Genetic variation among major human geographic groups supports a peculiar evolutionary trend in PAX9

A total of 172 persons from nine South Amerindian, three African and one Eskimo populations were studied in relation to the Paired box gene 9 (PAX9) exon 3 (138 base pairs) as well as its 59and 39flanking intronic segments (232 bp and 220 bp, respectively) and integrated with the information available for the same genetic region from individuals of different geographical origins. Nine mutations were scored in exon 3 and six in its flanking regions; four of them are new South American tribe-specific singletons. Exon3 nucleotide diversity is several orders of magnitude higher than its intronic regions. Additionally, a set of variants in the PAX9 and 101 other genes related with dentition can define at least some dental morphological differences between Sub-Saharan Africans and non-Africans, probably associated with adaptations after the modern human exodus from Africa. Exon 3 of PAX9 could be a good molecular example of how evolvability works

Giant hepatic hemangioma in a patient with cirrhosis: challenging to manage

Giant hepatic hemangiomas are occasional in patients with cirrhosis. It remains a challenge to decide on the need for treatment and choose the most appropriate intervention. A 62-year-old woman was recently diagnosed with cirrhosis and complained of upper abdominal fullness, reduction in oral food intake, and weight loss of 6 kg over the last three years. Upper digestive endoscopy evidenced thin-caliber esophageal varices and significant extrinsic compression of the lesser gastric curvature. Abdominal computed tomography revealed an exophytic tumor in the left hepatic lobe, measuring 11.5 cm, which had progressive centripetal contrast enhancement from the arterial phase, compatible with hepatic hemangioma. Serum tumor markers were negative, and her liver function was unimpaired. The patient underwent surgical resection (non-anatomical hepatectomy of segments II and III) which had no immediate complications, and the histopathological evaluation confirmed cavernous hepatic hemangioma. Two weeks later, she was admitted to the emergency room with jaundice, signs of hepatic encephalopathy, and moderate ascites, and was further diagnosed with secondary bacterial peritonitis. As no perforations, abscesses, or fistulas were observed on subsequent imaging tests, clinical management was successfully carried out. This case highlights that giant hepatic hemangiomas may be symptomatic and warrant treatment. In the setting of cirrhosis and portal hypertension, physicians should be aware of the risk of hepatic decompensation following surgical resection, even in patients with Child-Pugh class A

Gastric bypass versus best medical treatment for diabetic kidney disease: 5 years follow up of a single-centre open label randomised controlled trial

BACKGROUND: We compared the albuminuria-lowering effects of Roux-en-Y gastric bypass (RYGB) to best medical treatment in patients with diabetic kidney disease and obesity to determine which treatment is better. METHODS: A 5 year, open-label, single-centre, randomised trial studied patients with diabetic kidney disease and class I obesity after 1:1 randomization to best medical treatment (n = 49) or RYGB (n = 51). The primary outcome was the proportion of patients achieving remission of microalbuminuria after 5 years. Secondary outcomes included improvements in diabetic kidney disease, glycemic control, quality of life, and safety. For efficacy outcomes, we performed an intention-to-treat (ITT) analysis. This study was registered with ClinicalTrials.gov, NCT01821508. FINDINGS: 88% of patients (44 per arm) completed 5-year follow-up. Remission of albuminuria occurred in 59.6% (95% CI = 45.5–73.8) after best medical treatment and 69.7% (95% CI = 59.6–79.8) after RYGB (risk difference: 10%, 95% CI, −7 to 27, P = 0.25). Patients after RYGB were twice as likely to achieve an HbA1c ≤ 6.5% (60.2% versus 25.4%, risk difference, 34.9%; 95% CI = 15.8–53.9, P < 0.001). Quality of life after five years measured by the 36-Item Short Form Survey questionnaire (standardized to a 0-to-100 scale) was higher in the RYGB group than in the best medical treatment group for several domains. The mean differences were 13.5 (95% CI, 5.5–21.6, P = 0.001) for general health, 19.7 (95% CI, 9.1–30.3, P < 0.001) for pain, 6.1 (95% CI, −4.8 to 17.0, P = 0.27) for social functioning, 8.3 (95% CI, 0.23 to 16.3, P = 0.04) for emotional well-being, 12.2 (95% CI, 3.9–20.4, P = 0.004) for vitality, 16.8 (95% CI, −0.75 to 34.4, P = 0.06) for mental health, 21.8 (95% CI, 4.8–38.7, P = 0.01) for physical health and 11.1 (95% CI, 2.24–19.9, P = 0.01) for physical functioning. Serious adverse events were experienced in 7/46 (15.2%) after best medical treatment and 11/46 patients (24%) after RYGB (P = 0.80). INTERPRETATION: Albuminuria remission was not statistically different between best medical treatment and RYGB after 5 years in participants with diabetic kidney disease and class 1 obesity, with 6–7 in ten patients achieving remission of microalbuminuria (uACR <30 mg/g) in both groups. RYGB was superior in improving glycemia, diastolic blood pressure, lipids, body weight, and quality of life. FUNDING: The study was supported by research grants from Johnson & Johnson Brasil, Oswaldo Cruz German Hospital, and by grant 12/YI/B2480 from Science Foundation Ireland (Dr le Roux) and grant 2015-02733 from the Swedish Medical Research Council (Dr le Roux). Dr Pereira was funded by the Chevening Scholarship Programme (Foreign and Commonwealth Office, UK)

