False-Positive Uptake on Radioiodine Whole-Body Scan Due to Bronchiectasis

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Stable isotopes as ecological tracers: an efficient method for assessing the contribution of multiple sources to mixtures

Stable isotopes are increasingly being used as tracers of ecological processes potentially providing relevant information to environmental management issues. An application of the methodology consists in relating the stable isotopic composition of a sample mixture to that of sources. The number of stable isotopes, however, is usually lower than that of potential sources existing in an ecosystem, which creates mathematical difficulties in correctly tracing sources. We discuss a linear programming model which efficiently derives information on the contribution of sources to mixtures for any number of stable isotopes and any number of sources by addressing multiple sources simultaneously. The model identifies which sources are present in all, present in a subset of the samples or absent from all samples simultaneously and calculates minimum and maximum values of each source in the mixtures. We illustrate the model using a data set consisting of the isotopic signatures of different plant sources ingested by primary consumers in tropical riverine habitat in Asia. The model discussed may contribute to extend the scope of stable isotopes methodology to a range of new problems dealing with multiple sources and multiple tracers. For instance, in food web studies, if particular organic matter sources disappear or decrease in availability (e.g. climate change scenarios) the model allows simulation of alternative diets of the consumers providing potentially relevant information for managers and decision makers

Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach

<p>Abstract</p> <p>Background</p> <p>Multilocus Sequence Typing (MLST) is a frequently used typing method for the analysis of the clonal relationships among strains of several clinically relevant microbial species. MLST is based on the sequence of housekeeping genes that result in each strain having a distinct numerical allelic profile, which is abbreviated to a unique identifier: the sequence type (ST). The relatedness between two strains can then be inferred by the differences between allelic profiles. For a more comprehensive analysis of the possible patterns of evolutionary descent, a set of rules were proposed and implemented in the eBURST algorithm. These rules allow the division of a data set into several clusters of related strains, dubbed clonal complexes, by implementing a simple model of clonal expansion and diversification. Within each clonal complex, the rules identify which links between STs correspond to the most probable pattern of descent. However, the eBURST algorithm is not globally optimized, which can result in links, within the clonal complexes, that violate the rules proposed.</p> <p>Results</p> <p>Here, we present a globally optimized implementation of the eBURST algorithm – goeBURST. The search for a global optimal solution led to the formalization of the problem as a graphic matroid, for which greedy algorithms that provide an optimal solution exist. Several public data sets of MLST data were tested and differences between the two implementations were found and are discussed for five bacterial species: <it>Enterococcus faecium</it>, <it>Streptococcus pneumoniae</it>, <it>Burkholderia pseudomallei</it>, <it>Campylobacter jejuni </it>and <it>Neisseria spp.</it>. A novel feature implemented in goeBURST is the representation of the level of tiebreak rule reached before deciding if a link should be drawn, which can used to visually evaluate the reliability of the represented hypothetical pattern of descent.</p> <p>Conclusion</p> <p>goeBURST is a globally optimized implementation of the eBURST algorithm, that identifies alternative patterns of descent for several bacterial species. Furthermore, the algorithm can be applied to any multilocus typing data based on the number of differences between numeric profiles. A software implementation is available at <url>http://goeBURST.phyloviz.net</url>.</p

Psychosis Assessment in Early-Stage Parkinson's Disease: Comparing Parkinson's Psychosis Questionnaire with the Brief Psychiatric Rating Scale in a Portuguese Sample

Psychotic symptoms in Parkinson's disease (PD) are frequent, disabling, and an important prognostic factor. Thus, screening instruments for detecting psychosis in PD are needed. For this purpose, we applied the Parkinson's Psychosis Questionnaire (PPQ), a short structured questionnaire, which requires no specific training, along with the Brief Psychiatric Rating Scale, expanded version (BPRS-E), for rating general psychopathology, including psychotic symptoms. We evaluated, in a cross-sectional study, a Portuguese sample of 36 early-stage PD patients (mean age of 73 years; mean duration of illness of 3.2 years). The PPQ total score correlated with the BPRS-E total score (0.359; P = 0.032) and with the BPRS-E-positive symptoms score (0.469; P = 0.004). The prevalence of psychosis (41.7%) was higher than expected. Sampling bias and detection of minor psychotic phenomena may have contributed to this result. These findings suggest that the PPQ should be further evaluated as a feasible assessment for psychotic symptoms in PD

Cyto-Histological Profile of MicroRNAs as Diagnostic Biomarkers in Differentiated Thyroid Carcinomas

