Meta-analysis of type 2 Diabetes in African Americans Consortium

Type 2 diabetes (T2D) is more prevalent in African Americans than in Europeans. However, little is known about the genetic risk in African Americans despite the recent identification of more than 70 T2D loci primarily by genome-wide association studies (GWAS) in individuals of European ancestry. In order to investigate the genetic architecture of T2D in African Americans, the MEta-analysis of type 2 DIabetes in African Americans (MEDIA) Consortium examined 17 GWAS on T2D comprising 8,284 cases and 15,543 controls in African Americans in stage 1 analysis. Single nucleotide polymorphisms (SNPs) association analysis was conducted in each study under the additive model after adjustment for age, sex, study site, and principal components. Meta-analysis of approximately 2.6 million genotyped and imputed SNPs in all studies was conducted using an inverse variance-weighted fixed effect model. Replications were performed to follow up 21 loci in up to 6,061 cases and 5,483 controls in African Americans, and 8,130 cases and 38,987 controls of European ancestry. We identified three known loci (TCF7L2, HMGA2 and KCNQ1) and two novel loci (HLA-B and INS-IGF2) at genome-wide significance (4.15 × 10(-94)<P<5 × 10(-8), odds ratio (OR)  = 1.09 to 1.36). Fine-mapping revealed that 88 of 158 previously identified T2D or glucose homeostasis loci demonstrated nominal to highly significant association (2.2 × 10(-23) < locus-wide P<0.05). These novel and previously identified loci yielded a sibling relative risk of 1.19, explaining 17.5% of the phenotypic variance of T2D on the liability scale in African Americans. Overall, this study identified two novel susceptibility loci for T2D in African Americans. A substantial number of previously reported loci are transferable to African Americans after accounting for linkage disequilibrium, enabling fine mapping of causal variants in trans-ethnic meta-analysis studies.Peer reviewe

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of SARS-CoV-2 genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three available genomic nomenclature systems for SARS-CoV-2 to all sequence data from the WHO European Region available during the COVID-19 pandemic until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation. We provide a comparison of the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2.Peer reviewe

Geology And Shrimp U-pb Geochronology Of The Igarapé Bahia Deposit, Carajás Copper-gold Belt, Brazil: An Archean (2.57 Ga) Example Of Iron-oxide Cu-au-(u-ree) Mineralization

Striking feature of the Carajás region, Brazil, is the clustering of a variety of different types of Cu-Au deposits. The most abundant in the belt are the &gt;200 million metric tons (Mt) of Fe oxide Cu-Au-(U-REE) deposits, which, despite the variety of host rocks and different orebody morphologies, share a number of diagnostic features, including (1) intense Fe metasomatism leading to the formation of grunerite, fayalite, and/or Fe oxides (magnetite and/or hematite); (2) intense carbonate alteration (mainly siderite); (3) sulfur-poor ore mineralogy (chalcopyrite and bornite); (4) quartz-deficient gangue; (5) extreme low REE enrichment, and (6) enrichment in U and Co. The Igarapé Bahia deposit is perhaps the best documented Fe oxide Cu-Au-(U-REE) deposit of the belt, containing about 219 Mt at 1.4 percent Cu and 0.86 g/t Au. The Cu-Au ore consists of steeply dipping breccia bodies that are hosted by hydrothermally altered metavolcano-sedimentary rocks. SHRIMP II zircon dating of the host metavolcanic rocks gives a 207Pb/ 206Pb age of 2748 ± 34 Ma. This suggests a correlation between the Igarapé Bahia volcano-sedimentary sequence and the Grão Pará volcanic rocks, which have published ages of ca. 2.75 Ga. SHRIMP dating of monazite from the matrix of ore-bearing magnetite breccias gives a 207Pb/ 206Pb age of 2575 ± 12 Ma, confirming the epigenetic nature of the mineralization and placing it ∼175 m.y. after accumulation of the host volcano-sedimentary sequence. The 2575 ± 12 Ma SHRIMP age of hydrothermal monazite from the Igarapé Bahia mineralization is indistinguishable from published conventional 207Pb/ 206Pb ages for zircons from the Archean A-type granites of the Carajás belt, indicating that mineralization processes at Igarapé Bahia were temporally related