Análise ambiental de um fragmento florestal urbano, no município de Alvorada, Rio Grande do Sul

This study was developed in a forest fragment named “Cinturão Verde”, in an urban area of Alvorada municipality, Rio Grande do Sul State. It is an area with irregular topography and illegal habitations, with consequent problems related to garbage deposition, sewerage and deforestation. The objective of this study was to characterize social and environmentally the local human population and to identify the influence of urbanization over this time. From the prodution of land use images, five sample stations were demarcated along Nunes creek. Water quality characterization of the creek, floristic and phytophysionomy composition and richness and abundance of birds and arthropods were sampled during October and November 2003, with a characterization of local human population concerning its sociocultural and environmental perception about the forest fragment. Regarding chemical and biological water analysis, results indicated high eutrophization degree due, probably, to lack of basic sanitation. Despite the impacts, the forest fragment still presents some biotical integrity, reflected by the representativity of the considered groups. It was verified, for example, that 14.8% of bird species contribute to seed dispersion of 67% of tree species. However, we evidenced loss of forested area due to urbanization. Trails and garbage deposition in the forest decrease undestory area, restricting its natural regeneration. Results obtained from the environmental perception analysis indicated lack of integration of the local human population with the forest fragment. The increase of local insecurity was the main negative aspect pointed, but inhabitants wished a suitable recreation area. The long term sustainability of this forest fragment will occur through a conection with other near forested areas. Also, it is important for conservation area to stimulate environment educational programs to sensitize the people about the value of the local environment.Este estudo foi desenvolvido em um fragmento florestal denominado “Cinturão Verde”, em uma área urbana no município de Alvorada, no Estado do Rio Grande do Sul. É uma área que apresenta topografia acidentada e ocupações irregulares, com conseqüentes problemas relacionados à deposição de lixo, esgoto e desmatamento. O objetivo do estudo foi caracterizar sócio-ambientalmente e identificar a influência da urbanização sobre este fragmento. A partir da produção de imagens de uso do solo, foram definidos cinco pontos ao longo do Arroio Nunes, nos quais amostrou-se, durante o período de outubro e novembro de 2003, a qualidade da água do arroio, as composições florística e fitofisionômica e a riqueza e abundância de artrópodos e aves. Além disso, buscou-se caracterizar a comunidade de moradores do entorno do fragmento acerca de suas condições sócio-culturais e de sua percepção em relação ao fragmento. Em relação às análises químicas e biológicas da água, os resultados obtidos indicaram alto grau de eutrofização devido, provavelmente, à falta de saneamento básico. Apesar do impacto antrópico, o fragmento apresenta ainda uma certa integridade biótica refletida pela representatividade dos grupos avaliados. Verificou-se, por exemplo, que 14,8% da avifauna contribui para a dispersão de cerca de 67% das espécies de árvores. No entanto, constatou-se perda de área florestada devido à urbanização. Trilhas e deposição de lixo no interior da floresta diminuem a área de sub-bosque, restringindo sua regeneração natural. Os resultados obtidos nas análises de percepção ambiental indicaram a falta de integração da população do entorno em relação ao fragmento. O aumento da insegurança local foi o principal aspecto negativo, porém os moradores do entorno mostraramse desejosos de poder contar com uma área adequada de lazer. Provavelmente, só será possível a sustentabilidade a longo prazo do fragmento florestal através da conexão com outras áreas florestadas próximas. Além disso, é importante para a conservação da área, incentivo à programas de educação ambiental que sensibilizem a comunidade em relação à valorização do meio ambiente local

