Novel Bayesian Networks for Genomic Prediction of Developmental Traits in Biomass Sorghum.

The ability to connect genetic information between traits over time allow Bayesian networks to offer a powerful probabilistic framework to construct genomic prediction models. In this study, we phenotyped a diversity panel of 869 biomass sorghum (Sorghum bicolor (L.) Moench) lines, which had been genotyped with 100,435 SNP markers, for plant height (PH) with biweekly measurements from 30 to 120 days after planting (DAP) and for end-of-season dry biomass yield (DBY) in four environments. We evaluated five genomic prediction models: Bayesian network (BN), Pleiotropic Bayesian network (PBN), Dynamic Bayesian network (DBN), multi-trait GBLUP (MTr-GBLUP), and multi-time GBLUP (MTi-GBLUP) models. In fivefold cross-validation, prediction accuracies ranged from 0.46 (PBN) to 0.49 (MTr-GBLUP) for DBY and from 0.47 (DBN, DAP120) to 0.75 (MTi-GBLUP, DAP60) for PH. Forward-chaining cross-validation further improved prediction accuracies of the DBN, MTi-GBLUP and MTr-GBLUP models for PH (training slice: 30-45 DAP) by 36.4-52.4% relative to the BN and PBN models. Coincidence indices (target: biomass, secondary: PH) and a coincidence index based on lines (PH time series) showed that the ranking of lines by PH changed minimally after 45 DAP. These results suggest a two-level indirect selection method for PH at harvest (first-level target trait) and DBY (second-level target trait) could be conducted earlier in the season based on ranking of lines by PH at 45 DAP (secondary trait). With the advance of high-throughput phenotyping technologies, our proposed two-level indirect selection framework could be valuable for enhancing genetic gain per unit of time when selecting on developmental traits

Case Report: Pheochromocytoma and Synchronous Neuroblastoma in a Family With Hereditary Pheochromocytoma Associated With a MAX Deleterious Variant

Introduction: Pheochromocytomas are rare catecholamine-producing neuroendocrine tumours arising from chromaffin cells of the adrenal medulla or extra-adrenal sympathetic paraganglia. Recent studies have indicated that up to 40% of pheochromocytomas could be attributable to an inherited germline variant in an increasing list of susceptibility genes. Germline variants of the MYC-associated factor (MAX) gene have been associated with familial pheochromocytomas and paragangliomas with an autosomal dominant pattern of inheritance, a median age at onset of 33 years and an overall frequency estimated at 1.9%. We describe a deleterious MAX variant associated with hereditary pheochromocytoma in a family with four affected individuals. Case presentation: The first patient presented with bilateral pheochromocytoma in 1995; genetic testing was proposed to his oldest son, when he was diagnosed with a bilateral pheochromocytoma with a synchronous neuroblastoma. Upon the identification of the MAX variant c.97C>T, p.(Arg33Ter), in the latter individual, his two siblings and their father were tested and the same variant was identified in all of them. Both siblings were subsequently diagnosed with pheochromocytoma (one of them bilateral) and choose to remain on active surveillance before they were submitted to adrenalectomy. All the tumours secreted predominantly norepinephrine, accordingly to the typical biochemical phenotype ascribed to variants in the MAX gene. Conclusion: This case series is, to our knowledge, the one with the largest number of individuals with hereditary pheochromocytoma with a deleterious MAX variant in the same family. It is also the first case with a synchronous pheochromocytoma and neuroblastoma in carriers of a MAX deleterious variant. This report draws attention to some ill-defined features of pheochromocytoma and other malignancies associated with a MAX variant and highlights the importance of understanding the genotype-phenotype correlation in hereditary pheochromocytoma and the impact of oriented genetic testing to detect, survey and treat patients and kindreds at risk

Non-Destructive Measurement of the Internal Quality of Citrus Fruits Using a Portable NIR Device

The citrus industry has grown exponentially as a result of increasing demand on its consumption, giving it high standing among other fruit crops. Therefore, the citrus sector seeks rapid, easy, and non-destructive approaches to evaluate in real time and in situ the external and internal changes in physical and nutritional quality at any stage of fruit development or storage. In particular, vitamin C is among the most important micronutrients for consumers, but its measurement relies on laborious analytical methodologies. In this study, a portable near infrared spectroscopy (NIRS) sensor was used in combination with chemometrics to develop robust and accurate models to study the ripeness of several citrus fruits (oranges, lemons, clementines, tangerines, and Tahiti limes) and their vitamin C content. Ascorbic acid, dehydroascorbic acid, and total vitamin C were determined by HILIC-HPLC-UV, while soluble solids and total acidity were evaluated by standard analytical procedures. Partial least squares regression (PLSR) was used to build regression models which revealed suitable performance regarding the prediction of quality and ripeness parameters in all tested fruits. Models for ascorbic acid, dehydroascorbic acid, total vitamin C, soluble solids, total acidity, and juiciness showed R2cv = 0.77–0.87, R2cv = 0.29–0.79, R2cv = 0.77–0.86, R2cv = 0.75–0.97, R2cv = 0.24–0.92, and R2cv = 0.38–0.75, respectively. Prediction models of oranges and Tahiti limes showed good to excellent performance regarding all tested conditions. The resulting models confirmed that NIRS technology is a time- and cost-effective approach for predicting citrus fruit quality, which can easily be used by the various stakeholders from the citrus industry.This work received support from Fundação para a Ciência e Tecnologia under the Partnership Agreement UIDB/50006/2020/PT