to these A-type Archean granites. The wide range of highly radiogenic 87Sr/ 86Sr ratios (0.714-0.755) of carbonates from the Igarapé Bahia deposit suggests multiple crustal sources, consistent with a magmatic-hydrothermal origin. SHRIMP dating of zircon xenocrysts recovered from crosscutting diabase dikes indicates a maximum 207Pb/ 206Pb age of ∼2670 Ma, consistent with field evidence and the age of host rocks, but does not unequivocably constrain the age of the ores. The styles of hydrothermal alteration, mineralogy, and geochemistry of the Igarapé Bahia ore, as well as published fluid inclusion and stable isotope data, support its classification as a member of the world-class Olympic Dam-type Fe oxide Cu-Au-(U-REE) group of deposits, as previously argued by several authors. The SHRIMP age of 2575 ± 12 Ma for hydrothermal monazite indicates that Igarapé Bahia is an Archean example of this deposit group. © 2005 Society of Economic Geologists, Inc.1001728Almada, M.C.O., O Corpo Acampamento Sul do depósito Bahia, Carajás: Características geológicas e fluidos hidrotermais (1998), p. 99. , Unpublished M.Sc. thesis, Belém, Brazil, Universidade Federal do ParáAlthoff, A.M.R., Villas, R.N., Giuliani, G., A mineralização cuprífera da Área Bahia, Serra dos Carajás (PA): Evolução dos fluidos hidrotermais e modelo metalogenético (1994) Geochemica Brasiliense, 8, pp. 135-155Angélica, R.S., Mineralogia e geoquímica dos gossans e lateritos auríferos na Região de Carajás, Estado do Pará: Os depósitos de Igarapé Bahia e Águas Claras (1996), p. 115. , Unpublished Ph.D. thesis, Belém, Brazil, Universidade Federal do ParáAraújo, O.J.B., Maia, R.G.N., Xafi, J.J.S., Costa, J.B.S., A megaestruturação arqueana da folha Serra dos Carajás (1988), pp. 324-333. , Congresso Latino-Americano de Geologia, VII, Belém, Sociedade Brasileira de Geologia, AnaisBarreira, C.F., Soares, A.D.V., Ronzê, P.C., Descoberta do Depósito Cu-Au Alemão-Província Mineral de Carajás (PA) (1999) Simpósio De Geologia Da Amazônia, VI, pp. 136-139. , [ext. abs.]: Manaus, Sociedade Brasilaira de Geologia, Extended Abstract BulletinBarrie, C.T., Hannington, M.D., Classification of volcanic-associated massive sulfide deposits based on host-rock composition (1999) Reviews in Economic Geology, 8, pp. 1-11Barros, C.E.M., Barbey, P., A importância da granitogênese tardiarqueana (2.5 Ga) na evolução tectono-metamórfica da Província Mineral de Carajás-O Complexo Granítico Estrela e sua auréola de contato (1998) Revista Brasileira De Geociências, 28, pp. 513-522Barros, C.E.M., Dall'Agnoll, R., Lafon, J.M., Teixeira, N.P., Ribeiro, J.W., Geologia e geocronologia Rb-Sr do Gnaisse Estrela, Curionópolis, PA (1992) Boletin Do Museu Paraense Emílio Goeldi, Ciências Da Terra, 4, pp. 83-104Barros, C.E.M., Dall'Agnoll, R., Barbey, P., Boullier, A.M., Geochemistry of the Estrela Complex, Carajás region, Brazil: An example of an Archean A-type granite (1997) Journal of South American Earth Sciences, 10, pp. 321-330Barros, C.E.M., Barbey, P., Boullier, A.M., Role of magma pressure, tectonic stress and crystallization progress in the emplacement of syntectonic granites. The A-type Estrela Granite Complex (Carajás mineral province, Brazil) (2001) Tectonophysics, 343, pp. 93-109Barton, M.D., Johnson, D.A., Evaporitic-source model for igneous-related Fe oxide-(REE-Cu-Au-U) mineralization (1996) Geology, 24, pp. 259-262Campbell, I.H., Compston, D.M., Richards, J.P., Johnson, J.P., Kent, A.J.R., Review of the application of isotopic studies to the genesis of Cu-Au mineralization at Olympic Dam and Au mineralization at Porgera, Tennant Creek district and Yilgarn craton (1998) Australian Journal of Earth Sciences, 45, pp. 201-218Compston, W., Williams, I.S., Campbell, I.H., Gresham, J.J., Zircon xenocrysts from the Kambalda volcanics: Age constraints and direct evidence for the older continental crust below the Kambalda-Norseman greenstones (1986) Earth and Planetary Science Letters, 76, pp. 299-311Cordeiro, A.A.C., Pesquisa mineral: Panorama atual da CVRD na Amazônia (1999) Simpósio De Geologia Da Amazônia, VI, pp. 80-83. , [ext. abs.]: Manaus, Sociedade Brasilaira de Geologia, Extended Abstract BulletinCross, K.C., Daly, S.J., Flint, R.B., Mineralization associated with the GRV and Hiltaba Suite granitoids (1993) Geological Survey of Southern Australia Bulletin, 54, p. 242Davidson, G.J., Large, R.R., Gold metallogeny and the copper-gold association of Australian Proterozoic (1994) Mineralium Deposita, 29, pp. 208-223Dias, G.S., Macambira, M.J.B., Dall'Agnol, R., Soares, A.D.V., Barros, C.E.M., Datação de zircões de Sill de metagabro: Comprovação da idade arqueana da Formação Águas Claras, Carajás, Pará (1996) Simpósio De Geologia Da Amazônia, V, pp. 376-379. , [ext. abs.]: Belém, Sociedade Brasileira de Geologia, Extended Abstracts BulletinProvíncia Mineral de Carajás. 