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear un derstanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5–7 vast areas of the tropics remain understudied.8–11 In the American tropics, Amazonia stands out as the world’s most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepre sented in biodiversity databases.13–15 To worsen this situation, human-induced modifications16,17 may elim inate pieces of the Amazon’s biodiversity puzzle before we can use them to understand how ecological com munities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple or ganism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region’s vulnerability to environmental change. 15%–18% of the most ne glected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lostinfo:eu-repo/semantics/publishedVersio

SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal

Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. Methods By applying recent phylodynamic models that allow integration of individual-based travel history, we reconstructed and characterized the spatio-temporal dynamics of SARSCoV-2 introductions and early dissemination in Portugal. Results We detected at least 277 independent SARS-CoV-2 introductions, mostly from European countries (namely the United Kingdom, Spain, France, Italy, and Switzerland), which were consistent with the countries with the highest connectivity with Portugal. Although most introductions were estimated to have occurred during early March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal throughout February, before the first cases were confirmed. Conclusions Here we conclude that the earlier implementation of measures could have minimized the number of introductions and subsequent virus expansion in Portugal. This study lays the foundation for genomic epidemiology of SARS-CoV-2 in Portugal, and highlights the need for systematic and geographically-representative genomic surveillance.We gratefully acknowledge to Sara Hill and Nuno Faria (University of Oxford) and Joshua Quick and Nick Loman (University of Birmingham) for kindly providing us with the initial sets of Artic Network primers for NGS; Rafael Mamede (MRamirez team, IMM, Lisbon) for developing and sharing a bioinformatics script for sequence curation (https://github.com/rfm-targa/BioinfUtils); Philippe Lemey (KU Leuven) for providing guidance on the implementation of the phylodynamic models; Joshua L. Cherry (National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health) for providing guidance with the subsampling strategies; and all authors, originating and submitting laboratories who have contributed genome data on GISAID (https://www.gisaid.org/) on which part of this research is based. The opinions expressed in this article are those of the authors and do not reflect the view of the National Institutes of Health, the Department of Health and Human Services, or the United States government. This study is co-funded by Fundação para a Ciência e Tecnologia and Agência de Investigação Clínica e Inovação Biomédica (234_596874175) on behalf of the Research 4 COVID-19 call. Some infrastructural resources used in this study come from the GenomePT project (POCI-01-0145-FEDER-022184), supported by COMPETE 2020 - Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by Fundação para a Ciência e a Tecnologia (FCT).info:eu-repo/semantics/publishedVersio

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear understanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5,6,7 vast areas of the tropics remain understudied.8,9,10,11 In the American tropics, Amazonia stands out as the world's most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepresented in biodiversity databases.13,14,15 To worsen this situation, human-induced modifications16,17 may eliminate pieces of the Amazon's biodiversity puzzle before we can use them to understand how ecological communities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple organism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region's vulnerability to environmental change. 15%–18% of the most neglected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lost

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear understanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5,6,7 vast areas of the tropics remain understudied.8,9,10,11 In the American tropics, Amazonia stands out as the world's most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepresented in biodiversity databases.13,14,15 To worsen this situation, human-induced modifications16,17 may eliminate pieces of the Amazon's biodiversity puzzle before we can use them to understand how ecological communities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple organism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region's vulnerability to environmental change. 15%–18% of the most neglected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lost