Forecasting the dynamics of a complex microbial community using integrated meta-omics.

Predicting the behaviour of complex microbial communities is challenging. However, this is essential for complex biotechnological processes such as those in biological wastewater treatment plants (BWWTPs), which require sustainable operation. Here we summarize 14 months of longitudinal meta-omics data from a BWWTP anaerobic tank into 17 temporal signals, explaining 91.1% of the temporal variance, and link those signals to ecological events within the community. We forecast the signals over the subsequent five years and use 21 extra samples collected at defined time intervals for testing and validation. Our forecasts are correct for six signals and hint on phenomena such as predation cycles. Using all the 17 forecasts and the environmental variables, we predict gene abundance and expression, with a coefficient of determination ≥0.87 for the subsequent three years. Our study demonstrates the ability to forecast the dynamics of open microbial ecosystems using interactions between community cycles and environmental parameters.

Association between Elevated Iodine Intake and IQ among School Children in Portugal.

The goal of this work was to examine whether elevated iodine intake was associated with adverse effects on IQ among school-age children in Portugal. In a representative sample of children from the north of the country, IQ percentiles by age (assessed with Raven's Colored Progressive Matrices) were dichotomized to <50 ("below-average" IQs) and ≥50. Morning urine iodine concentrations, corrected for creatinine, were dichotomized to <250 µg/g and ≥250 µg/g, according to the European Commission/Scientific Committee on Food's tolerable upper level of daily iodine intake for young children. Data were examined with Chi-square tests, logistic regression, and GLM univariate analysis. The sample (N = 1965) was classified as generally iodine-adequate (median urinary iodine concentration = 129 µg/L; median iodine-to-creatinine ratio = 126 µg/g) according to the WHO's criteria. A greater proportion of children in the ≥250 µg/g group had below-average IQs, compared to children with less than 250 µg/g (p = 0.037), despite a sizable (though non-significant) proportion of children in the less-than-250 µg/g group also presenting below-average IQs, at the bottom of the iodine distribution (<50 µg/g). The proportion of below-average IQs increased with increasingly elevated iodine concentrations (p = 0.047). The association remained significant after the adjustment for confounders, with the elevated iodine group showing increased odds of having below-average IQs when compared with the non-elevated iodine group (OR 1.55; 95% CI 1.11−2.17; p = 0.011). Consistently, the former group presented a lower mean IQ than the latter (p = 0.006). High iodine intake was associated with lower IQs even in a population classified as iodine-adequate. These results bear on child cognition and on initiatives involving iodine supplementation.

Staging cardiac damage in patients with aortic regurgitation.

The impact of "downstream" pathophysiological cardiac consequences in aortic regurgitation patients were not well established. The aim of our study was to validate a staging system built for severe aortic stenosis in a large real-world cohort of aortic regurgitation (AR) patients, evaluating the prevalence of different stages of cardiac damage and assess its prognostic impact. Clinical, echocardiographic and outcome data of patients with moderate-severe AR who underwent transthoracic echocardiography between January/2014 and September/2019 were retrospectively analysed. Patients were classified according to the extent of cardiac damage: Stage 0 (no cardiac damage), Stage 1 (left ventricular damage), Stage 2 (mitral valve or left atrial damage), Stage 3 (tricuspid valve or pulmonary artery vasculature damage) and Stage 4 (right ventricular damage). The primary endpoint was all-cause mortality. A total of 571 patients (median age 73, 51% male) were enrolled: Stage 0 (14.0%), Stage 1 (21.5%), Stage 2 (49.2%), Stage 3 (12.3%) and Stage 4 (3.0%). Median follow-up time was 39.5 months (IQR 22.2 to 61.0). At the end of follow-up, cumulative death was significantly higher in more advanced disease stages (log-rank p < 0.001). On multivariable analysis, Stage 3-4 was associated with increased risk of all-cause mortality (HR 3.20; 95% CI 1.48-6.93; p = 0.003). Our study suggests that extra-valvular damage is common in patients with significant AR and that a staging system developed for aortic stenosis also provides prognostic information in these patients. This staging system may be helpful for clinical decision-making regarding the time of valvular intervention.

binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets.

