Publications by authors named "Ana M Rocha"

6 Publications

  • Page 1 of 1

Dynamics of a Dual SARS-CoV-2 Lineage Co-Infection on a Prolonged Viral Shedding COVID-19 Case: Insights into Clinical Severity and Disease Duration.

Microorganisms 2021 Feb 2;9(2). Epub 2021 Feb 2.

CHUSJ-Centro Hospitalar Universitário S. João, 4200-319 Porto, Portugal.

A few molecularly proven severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cases of symptomatic reinfection are currently known worldwide, with a resolved first infection followed by a second infection after a 48 to 142-day intervening period. We report a multiple-component study of a clinically severe and prolonged viral shedding coronavirus disease 2019 (COVID-19) case in a 17-year-old Portuguese female. She had two hospitalizations, a total of 19 RT-PCR tests, mostly positive, and criteria for releasing from home isolation at the end of 97 days. The viral genome was sequenced in seven serial samples and in the diagnostic sample from her infected mother. A human genome-wide array (>900 K) was screened on the seven samples, and in vitro culture was conducted on isolates from three late samples. The patient had co-infection by two SARS-CoV-2 lineages, which were affiliated in distinct clades and diverging by six variants. The 20A lineage was absolute at the diagnosis (shared with the patient's mother), but nine days later, the 20B lineage had 3% frequency, and two months later, the 20B lineage had 100% frequency. The 900 K profiles confirmed the identity of the patient in the serial samples, and they allowed us to infer that she had polygenic risk scores for hospitalization and severe respiratory disease within the normal distributions for a Portuguese population cohort. The early-on dynamic co-infection may have contributed to the severity of COVID-19 in this otherwise healthy young patient, and to her prolonged SARS-CoV-2 shedding profile.
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http://dx.doi.org/10.3390/microorganisms9020300DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7912897PMC
February 2021

Analysis of Long Period Gratings Inscribed by CO Laser Irradiation and Estimation of the Refractive Index Modulation.

Sensors (Basel) 2020 Nov 10;20(22). Epub 2020 Nov 10.

Department of Physics and I3N, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.

Long period gratings (LPGs) inscribed in single mode fibers (SMFs) using CO laser irradiation were modelled numerically using the coupled mode method. The model considers the specifications of the inscription technique, such as the shape of the refractive index modulation that mimics the circularly symmetric point-to-point laser irradiation profile. A simple expression for predicting the resonant wavelength was obtained assuming a two-mode coupling model. However, to explain the spectra of the experimental LPGs, it was necessary to assume a reasonably high refractive index change and a multimode coupling model. Furthermore, using the developed model and a genetic algorithm to fit experimental resonances to simulated ones, we were able to estimate the maximum refractive index change, obtaining a value of 2.2 × 10, confirming the high refractive index change. The proposed model also predicts a second order resonance for this high value of refractive index change that was confirmed experimentally. Hence, with this model, we found some significant differences in the LPGs behavior when compared with conventional ones, namely, the emergence of coupling between different cladding modes and the competition of first and second order resonances which change the LPG transmission spectrum.
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http://dx.doi.org/10.3390/s20226409DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7697559PMC
November 2020

H3K27me3 expression and methylation status in histological variants of malignant peripheral nerve sheath tumours.

J Pathol 2020 10 1;252(2):151-164. Epub 2020 Sep 1.

Research Department of Pathology, University College London, London, UK.

Diagnosing MPNST can be challenging, but genetic alterations recently identified in polycomb repressive complex 2 (PRC2) core component genes, EED and SUZ12, resulting in global loss of the histone 3 lysine 27 trimethylation (H3K27me3) epigenetic mark, represent drivers of malignancy and a valuable diagnostic tool. However, the reported loss of H3K27me3 expression ranges from 35% to 84%. We show that advances in molecular pathology now allow many MPNST mimics to be classified confidently. We confirm that MPNSTs harbouring mutations in PRC2 core components are associated with loss of H3K27me3 expression; whole-genome doubling was detected in 68%, and SSTR2 was amplified in 32% of MPNSTs. We demonstrate that loss of H3K27me3 expression occurs overall in 38% of MPNSTs, but is lost in 76% of histologically classical cases, whereas loss was detected in only 23% cases with heterologous elements and 14% where the diagnosis could not be provided on morphology alone. H3K27me3 loss is rarely seen in other high-grade sarcomas and was not found to be associated with an inferior outcome in MPNST. We show that DNA methylation profiling distinguishes MPNST from its histological mimics, was unrelated to anatomical site, and formed two main clusters, MeGroups 4 and 5. MeGroup 4 represents classical MPNSTs lacking H3K27me3 expression in the majority of cases, whereas MeGroup 5 comprises MPNSTs exhibiting non-classical histology and expressing H3K27me3 and cluster with undifferentiated sarcomas. The two MeGroups are distinguished by differentially methylated PRC2-associated genes, the majority of which are hypermethylated in the promoter regions in MeGroup 4, indicating that the PRC2 target genes are not expressed in these tumours. The methylation profiles of MPNSTs with retention of H3K27me3 in MeGroups 4 and 5 are independent of mutations in PRC2 core components and the driver(s) in these groups remain to be identified. Our results open new avenues of investigation. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
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http://dx.doi.org/10.1002/path.5507DOI Listing
October 2020

