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Genome annotation has historically ignored small open reading frames (smORFs), which encode a class of proteins shorter than 100 amino acids, collectively referred to as microproteins. This cutoff was established to avoid thousands of false positives due to limitations of pure genomics pipelines. Proteogenomics, a computational approach that combines genomics, transcriptomics, and proteomics, makes it possible to accurately identify these short sequences by overlaying different levels of omics evidence. In this chapter, we showcase the use of µProteInS, a bioinformatics pipeline developed for the identification of unannotated microproteins encoded by smORFs in bacteria. The workflow covers all the steps from quality control and transcriptome assembly to the scoring and post-processing of mass spectrometry data. Additionally, we provide an example on how to apply the pipeline's machine learning method to identify high-confidence spectra and pinpoint the most reliable identifications from large datasets.

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Fungal diseases are often linked to poverty, which is associated with poor hygiene and sanitation conditions that have been severely worsened by the COVID-19 pandemic. Moreover, COVID-19 patients are treated with Dexamethasone, a corticosteroid that promotes an immunosuppressive profile, making patients more susceptible to opportunistic fungal infections, such as those caused by Candida species. In this study, we analyzed the prevalence of Candida yeasts in wastewater samples collected to track viral genetic material during the COVID-19 pandemic and identified the yeasts using polyphasic taxonomy. Furthermore, we investigated the production of biofilm and hydrolytic enzymes, which are known virulence factors. Our findings revealed that all Candida species could form biofilms and exhibited moderate hydrolytic enzyme activity. We also proposed a workflow for monitoring wastewater using Colony PCR instead of conventional PCR, as this technique is fast, cost-effective, and reliable. This approach enhances the accurate taxonomic identification of yeasts in environmental samples, contributing to environmental monitoring as part of the One Health approach, which preconizes the monitoring of possible emergent pathogenic microorganisms, including fungi.

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Natural products (or specialized metabolites) are historically the main source of new drugs. However, the current drug discovery pipelines require miniaturization and speeds that are incompatible with traditional natural product research methods, especially in the early stages of the research. This article introduces the NP3 MS Workflow, a robust open-source software system for liquid chromatography-tandem mass spectrometry (LC-MS/MS) untargeted metabolomic data processing and analysis, designed to rank bioactive natural products directly from complex mixtures of compounds, such as bioactive biota samples. NP3 MS Workflow allows minimal user intervention as well as customization of each step of LC-MS/MS data processing, with diagnostic statistics to allow interpretation and optimization of LC-MS/MS data processing by the user. NP3 MS Workflow adds improved computing of the MS2 spectra in an LC-MS/MS data set and provides tools for automatic [M + H]+ ion deconvolution using fragmentation rules; chemical structural annotation against MS2 databases; and relative quantification of the precursor ions for bioactivity correlation scoring. The software will be presented with case studies and comparisons with equivalent tools currently available. NP3 MS Workflow shows a robust and useful approach to select bioactive natural products from complex mixtures, improving the set of tools available for untargeted metabolomics. It can be easily integrated into natural product-based drug-discovery pipelines and to other fields of research at the interface of chemistry and biology.

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OBJECTIVE: This scoping review aimed to map the literature on the utilization of intraoral scanners (IOS) in fabricating post and core restorations. DATA: The study protocol is available at https://osf.io/ja9xh/. This scoping review followed Joanna Briggs Institute guidelines, and reporting was based on the checklist proposed by PRISMA-ScR. SOURCES: Searches were conducted in PubMed/MEDLINE, Web of Science, Scopus, and grey literature up to August 2023. RESULTS: A total of 455 studies were identified. After screening, 16 studies were deemed suitable for scoping review. Of these, 13 were in vitro studies, two were case reports, and one was a clinical study. Different IOS systems for scanning post spaces were evaluated, with Trios being most prevalent, followed by Prismescan. While most studies did not use any intraoral scanning devices, five studies reported the use of scan posts. Results regarding retention favored fully digital workflows. However, results about the adaptation and accuracy varied between included studies, highlighting the importance of standardized approaches. Future clinical studies should encompass variations in IOS systems, post space depths, scanner depth of field, light conditions, scan post utilization, operator experience, scanning time and strategy, and direct comparison with conventional techniques. CONCLUSION: IOS is increasingly important in capturing digital impressions for post spaces and provides valuable insights for clinicians and researchers. Although included studies, primarily in vitro, demonstrated promising results for the utilization of IOS systems in fully digital workflows for post and core restorations, further well-conducted studies, particularly clinical trials, are recommended due to data heterogeneity and limitations. CLINICAL SIGNIFICANCE: This mapping highlights the potential of modern IOS in fully digital workflows for post and core restorations. Despite promising results, challenges related to different variables associated with IOS require careful consideration. Standardization and additional clinical validation are essential for optimize IOS benefits in post and core restorations.