The reconstruction of genomes is a critical step in genome-resolved metagenomics and for multi-omic data integration from microbial communities. Here, we present binny, a binning tool that produces high-quality metagenome-assembled genomes (MAG) from both contiguous and highly fragmented genomes. Based on established metrics, binny outperforms or is highly competitive with commonly used and state-of-the-art binning methods and finds unique genomes that could not be detected by other methods. binny uses k-mer-composition and coverage by metagenomic reads for iterative, nonlinear dimension reduction of genomic signatures as well as subsequent automated contig clustering with cluster assessment using lineage-specific marker gene sets. When compared with seven widely used binning algorithms, binny provides substantial amounts of uniquely identified MAGs and almost always recovers the most near-complete ($\gt 95\%$ pure, $\gt 90\%$ complete) and high-quality ($\gt 90\%$ pure, $\gt 70\%$ complete) genomes from simulated datasets from the Critical Assessment of Metagenome Interpretation initiative, as well as substantially more high-quality draft genomes, as defined by the Minimum Information about a Metagenome-Assembled Genome standard, from a real-world benchmark comprised of metagenomes from various environments than any other tested method.

Fighting the pandemic with collaboration at heart: Report from cardiologists in a COVID-19-dedicated Portuguese intensive care unit.

INTRODUCTION AND OBJECTIVES: The coronavirus disease 2019 (COVID-19) spread quickly around the world. Although mainly a respiratory illness, there is growing interest in non-respiratory manifestations, particularly cardiovascular ones. At our center, mobilization of cardiologists with intensive care training was needed. Our aim is to describe patients with severe COVID-19 admitted to a Portuguese intensive care unit (ICU), the cardiovascular impact of the disease and the experience of cardiologists working in a COVID-19 ICU. METHODS: Data from adult patients with COVID-19 admitted to the ICU of Centro Hospitalar de Vila Nova de Gaia/Espinho between 16 March 2020 and 21 April 2020 were analyzed retrospectively. RESULTS: Thirty-five patients were admitted. Mean age was 62.6±6.0 years and 23 (65.7%) were male. Dyslipidemia was the most common cardiovascular risk factor (65.7%, n=23), followed by hypertension (57.1%, n=20). Mean ICU stay time was 15.9±10.0 days. Patients had high rates of mechanical ventilation (88.6%, n=31) and vasopressor support (88.6%, n=31). Low rates of new onset left systolic dysfunction were detected (8.5%, n=2). One patient required venoarterial extra-corporeal membrane oxygenation. Mortality was 25% (n=9). Acute myocardial injury and N-terminal pro-B-type natriuretic peptide (NT-proBNP) elevation was detected in 62.9% (n=22). Patients that died had higher NT-proBNP compared to those discharged alive (p<0.05). Care by cardiologists frequently changed decision making. CONCLUSIONS: The cardiovascular impact of COVID-19 seems relevant but is still widely unknown. Studies are needed to clarify the role of cardiac markers in COVID-19 prognosis. Multidisciplinary care most likely results in improved patient care.

Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows.

Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out a community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluate the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample. We observe that variability at the peptide level is predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappear at the protein group level. While differences are observed for predicted community composition, similar functional profiles are obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.

Incessant Atrial Tachycardia: Problem Solving With Minimally Invasive Surgery.

A 35-year-old female with sarcoidosis sought medical attention due to palpitations. The ECG showed an atrial tachycardia (AT), apparently originating in the left atrium. A 24-hour Holter monitoring revealed AT to be present during the entire day. Cardiac magnetic resonance exhibited no cardiac involvement by sarcoidosis but registered a mildly depressed left ventricular ejection fraction (LVEF). Atrial electroanatomical mapping showed the earliest activation zone on the distal portion of the left atrial appendage (LAA). Considering the high risk for perforation with catheter ablation in this region, she was sent to thoracoscopic surgical LAA exclusion with a clip device; it was possible to witness the termination of the arrhythmia during the procedure. She was safely discharged two days after surgery and has completed a one-year follow-up without recurrence of AT or symptoms, and with normalization of LVEF.

