreneurial education, explores economic impact and job opportunities generated, analyzes how innovation and entrepreneurship can contribute to regional development, reduces inequalities by offering inclusive economic opportunities, encourages sustainable consumption and production practices, and underscores the importance of cross-sector partnerships for effective SDG implementation. Keywords Entrepreneurship; Innovation; Entrepreneurial Education; Business Incubator; Regionalism.