Switching in multicore fibers using flexural acoustic waves.

Opt Express 2015 Oct;23(20):26313-25

We propose an in-line wavelength selective core switch for multicore fiber (MCF) transmission systems, based on the acousto-optic effect. A theoretical model addressing the interaction between flexural acoustic waves and the optical signal in MCFs is developed. We show that an optical signal propagating in a particular core can be switched to any other core or distributed over all the cores. By tuning the acoustic wave amplitude, we can adjust the amount of optical power transferred between the cores.
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http://dx.doi.org/10.1364/OE.23.026313DOI Listing
October 2015

Portuguese mitochondrial DNA genetic diversity-An update and a phylogenetic revision.

Forensic Sci Int Genet 2015 Mar 14;15:27-32. Epub 2014 Oct 14.

Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.

In recent years a large amount of mitochondrial population data for forensic purposes has been produced. Current efforts are focused at increasing the number of studied populations while generating updated genetic information of forensic quality. However, complete mitochondrial control region sequences are still scarce for most populations and even more so for complete mitochondrial genomes. In the case of Portugal, previous population genetics studies have already revealed the general portrait of HVS-I and HVS-II mitochondrial diversity, becoming now important to update and expand the mitochondrial region analysed. Accordingly, a total of 292 complete control region sequences from continental Portugal were obtained, under a stringent experimental design to ensure the quality of data through double sequencing of each target region. Furthermore, H-specific coding region SNPs were examined to detail haplogroup classification and complete mitogenomes were obtained for all sequences belonging to haplogroups U4 and U5. In general, a typical Western European haplogroup composition was found in mainland Portugal, associated to high level of mitochondrial genetic diversity. Within the country, no signs of substructure were detected. The typing of extra coding region SNPs has provided the refinement or confirmation of the previous classification obtained with EMMA tool in 96% of the cases. Finally, it was also possible to enlarge haplogroup U phylogeny with 28 new U4 and U5 mitogenomes.
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http://dx.doi.org/10.1016/j.fsigen.2014.10.004DOI Listing
March 2015

Galectin-3 overexpression in invasive laryngeal carcinoma, assessed by computer-assisted analysis.

J Histochem Cytochem 2009 Jul 30;57(7):665-73. Epub 2009 Mar 30.

Department of Pathology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, 14049-900, Ribeirão Preto, São Paulo, Brazil.

The larynx is the most common site of malignancy in the upper aerodigestive tract. In Brazil, malignant laryngeal lesions represent 2% of all cancers, with approximately 3000 annual deaths. The association between human papillomavirus (HPV) and laryngeal cancer is still controversial. The aim of the present retrospective study was to determine the expression of galectin-3 immunoperoxidase in laryngeal carcinoma by examining paraffin-embedded larynx biopsies from 65 patients, 10 in situ laryngeal carcinomas, 27 laryngeal carcinomas without metastases, and 28 with metastases. Twenty-eight cervical lymph nodes from patients with metastatic lesions were also evaluated. Nested PCR was performed to detect and type HPV DNA. Galectin-3 expression was assessed by immunohistochemistry using a computer-assisted system. Among 65 patients, 55 (84.6%) were positive to beta-globin (internal control); 10 (15.4%) patients were beta-globin negative and were excluded from the HPV evaluation. Thus, 7 (12.7%) out of 55 patients were HPV positive and 48 (87.3%) out of 55 patients were HPV negative. High expression of galectin-3 was observed in invasive laryngeal tumors, suggesting that galectin-3 could be associated with the invasiveness and aggressiveness of laryngeal carcinomas.
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http://dx.doi.org/10.1369/jhc.2009.952960DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2699322PMC
July 2009