Management of Coronavirus Disease 2019 Patients With Lung Cancer: Experience From a Thoracic Oncology Center

Background: Cancer patients appear to be at a higher risk of complications from coronavirus disease 2019 (COVID-19). Specific data related to lung cancer (LC) patient management, active treatment, and/or recent diagnosis are still very limited. Here, we aimed to investigate the clinical presentation, baseline features, and clinical outcomes of LC patients with COVID-19. Methods: A retrospective case study was performed at Centro Hospitalar Universitário de São Joao, a tertiary hospital in the North of Portugal. Data from LC patients diagnosed with COVID-19 were collected during the first 10 months of the COVID-19 pandemic (March 2020–January 2021). Results: Twenty-eight patients with active LC were diagnosed with COVID-19, being adenocarcinoma the most common histological type present (n = 13, 46.4%). Sixteen patients had metastatic stage IV LC (61.5%). Twenty-five patients (89.3%) had relevant comorbidities including hypertension (39.3%) and chronic obstructive pulmonary disease (32.1%). For patients undergoing antineoplastic treatment, the median time from the last chemotherapy administration to COVID-19 diagnosis was of 16 days (interquartile range = 13–41 days). Half of patients were previously on corticosteroid therapy. Twenty patients (71.4%) needed hospitalization, 18 received oxygen therapy (64.3%), 3 (10.7%) of them received high-flow nasal cannula with good tolerability, and 1 (3.6%) needed non-invasive ventilation. Hydroxychloroquine and antibiotics were given to 4 (14.3%) and 12 (42.9%) patients, respectively. Seven patients (25%) died at a median time of 5 days following COVID-19 diagnosis. Conclusion: This is one of the first studies reporting the adverse outcomes associated with COVID-19 in LC patients at same time that adds evidence regarding the need to create protocols and guidelines to reduce the infection risk in such patients.NC-M acknowledges the Portuguese Foundation for Science and Technology under the Horizon 2020 Program (PTDC/PSI-GER/28076/2017)

Enhanced lithium depletion in Sun-like stars with orbiting planets

The surface abundance of lithium on the Sun is 140 times less than protosolar, yet the temperature at the base of the surface convective zone is not hot enough to burn Li. A large range of Li abundances in solar type stars of the same age, mass and metallicity is observed, but theoretically difficult to understand. An earlier suggestion that Li is more depleted in stars with planets was weakened by the lack of a proper comparison sample of stars without detected planets. Here we report Li abundances for an unbiased sample of solar-analogue stars with and without detected planets. We find that the planet-bearing stars have less than 1 per cent of the primordial Li abundance, while about 50 per cent of the solar analogues without detected planets have on average 10 times more Li. The presence of planets may increase the amount of mixing and deepen the convective zone to such an extent that the Li can be burned.Comment: 13 pages, 2 figure

Mortality among over 6 million internal and international migrants in Brazil: a study using the 100 Million Brazilian Cohort

Background: To understand if migrants living in poverty in low and middle-income countries (LMICs) have mortality advantages over the non-migrant population, we investigated mortality risk patterns among internal and international migrants in Brazil over their life course. / Methods: We linked socio-economic and mortality data from 1st January 2011 to 31st December 2018 in the 100 Million Brazilian Cohort and calculated all-cause and cause-specific age-standardised mortality rates according to individuals' migration status for men and women. Using Cox regression models, we estimated the age- and sex-adjusted mortality hazard ratios (HR) for internal migrants (i.e., Brazilian-born individuals living in a different Brazilian state than their birth) compared to Brazilian-born non-migrants; and for international migrants (i.e., people born in another country) compared to Brazilian-born individuals. / Findings: The study followed up 45,051,476 individuals, of whom 6,057,814 were internal migrants, and 277,230 were international migrants. Internal migrants had similar all-cause mortality compared to Brazilian non-migrants (aHR = 0.99, 95% CI = 0.98–0.99), marginally higher mortality for ischaemic heart diseases (aHR = 1.04, 95% CI = 1.03–1.05) and higher for stroke (aHR = 1.11, 95% CI = 1.09–1.13). Compared to Brazilian-born individuals, international migrants had 18% lower all-cause mortality (aHR = 0.82, 95% CI = 0.80–0.84), with up to 50% lower mortality from interpersonal violence among men (aHR = 0.50, 95% CI = 0.40–0.64), but higher mortality from avoidable causes related to maternal health (aHR = 2.17, 95% CI = 1.17–4.05). / Interpretation: Although internal migrants had similar all-cause mortality, international migrants had lower all-cause mortality compared to non-migrants. Further investigations using intersectional approaches are warranted to understand the marked variations by migration status, age, and sex for specific causes of death, such as elevated maternal mortality and male lower interpersonal violence-related mortality among international migrants

