RCIPL
Repositório Institucional do Politécnico de Lisboa
Entradas recentes
Diaphragm ultrasonography during respiratory manoeuvres
Publication . Leote, João; Costa, Carolina; Ferreira, Edgar; Parxotamo, André; Batista, Maria; Loução, Ricardo; Gonzalez, Filipe; Bacariza, Jacobo; Dias, Maria Hermínia Monteiro Brites
This study aimed to describe diaphragm ultrasonography (DU) during mouth occlusion pressure (P0.1) and maximal inspiratory pressure (MIP) in healthy participants. Four participants performed: (i) neurophysiological tests and then (ii) simultaneous DU with P0.1 and MIP. Diaphragm excursion was 2.37 cm (median) during tidal volume of 0.74 L. Additionally, a median diaphragm excursion of 1.25 cm was associated with a median P0.1 of 1.39 cm H2O, while a median diaphragm excursion of 3.10 cm was associated with a median MIP of 125.88 cm H2O. DU showed a hold-back movement during P0.1 and a plateau during MIP, providing novel insights into diaphragm movement with potential clinical practice implications.
Impact of epigallocatechinn-3-gallate on Staphylococcus aureus molecular profile
Publication . Inácio, Raquel; Ribeiro, Edna; Calado, Cecília R. C.
The discovery of new antimicrobial compounds is critical for the control of severe nosocomial infections, as those associated with methicillin-sensitive (MSSA) and resistant (MRSA) Staphylococcus aureus strains. In order to enhance new therapeutic approaches, it is crucial to develop new platforms to screen innovative compounds. Here, we evaluated how Fourier Transform Infra-Red (FTIR)-spectroscopy enables the prediction of antibiotic resistance and monitors the impact of epigallocatechin-3-gallate (EGCG) on the metabolism of MRSA and MSSA strains. Data showed that EGCG impacts the bacteria's metabolism, and that MRSA strains are more sensitive to EGCG. The high sensitivity of the technique also enabled us to discriminate the impact of EGCG concentrations, i.e., between 25 and 50, and between 50 and 100μg/ml. On the other hand, EGCG's impact on cellular molecular composition was lower than the differences between MSSA and MRSA strains. Furthermore, it was possible to predict these strains' resistance towards the antibiotics methicillin, amoxicillin, imipenem, and gentamicin. Since the spectra were acquired in a rapid, simple, economic, and high-throughput mode, this methodology may strongly promote the surveillance of nosocomial infection caused by S. aureus, and to screen new antimicrobial compounds.
From scans to steps: elevating stroke rehabilitation with 3D-printed ankle-foot orthoses
Publication . Silva, Rui; Morouço, Pedro; Ricardo, Diogo; Campos, Inês; Alves, Nuno; Veloso, António P.
Background: The integration of advanced 3D scanning and additive manufacturing technologies in stroke rehabilitation offers promising advancements in the design and production of ankle-foot orthoses. These technological innovations are progressively recognized for their potential to provide more precise and customized orthotic solutions for individuals with stroke-related impairments. Objectives: The primary aim of this study was to biomechanically test and validate the effectiveness of custom ankle-foot orthoses produced through additive manufacturing technology using data captured by a novel photogrammetric scanning system. The customized orthosis was compared with a standard prefabricated orthosis to assess their relative effectiveness in improving gait dynamics and patient satisfaction in stroke rehabilitation. Methods: Participants with equinovarus deformity, a common consequence of stroke, were fitted with custom ankle-foot orthoses, alongside conventional prefabricated orthoses. The study utilized the Qualisys® motion analysis system for comprehensive biomechanical gait analysis, and the QUEST questionnaire was employed to capture participant feedback on both types of orthoses. Detailed comparisons of gait dynamics were conducted using Statistical Parametric Mapping with each orthosis. Results: The study revealed notable kinematic and kinetic differences between the custom and prefabricated orthoses. The custom orthoses demonstrated superior performance in enhancing gait efficiency, symmetry, and safety. Patient feedback favored the customized orthoses over the prefabricated variants, with higher scores in comfort, fit, and overall effectiveness. Conclusions: This research underscores the effectiveness of custom orthoses produced through additive manufacturing technology for stroke rehabilitation. By offering a comprehensive evaluation of orthotic interventions and establishing a comparative framework, the study serves as a reference point for future research, advocating for a more personalized and evidence-based approach in orthotic design for improving the quality of life of stroke survivors.