Fighting the pandemic with collaboration at heart: Report from cardiologists in a COVID-19-dedicated Portuguese intensive care unit.

INTRODUCTION AND OBJECTIVES: The coronavirus disease 2019 (COVID-19) spread quickly around the world. Although mainly a respiratory illness, there is growing interest in non-respiratory manifestations, particularly cardiovascular ones. At our center, mobilization of cardiologists with intensive care training was needed. Our aim is to describe patients with severe COVID-19 admitted to a Portuguese intensive care unit (ICU), the cardiovascular impact of the disease and the experience of cardiologists working in a COVID-19 ICU. METHODS: Data from adult patients with COVID-19 admitted to the ICU of Centro Hospitalar de Vila Nova de Gaia/Espinho between 16 March 2020 and 21 April 2020 were analyzed retrospectively. RESULTS: Thirty-five patients were admitted. Mean age was 62.6±6.0 years and 23 (65.7%) were male. Dyslipidemia was the most common cardiovascular risk factor (65.7%, n=23), followed by hypertension (57.1%, n=20). Mean ICU stay time was 15.9±10.0 days. Patients had high rates of mechanical ventilation (88.6%, n=31) and vasopressor support (88.6%, n=31). Low rates of new onset left systolic dysfunction were detected (8.5%, n=2). One patient required venoarterial extra-corporeal membrane oxygenation. Mortality was 25% (n=9). Acute myocardial injury and N-terminal pro-B-type natriuretic peptide (NT-proBNP) elevation was detected in 62.9% (n=22). Patients that died had higher NT-proBNP compared to those discharged alive (p<0.05). Care by cardiologists frequently changed decision making. CONCLUSIONS: The cardiovascular impact of COVID-19 seems relevant but is still widely unknown. Studies are needed to clarify the role of cardiac markers in COVID-19 prognosis. Multidisciplinary care most likely results in improved patient care.

INTRODUÇÃO E OBJETIVOS: A doença pelo novo coronavirus (COVID-19) espalhou-se rapidamente pelo globo. Embora tenha atingimento essencialmente respiratório, existe interesse nas manifestações extrarrespiratórias, nomeadamente nas cardiovasculares. No nosso centro, foi necessária a mobilização de cardiologistas com experiência em cuidados intensivos para enfrentar este desafio. O objetivo desta investigação é descrever a população internada com COVID-19 grave numa UCI portuguesa, o impacto cardiovascular desta doença e a nossa experiência enquanto cardiologistas numa UCI COVID-19. MÉTODOS: Dados de adultos com COVID-19 internados na UCI do Centro Hospitalar de Vila Nova de Gaia/Espinho entre 16/03/2020 e 21/04/2020 foram analisados retrospetivamente. RESULTADOS: Foram internados 35 doentes. A média de idade foi 62,6±6,0 anos e 23 (65,7%) doentes eram homens. A dislipidemia foi o fator de risco cardiovascular mais prevalente (65,7%, n=23), seguida pela hipertensão (57,1%, n=20). O tempo médio de internamento em UCI foi 15,9±10,0 dias. A necessidade de ventilação mecânica (88,6%, n=31) e suporte vasopressor (88,6%, n=31) foi alta, mas poucos doentes desenvolveram disfunção sistólica de novo (n=2,85%). A mortalidade foi de 25% (n=9). Foi detetada lesão miocárdica aguda e elevação do NT-proBNP em 62,9% (n=22) dos doentes, sendo os níveis de NT-proBNP mais elevados nos doentes que faleceram (p<0,05). A participação de cardiologistas na UCI alterou frequentemente a decisão clínica. CONCLUSÃO: O impacto cardiovascular da COVID-19 parece relevante mas é parcamente conhecido, sendo necessários mais estudos para clarificar o papel dos marcadores cardíacos no prognóstico da COVID-19. As equipas multidisciplinares provavelmente melhoram os cuidados de saúde prestados a estes doentes.