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Thanks to advancements in genome sequencing and bioinformatics, thousands of bacterial genome sequences are available in public databases. This presents an opportunity to study bacterial diversity in unprecedented detail. This chapter describes a complete bioinformatics workflow for comparative genomics of bacterial genomes, including genome annotation, pangenome reconstruction and visualization, phylogenetic analysis, and identification of sequences of interest such as antimicrobial-resistance genes, virulence factors, and phage sequences. The workflow uses state-of-the-art, open-source tools. The workflow is presented by means of a comparative analysis of Salmonella enterica serovar Typhimurium genomes. The workflow is based on Linux commands and scripts, and result visualization relies on the R environment. The chapter provides a step-by-step protocol that researchers with basic expertise in bioinformatics can easily follow to conduct investigations on their own genome datasets.

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This case report focuses on the replacement of ceramic laminate veneers with suboptimal marginal fit and design, employing a digital workflow and CAD-CAM technology. The patient, a woman in her 30s, expressed concerns about the appearance and hygiene challenges of her existing veneers. A comprehensive assessment, including clinical examination, facial photographs and intraoral scanning, was conducted. Utilising CAD software, facial photographs and 3D models merged to create a digital wax-up, crucial in designing suitable veneers and addressing issues like overcontouring and a poor emergence profile. Following the removal of old veneers, a mock-up was performed and approved. Preparations ensured space for restorations with well-defined margins. The final restorations, milled with Leucite-reinforced vitreous ceramic, were cemented. At the 1 year follow-up, improved aesthetics, gingival health and functional restorations were observed. This report highlights the efficacy of digital workflows in achieving consistent and aesthetically pleasing outcomes in ceramic laminate veneer replacement.

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Objetivo: descrever a experiência da reorganização do processo de trabalho de enfermeiros que atuam na Atenção Primária à Saúde no enfrentamento da covid-19, no município de João Pessoa - Paraíba. Métodos: Trata-se de um estudo descritivo com abordagem qualitativa, desenvolvido com um total de 15 enfermeiras atuantes no município de João Pessoa com idade entre 41 e 67 anos (média de 56 anos) e com tempo médio de 12 anos e 8 meses de atuação na Estratégia Saúde da Família. Resultados: foram evidenciados um campo amplo de alterações na dinâmica das Unidades Básicas de Saúde devido a pandemia, dentre elas, modificações no processo de trabalho da equipe, a estagnação das atividades coletivas, como também a implementação de ações destinadas para a covid-19. Conclusão: As experiências relatadas das participantes do estudo ressaltam o grande impacto que a pandemia trouxe para o cotidiano de uma equipe de Atenção Básica, sendo fundamental o fortalecimento da atenção primária à saúde, com recursos financeiros, incentivo e qualificação profissional, garantindo uma maior adequação da nova realidade vivida, a fim de garantir continuidade do cuidado. (AU)