Towards a validation of the standard and enzyme-linked comet assay: a retrospective variability analysis
Publication . Møller, Peter; Ladeira, Carina; Ziemann, Christina; Knasmueller, Siegfried; Mišík, Miroslav; Louro, Henriqueta; Silva, Maria João; Olsen, Ann Karin; Azqueta, Amaya; Langie, Sabine A.; Bonassi, Stefano; Dusinska, Maria; Gajski, Goran; Collins, Andrew
The comet assay is one of the most popular tests for genotoxicity in cell cultures, non-animal species, animals, and humans. It has high sensitivity to detect low levels of DNA damage, can be applied to non-proliferating cells, requires relatively few cells, is technically simple, and is low-cost. The Organisation for Economic Co-operation and Development (OECD) adopted in 2016 the in vivo comet assay for measurement of DNA strand breaks in animal tissues. There is a desire to expand the comet assay to genotoxicity testing in cell cultures, including the detection of oxidatively damaged DNA by incubation of gel-embedded nucleoids with DNA repair enzymes, especially formamidopyrimidine DNA glycosylase (Fpg), which converts oxidised purines to DNA breaks. Based on available information in the literature, this review provides a retrospective evaluation of the validation status of this assay, focusing on accuracy and reliability in genotoxicity testing in vitro. Information on accuracy is scarce, although limited evidence suggests levels of Fpg-sensitive sites are similar to those obtained by Fpg-linked alkaline unwinding and alkaline elution assays. Several ring studies have shown that estimated background levels of DNA breaks vary within and between laboratories. However, ring studies indicate good intra- and inter-laboratory reproducibility of the standard assay on ionizing radiation-exposed and the Fpg-linked assay on potassium bromate-exposed cells. Further studies are needed to assess the reproducibility in multiple laboratories using coded samples of non-genotoxins and genotoxins. Nevertheless, the available results indicate the comet assay is a reliable in vitro genotoxicity test.
Variant calling in genomics: a comparative performance analysis and decision guide
Publication . Pinto, Vera; Sousa, Lisete; Silva, Carina; Nejat Mahdieh
The accurate detection of genetic variants is critical for advancing genomics research and precision medicine. However, this task remains challenging due to pervasive sequencing errors and complex genomic regions. The choice of variant calling software significantly influences results, creating a need for clear, evidence-based guidance. This study aims to provide a performance evaluation and a clear, evidence-based guide for selecting variant callers by benchmarking seven widely used tools, GATK, FreeBayes, DeepVariant, Samtools, Strelka2, Octopus, and Varscan2, highlighting their algorithmic trade-offs. The well-characterized NA12878 genome from the Genome in a Bottle consortium was analyzed. High-coverage whole-genome sequencing data were processed with each variant caller, and the resulting variant calling files were benchmarked against a gold-standard reference. Performance was assessed using precision, recall, and F1-score on a chromosome 20 subset and on full whole-genome data. The analysis revealed that DeepVariant's deep learning approach achieved the highest precision (0.7869) and F1-score (0.8754) on chromosome 20. For whole-genome analysis, Strelka2 excelled in precision (0.8326), while Octopus demonstrated superior recall (0.9838). FreeBayes exhibited high sensitivity but lower precision, underscoring a key trade-off. There is no universally superior variant caller; the optimal choice depends on the specific research objectives, whether prioritizing precision, recall, or computational efficiency. This study serves as a crucial evidence-based resource for researchers and clinicians, enabling informed tool selection.