Challenges, Strategies, and Perspectives for Reference-Independent Longitudinal Multi-Omic Microbiome Studies.

In recent years, multi-omic studies have enabled resolving community structure and interrogating community function of microbial communities. Simultaneous generation of metagenomic, metatranscriptomic, metaproteomic, and (meta) metabolomic data is more feasible than ever before, thus enabling in-depth assessment of community structure, function, and phenotype, thus resulting in a multitude of multi-omic microbiome datasets and the development of innovative methods to integrate and interrogate those multi-omic datasets. Specifically, the application of reference-independent approaches provides opportunities in identifying novel organisms and functions. At present, most of these large-scale multi-omic datasets stem from spatial sampling (e.g., water/soil microbiomes at several depths, microbiomes in/on different parts of the human anatomy) or case-control studies (e.g., cohorts of human microbiomes). We believe that longitudinal multi-omic microbiome datasets are the logical next step in microbiome studies due to their characteristic advantages in providing a better understanding of community dynamics, including: observation of trends, inference of causality, and ultimately, prediction of community behavior. Furthermore, the acquisition of complementary host-derived omics, environmental measurements, and suitable metadata will further enhance the aforementioned advantages of longitudinal data, which will serve as the basis to resolve drivers of community structure and function to understand the biotic and abiotic factors governing communities and specific populations. Carefully setup future experiments hold great potential to further unveil ecological mechanisms to evolution, microbe-microbe interactions, or microbe-host interactions. In this article, we discuss the challenges, emerging strategies, and best-practices applicable to longitudinal microbiome studies ranging from sampling, biomolecular extraction, systematic multi-omic measurements, reference-independent data integration, modeling, and validation.

Mantis: flexible and consensus-driven genome annotation.

BACKGROUND: The rapid development of the (meta-)omics fields has produced an unprecedented amount of high-resolution and high-fidelity data. Through the use of these datasets we can infer the role of previously functionally unannotated proteins from single organisms and consortia. In this context, protein function annotation can be described as the identification of regions of interest (i.e., domains) in protein sequences and the assignment of biological functions. Despite the existence of numerous tools, challenges remain in terms of speed, flexibility, and reproducibility. In the big data era, it is also increasingly important to cease limiting our findings to a single reference, coalescing knowledge from different data sources, and thus overcoming some limitations in overly relying on computationally generated data from single sources. RESULTS: We implemented a protein annotation tool, Mantis, which uses database identifiers intersection and text mining to integrate knowledge from multiple reference data sources into a single consensus-driven output. Mantis is flexible, allowing for the customization of reference data and execution parameters, and is reproducible across different research goals and user environments. We implemented a depth-first search algorithm for domain-specific annotation, which significantly improved annotation performance compared to sequence-wide annotation. The parallelized implementation of Mantis results in short runtimes while also outputting high coverage and high-quality protein function annotations. CONCLUSIONS: Mantis is a protein function annotation tool that produces high-quality consensus-driven protein annotations. It is easy to set up, customize, and use, scaling from single genomes to large metagenomes. Mantis is available under the MIT license at https://github.com/PedroMTQ/mantis.

Unification of functional annotation descriptions using text mining.

A common approach to genome annotation involves the use of homology-based tools for the prediction of the functional role of proteins. The quality of functional annotations is dependent on the reference data used, as such, choosing the appropriate sources is crucial. Unfortunately, no single reference data source can be universally considered the gold standard, thus using multiple references could potentially increase annotation quality and coverage. However, this comes with challenges, particularly due to the introduction of redundant and exclusive annotations. Through text mining it is possible to identify highly similar functional descriptions, thus strengthening the confidence of the final protein functional annotation and providing a redundancy-free output. Here we present UniFunc, a text mining approach that is able to detect similar functional descriptions with high precision. UniFunc was built as a small module and can be independently used or integrated into protein function annotation pipelines. By removing the need to individually analyse and compare annotation results, UniFunc streamlines the complementary use of multiple reference datasets.

Iodine Status and Iodised Salt Consumption in Portuguese School-Aged Children: The Iogeneration Study.