Objective: to describe the experience of the reorganization of the work process of nurses who work in Primary Health Care in the face of covid-19, in the city of João Pessoa - Paraíba. Methods: This is a descriptive study with a qualitative approach, developed with a total of 15 nurses working in the city of João Pessoa aged between 41 and 67 years (average of 56 years) and with an average time of 12 years and 8 months of performance in the Family Health Strategy. Results: a wide field of changes in the dynamics of Basic Health Units due to the pandemic were evidenced, among them, changes in the team's work process, the stagnation of collective activities, as well as the implementation of actions aimed at covid-19. Conclusion: The reported experiences of the study participants highlight the great impact that the pandemic has brought to the daily life of a Primary Care team, making it essential to strengthen primary health care, with financial resources, incentives and professional qualification, ensuring greater adequacy. of the new lived reality, in order to guarantee continuity of care. (AU)

Objetivo: describir la experiencia de la reorganización del proceso de trabajo de los enfermeros que actúan en la Atención Primaria de Salud frente a la covid-19, en la ciudad de João Pessoa - Paraíba. Métodos: Se trata de un estudio descriptivo con enfoque cualitativo, desarrollado con un total de 15 enfermeros que actúan en la ciudad de João Pessoa con edades entre 41 y 67 años (promedio de 56 años) y con tiempo promedio de 12 años y 8 meses de vida. desempeño en la Estrategia de Salud de la Familia. Resultados: Se evidenció un amplio campo de cambios en la dinámica de las Unidades Básicas de Salud debido a la pandemia, entre ellos, cambios en el proceso de trabajo del equipo, el estancamiento de las actividades colectivas, así como la implementación de acciones dirigidas a la covid-19. Conclusión: Las experiencias relatadas por los participantes del estudio resaltan el gran impacto que la pandemia trajo para el cotidiano de un equipo de Atención Primaria, siendo imprescindible fortalecer la atención primaria de salud, con recursos económicos, incentivos y calificación profesional, asegurando una mayor adecuación. de la nueva realidad vivida, para garantizar la continuidad de la atención. (AU)

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Molecular features play an important role in different bio-chem-informatics tasks, such as the Quantitative Structure-Activity Relationships (QSAR) modeling. Several pre-trained models have been recently created to be used in downstream tasks, either by fine-tuning a specific model or by extracting features to feed traditional classifiers. In this regard, a new family of Evolutionary Scale Modeling models (termed as ESM-2 models) was recently introduced, demonstrating outstanding results in protein structure prediction benchmarks. Herein, we studied the usefulness of the different-dimensional embeddings derived from the ESM-2 models to classify antimicrobial peptides (AMPs). To this end, we built a KNIME workflow to use the same modeling methodology across experiments in order to guarantee fair analyses. As a result, the 640- and 1280-dimensional embeddings derived from the 30- and 33-layer ESM-2 models, respectively, are the most valuable  since statistically better performances were achieved by the QSAR models built from them. We also fused features of the different ESM-2 models, and it was concluded that the fusion contributes to getting better QSAR models than using features of a single ESM-2 model. Frequency studies revealed that only a portion of the ESM-2 embeddings is valuable for modeling tasks since between 43% and 66% of the features were never used. Comparisons regarding state-of-the-art deep learning (DL) models confirm that when performing methodologically principled studies in the prediction of AMPs, non-DL based QSAR models yield comparable-to-superior performances to DL-based QSAR models. The developed KNIME workflow is available-freely at https://github.com/cicese-biocom/classification-QSAR-bioKom. This workflow can be valuable to avoid unfair comparisons regarding new computational methods, as well as to propose new non-DL based QSAR models.

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Liquid chromatography coupled with high-resolution mass spectrometry data-independent acquisition (LC-HRMS/DIA), including MSE, enable comprehensive metabolomics analyses though they pose challenges for data processing with automatic annotation and molecular networking (MN) implementation. This motivated the present proposal, in which we introduce DIA-IntOpenStream, a new integrated workflow combining open-source software to streamline MSE data handling. It provides 'in-house' custom database construction, allows the conversion of raw MSE data to a universal format (.mzML) and leverages open software (MZmine 3 and MS-DIAL) all advantages for confident annotation and effective MN data interpretation. This pipeline significantly enhances the accessibility, reliability and reproducibility of complex MSE/DIA studies, overcoming previous limitations of proprietary software and non-universal MS data formats that restricted integrative analysis. We demonstrate the utility of DIA-IntOpenStream with two independent datasets: dataset 1 consists of new data from 60 plant extracts from the Ocotea genus; dataset 2 is a publicly available actinobacterial extract spiked with authentic standard for detailed comparative analysis with existing methods. This user-friendly pipeline enables broader adoption of cutting-edge MS tools and provides value to the scientific community. Overall, it holds promise for speeding up metabolite discoveries toward a more collaborative and open environment for research.