Effects of external nutrient sources and extreme weather events on the nutrient budget of a Southern European coastal lagoon

The seasonal and annual nitrogen (N), phosphorus (P), and carbon (C) budgets of the mesotidal Ria Formosa lagoon, southern Portugal, were estimated to reveal the main inputs and outputs, the seasonal patterns, and how they may influence the ecological functioning of the system. The effects of extreme weather events such as long-lasting strong winds causing upwelling and strong rainfall were assessed. External nutrient inputs were quantified; ocean exchange was assessed in 24-h sampling campaigns, and final calculations were made using a hydrodynamic model of the lagoon. Rain and stream inputs were the main freshwater sources to the lagoon. However, wastewater treatment plant and groundwater discharges dominated nutrient input, together accounting for 98, 96, and 88 % of total C, N, and P input, respectively. Organic matter and nutrients were continuously exported to the ocean. This pattern was reversed following extreme events, such as strong winds in early summer that caused upwelling and after a period of heavy rainfall in late autumn. A principal component analysis (PCA) revealed that ammonium and organic N and C exchange were positively associated with temperature as opposed to pH and nitrate. These variables reflected mostly the benthic lagoon metabolism, whereas particulate P exchange was correlated to Chl a, indicating that this was more related to phytoplankton dynamics. The increase of stochastic events, as expected in climate change scenarios, may have strong effects on the ecological functioning of coastal lagoons, altering the C and nutrient budgets.Portuguese Science and Technology Foundation (FCT) [POCI/MAR/58427/2004, PPCDT/MAR/58427/2004]; Portuguese Science and Technology Foundation (FCT

Monitoring frequency influences the analysis of resting behaviour in a forest carnivore

Resting sites are key structures for many mammalian species, which can affect reproduction, survival, population density, and even species persistence in human-modified landscapes. As a consequence, an increasing number of studies has estimated patterns of resting site use by mammals, as well as the processes underlying these patterns, though the impact of sampling design on such estimates remain poorly understood. Here we address this issue empirically, based on data from 21 common genets radiotracked during 28 months in Mediterranean forest landscapes. Daily radiotracking data was thinned to simulate every other day and weekly monitoring frequencies, and then used to evaluate the impact of sampling regime on estimates of resting site use. Results showed that lower monitoring frequencies were associated with major underestimates of the average number of resting sites per animal, and of site reuse rates and sharing frequency, though no effect was detected on the percentage use of resting site types. Monitoring frequency also had a major impact on estimates of environmental effects on resting site selection, with decreasing monitoring frequencies resulting in higher model uncertainty and reduced power to identify significant explanatory variables. Our results suggest that variation in monitoring frequency may have had a strong impact on intra- and interspecific differences in resting site use patterns detected in previous studies. Given the errors and uncertainties associated with low monitoring frequencies, we recommend that daily or at least every other day monitoring should be used whenever possible in studies estimating resting site use patterns by mammals

Migrations and habitat use of the smooth hammerhead shark (Sphyrna zygaena) in the Atlantic Ocean

The smooth hammerhead shark, Sphyrna zygaena, is a cosmopolitan semipelagic shark captured as bycatch in pelagic oceanic fisheries, especially pelagic longlines targeting swordfish and/or tunas. From 2012 to 2016, eight smooth hammerheads were tagged with Pop-up Satellite Archival Tags in the inter-tropical region of the Northeast Atlantic Ocean, with successful transmissions received from seven tags (total of 319 tracking days). Results confirmed the smooth hammerhead is a highly mobile species, as the longest migration ever documented for this species (> 6600 km) was recorded. An absence of a diel vertical movement behavior was noted, with the sharks spending most of their time at surface waters (0-50 m) above 23 degrees C. The operating depth of the pelagic long-line gear was measured with Minilog Temperature and Depth Recorders, and the overlap with the species vertical distribution was calculated. The overlap is taking place mainly during the night and is higher for juveniles (similar to 40% of overlap time). The novel information presented can now be used to contribute to the provision of sustainable management tools and serve as input for Ecological Risk Assessments for smooth hammerheads caught in Atlantic pelagic longline fisheries.Oceanario de Lisboa through Project "SHARK-TAG: Migrations and habitat use of the smooth hammerhead shark in the Atlantic Ocean"; Investigador-FCT from the Portuguese Foundation for Science and Technology (FCT, Fundacao para a Ciencia e Tecnologia) [Ref: IF/00253/2014]; EU European Social Fund; Programa Operacional Potencial Human