The World Health Organization promotes salt iodisation to control iodine deficiency. In Portugal, the use of iodised salt in school canteens has been mandatory since 2013. The present study aimed to evaluate iodine status in school-aged children (6-12 years) and to monitor the use of iodised salt in school canteens. A total of 2018 participants were randomly selected to participate in a cross-sectional survey in northern Portugal. Children's urine and salt samples from households and school canteens were collected. A lifestyle questionnaire was completed by parents to assess children's eating frequency of iodine food sources. Urinary iodine concentration (UIC) was measured by inductively coupled plasma-mass spectrometry. The median UIC was 129 µg/L which indicates the adequacy of iodine status and 32% of the children had UIC < 100 µg/L. No school canteen implemented the iodised salt policy and only 2% of the households were using iodised salt. Lower consumption of milk, but not fish, was associated with a higher risk of iodine deficiency. Estimation of sodium intake from spot urine samples could be an opportunity for adequate monitoring of population means. Implementation of iodine deficiency control policies should include a monitoring program aligned with the commitment of reducing the population salt intake.

KRAS mutations in microsatellite instable gastric tumours: impact of targeted treatment and intratumoural heterogeneity.

In gastric cancer (GC), epidermal growth factor receptor (EGFR) overexpression associates with poor prognosis. Addition of a chimeric monoclonal antibody against EGFR (cetuximab) to first-line treatment of metastatic colorectal tumours improved outcomes of patients (stratified for KRAS wild-type cancers), whereas GC patients did not benefit from this approach. In GC, however, stratification based on KRAS mutations was not performed, and the 30 % KRAS mutation frequency in microsatellite instable cancers (MSI), which represents ∼4 % of total GC, was disregarded. Further, intratumoural heterogeneity regarding KRAS mutant subpopulations might also contribute to anti-EGFR therapy failure. We assessed the mutational status of the entire KRAS coding sequence in 19 MSI-GC cases by multiplex PCR/sequencing and used peak height ratio determined from electropherograms from KRAS heterozygous mutants and histopathological evaluation to infer tumour heterogeneity in GC. Using 2 multiplex reactions per sample, we found that 26 % (5/19) of MSI-GC cases harboured KRAS mutations (2 G12D, 2 G13D, 1 G12V). No mutations were found outside the codon 12 and 13 hotspots. Our analysis supported the co-existence of KRAS-positive and KRAS-negative tumour populations in 4/5 MSI-GC cases. In conclusion, the method developed stands as a cost-effective and practical way for mutation screening of the entire KRAS coding sequence. KRAS mutations are frequent in our series of MSI cases and are often found in a subpopulation of the tumour and not in the whole tumour. Further studies are needed to access the implications of this heterogeneity in KRAS mutant and wild-type tumour clones in anti-EGFR therapy response.

Fulguraçäo endocavitária de vias acessórias no tratamento da síndrome de Wolff-Parkinson-White / Endocavitary fulguration of accessory pathways in the treatment of Wolff-Parkinson-White syndrome

Apresentar nossa experiência inicial no tratamento definitivo da síndrome de Wolff-Parkinson-White, através de fulguraçäo endocavitária de vias acessórias. Quatorze sessöes de fulguraçäo endocavitária realizadas em 9 portadores de síndrome de Wolff-Parkinson-White. Cinco eram do sexo masculino e a média de idade foi de 35 anos. Obteve-se completa interrupçäo da conduçäo pela via anômala em 7 pacientes: 4 através de uma e 3 de duas sessöes. Um paciente (1§ da série) foi submetido a três sessöes, näo se conseguindo a interrupçäo definitiva da conduçäo pela via acessória, e encaminhado a cirurgia. O restante, näo responsivo à primeira tentativa, aguarda nova sessäo. Näo foram observadas complicaçöes cardiológicas inerentes ao procedimento. A fulguraçäo endocavitária de vias acessórias mostrou-se método seguro, eficaz e portanto passível de ser cogitado como primeira opçäo quando da indicaçäo de ablaçäo desses feixes anômalos