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Objective: to examine the nursing team's view of the repercussions of moving patients (admissions, transfers and discharges) on the organization of work and the delivery of care. Method: this is a qualitative study using the focus group technique, conducted with 23 professionals - 12 nurses, eight nurse technicians and three nurse assistants working in three inpatient units at a teaching hospital in the countryside of Sao Paulo. Four meetings took place between November 2021 and March 2022. The reports were analyzed thematically using MAXQDA software. Results: two thematic categories emerged: the influence of structural factors and work organization on the intra-hospital moving of patients; it demands time, generates work overload and interferes with the delivery of care. Conclusion: the volume of moving patient associated with unforeseen demands, care complexity and insufficient staff and resources have a negative impact on the delivery of care, with clinical risks and work overload. The findings make it possible to improve the regulation of patients entering and leaving the units, work organization and care management, avoiding clinical risks, delays, omissions and work overload.

Objetivo: examinar la perspectiva del equipo de enfermería sobre las repercusiones del movimiento de pacientes (admisiones, traslados y altas) en la organización del trabajo y en la prestación de cuidados. Método: estudio cualitativo utilizando la técnica de grupo focal llevado a cabo con 23 profesionales, incluyendo 12 enfermeros, ocho técnicos y tres auxiliares de enfermería de tres unidades de internación de un hospital universitario del interior de São Paulo. Se realizaron cuatro encuentros entre noviembre de 2021 y marzo de 2022. Los relatos fueron analizados en la modalidad temática con la ayuda del software MAXQDA. Resultados: surgieron dos categorías temáticas: la influencia de factores estructurales y de la organización del trabajo en el movimiento intrahospitalario de pacientes; y, el movimiento de pacientes demanda tiempo, genera sobrecarga de trabajo e interfiere en la prestación de cuidados. Conclusión: el volumen de movimientos de pacientes asociado a demandas imprevistas, complejidad asistencial e insuficiencia de personal y de recursos repercute negativamente en la prestación del cuidado con riesgos clínicos y sobrecarga laboral. Los hallazgos permiten mejorar la regulación de las entradas y salidas de pacientes en las unidades, la organización del trabajo y la gestión del cuidado, evitando riesgos clínicos, retrasos, omisiones y sobrecarga laboral.

Objetivo: examinar o olhar da equipe de enfermagem quanto às repercussões da movimentação de pacientes (admissões, transferências e altas) na organização do trabalho e na entrega do cuidado. Método: estudo qualitativo utilizando técnica de grupo focal conduzido junto a vinte e três profissionais sendo doze enfermeiros, oito técnicos e três auxiliares de enfermagem lotados em três unidades de internação de um hospital de ensino do interior de São Paulo. Ocorreram quatro encontros, entre novembro de 2021 e março de 2022. Os relatos foram analisados na modalidade temática com o auxílio do software MAXQDA. Resultados: emergiram duas categorias temáticas: a influência de fatores estruturais e da organização do trabalho na movimentação intra-hospitalar de pacientes; e a movimentação de pacientes demanda tempo, gera sobrecarga de trabalho e interfere na entrega do cuidado. Conclusão: o volume de movimentações de pacientes associado às demandas imprevistas, complexidade assistencial e insuficiência de pessoal e de recursos repercutem negativamente na entrega do cuidar com riscos clínicos e sobrecarga laboral. Os achados possibilitam aprimorar a regulação das entradas e saídas de pacientes nas unidades, organização do trabalho e gestão do cuidado evitando-se riscos clínicos, atrasos, omissões e sobrecarga laboral.

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