Introduction: The repertoire of microRNAs (miRNAs) in thyroid carcinomas starts to be elucidated. Among differentiated thyroid carcinomas (DTCs), papillary thyroid carcinoma (PTC) is the most frequent. The assessment of miRNAs expression may contribute to refine the pre-surgical diagnosis in order to obtain a personalized and more effective treatment for patients. Aims: This study aims to evaluate (1) the miRNAs in a series of DTCs, and their association with the presence of selected genetic mutations in order to improve diagnosis and predict the biologic behavior of DTC/PTC. (2) The reliability of molecular tests in Ultrasound-guided Fine Needle Aspiration Cytology (US-FNAC) for a more precise preoperative diagnosis. Material and methods: This series includes 176 samples (98 cytology and 78 histology samples) obtained from 106 patients submitted to surgery, including 13 benign lesions (controls) and 93 DTCs (cases). The microRNA expression was assessed for miR-146b, miR-221, miR-222, and miR-15a through quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR). The results were analyzed by the 2-ΔΔCT method, using miR16 as an endogenous control. Regarding PTC diagnosis, the discriminative ability of miRNAs expression was assessed by the area under the Receiver Operating Characteristic Curve (AUC). In PTCs, the association of miRNAs expression, clinicopathological features, and genetic mutations (BRAF, RAS, and TERTp) was evaluated. Results/discussion: All the analyzed miRNAs presented a tendency to be overexpressed in DTCs/PTCs when compared with benign lesions, both in cytology and histology samples. In cytology, miRNAs expression levels were higher in malignant tumors than in benign tumors. In histology, the discriminative abilities regarding PTC diagnosis were as follows: miR-146b (AUC 0.94, 95% CI 0.87-1), miR-221 (AUC 0.79, 95% CI 0.68-0.9), miR-222 (AUC 0.76, 95% CI 0.63-0.89), and miR-15a (AUC 0.85, 95% CI 0.74-0.97). miR-146b showed 89% sensitivity (se) and 87% specificity (sp); miR-221 se = 68.4, sp = 90; miR-222 se = 73, sp = 70; and mi-R15a se = 72, sp = 80. MicroRNAs were associated with worst-prognosis clinicopathological characteristics in PTCs (p < 0.05), particularly for miR-222. Our data reveal a significant association between higher expression levels of miR-146b, miR-221, and miR-222 in the presence of the BRAF mutation (p < 0.001) and miR-146b (p = 0.016) and miR-221 (p = 0.010) with the RAS mutation, suggesting an interplay of these mutations with miRNAs expression. Despite this study having a relatively small sample size, overexpression of miRNAs in cytology may contribute to a more precise preoperative diagnosis. The miRNAs presented a good discriminative ability in PTC diagnosis. The association between the miRNAs expression profile and genetic alterations can be advantageous for an accurate diagnosis of DTCs/PTCs in FNAC.info:eu-repo/semantics/publishedVersio

Assessment of a Large-Scale Unbiased Malignant Pleural Effusion Proteomics Study of a Real-Life Cohort

Background: Pleural effusion (PE) is common in advanced-stage lung cancer patients and is related to poor prognosis. Identification of cancer cells is the standard method for the diagnosis of a malignant PE (MPE). However, it only has moderate sensitivity. Thus, more sensitive diagnostic tools are urgently needed. Methods: The present study aimed to discover potential protein targets to distinguish malignant pleural effusion (MPE) from other non-malignant pathologies. We have collected PE from 97 patients to explore PE proteomes by applying state-of-the-art liquid chromatography-mass spectrometry (LC-MS) to identify potential biomarkers that correlate with immunohistochemistry assessment of tumor biopsy or with survival data. Functional analyses were performed to elucidate functional differences in PE proteins in malignant and benign samples. Results were integrated into a clinical risk prediction model to identify likely malignant cases. Sensitivity, specificity, and negative predictive value were calculated. Results: In total, 1689 individual proteins were identified by MS-based proteomics analysis of the 97 PE samples, of which 35 were diagnosed as malignant. A comparison between MPE and benign PE (BPE) identified 58 differential regulated proteins after correction of the p-values for multiple testing. Furthermore, functional analysis revealed an up-regulation of matrix intermediate filaments and cellular movement-related proteins. Additionally, gene ontology analysis identified the involvement of metabolic pathways such as glycolysis/gluconeogenesis, pyruvate metabolism and cysteine and methionine metabolism. Conclusion: This study demonstrated a partial least squares regression model with an area under the curve of 98 and an accuracy of 0.92 when evaluated on the holdout test data set. Furthermore, highly significant survival markers were identified (e.g., PSME1 with a log-rank of 1.68 × 10−6 ).info:eu-repo/semantics/publishedVersio

a consensus statement from the Portuguese Pulmonology Society

Coronavirus disease 2019 (COVID-19) is an emerging infectious disease caused by a novel SARS-CoV-2 pathogen. Its capacity for human-to-human transmission through respiratory droplets, coupled with a high-level of population mobility, has resulted in a rapid dissemination worldwide. Healthcare workers have been particularly exposed to the risk of infection and represent a significant proportion of COVID-19 cases in the worst affected regions of Europe. Like other open airway procedures or aerosol-generating procedures, bronchoscopy poses a significant risk of spreading contaminated droplets, and medical workers must adapt the procedures to ensure safety of both patients and staff. Several recommendation documents were published at the beginning of the pandemic, but as the situation evolves, our thoughts should not only focus on the present, but should also reflect on how we are going to deal with the presence of the virus in the community until there is a vaccine or specific treatment available. It is in this sense that this document aims to guide interventional pulmonology throughout this period, providing a set of recommendations on how to perform bronchoscopy or pleural procedures safely and efficiently.proofpublishe