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(2001) Mineralium Deposita, 36, pp. 189-194Haynes, D.W., Cross, K.C., Bills, R.T., Reed, M.H., Olympic Dam ore genesis: A fluid-mixing model (1995) Economic Geology, 90, pp. 281-307Hitzman, M.W., Oreskes, N., Einaudi, M.T., Geological characteristics and tectonic setting of Proterozoic iron oxide (Cu-U-Au-REE) deposits (1992) Precambrian Research, 58, pp. 241-287Holdsworth, R.E., Pinheiro, R.V.L., The anatomy of shallow-crustal transpressional structures: Insights from the Archean Carajás fault zone, Amazon, Brazil (2000) Journal of Structural Geology, 22, pp. 1105-1123Huhn, S.R.B., Santos, A.B.S., Amaral, A.F., Ledsham, E.J., Gougêa, J.L., Martins, L.P., Montalvao, R.G.M., Costa, V.G., O terreno "granito greenstone" da região de Rio Maria-Sul do Pará (1988), pp. 1438-1452. , [ext. abs.]: Congresso Brasileiro de Geologia, XXXV, Belém, Sociedade Brasileira de Geologia, AnaisHuhn, S.R.B., Souza, C.I.J., Albuquerque, M.C., Leal, E.D., Brustolin, V., Descoberta do depósito Cu(Au) Cristalino: Geologia e mineralização associada-Região da Serra do Rabo-Carajás-PA (1999) Simpósio De Geologia Da Amazônia, VI, pp. 140-143. , Manaus, BoletimHuhn, S.R.B., Macambira, M.J.B., Dall'Agnol, R., Geologia e geocronologia Pb/Pb do granito alcalino Arqueano Planalto, Região da Serra do Rabo, Carajás-PA (1999) Simpósio De Geologia Da Amazônia, VI, pp. 463-466. , Manaus, Sociedade Brasilaira de Geologia, Extended Abstract BulletinJaffey, A.H., Flynn, K.F., Glendenin, L.E., Bentley, W.C., Essling, A.M., Precision measurement of half lives and specific activities of 235U and 238U (1971) Physics Reviews, C4, pp. 1889-1906Kerrich, R., Goldfarb, R., Groves, D.I., Garwin, S., The geodynamics of world-class gold deposits: Characteristics, space-time distribution, and origins (2000) Reviews in Economic Geology, 13, pp. 501-551Lancaster, O.J., Fanton, J., Almeida, A.J., Leveille, R.A., Vieira, S., Discovery and geology of the Sossego copper-gold deposit, Carajás district, Pará State, Brazil (2000), [abs.]: International Geological Congress, 31st, Rio de Janeiro, Sociedade Brasileira de Geologia, Abstract volume (CDROM)Large, R.R., Australian volcanic-hosted massive sulfide deposits: Features, styles, and genetic model (1992) Economic Geology, 87, pp. 471-510Lindenmayer, Z.G., Salobo sequence, Carajás, Brazil: Geology, geochemistry and metamorphism (1990), p. 407. , Unpublished Ph.D. thesis, London, ON, University of Western OntarioLindenmayer, Z.G., Ronchi, L.H., Laux, J.H., Geologia e geoquímica da mineralização de Cu-Au primária da mina de Au do Igarapé Bahia, Serra dos Carajás (1998) Revista Brasileira De Geociências, 28, pp. 257-268Ludwig, K.R., (2001) SQUID 1.00 - A User's Manual, 2, p. 17. , Berkeley Geochronology Centre Special PublicationLudwig, K.R., User manual for Isoplot/Ex rev. 2.49 - A geochronological toolkit for Microsoft Excel (2001), 1 A, p. 56. , Berkeley Geochronology Centre Special PublicationMachado, N., Lindenmayer, Z., Krogh, T.E., Lindenmayer, D., U-Pb geochronology of Archean magmatism and basement reactivation in the Carajás area, Amazon Shield, Brazil (1991) Precambrian Research, 49, pp. 329-354Mellito, K.M., Aplicações dos sistemas Rb-Sr, Pb-Pb e Sm-Nd no depósito polimetálico do Salobo 3A, Província Mineral de Carajás, Pará (1998), p. 90. , Unpublished M.Sc. thesis, São Paulo, Brazil, Universidade de São PauloMontalvao, R.G.M., Tassinari, C.C.G., Bezerra, P.E.L., Geocronologia dos granitóides e gnaisses das regiões do Rio Maria, Fazenda Mata Geral e Rio Itacaiunas, Sul do Pará (Distrito Carajás-Cumaru) (1984), p. 153. , [abs.]: Congresso Brasileiro de Geologia, XXXIII, Rio de Janeiro, Sociedade Brasileira de Geologia, ResumosMuogeot, R., Respaut, J.P., Briqueu, L., Ledru, P., Milesi, P., Lerouge, C., Marcoux, E., Macambira, M.J.B., Isotope geochemistry constraints for Cu, Au mineralizations and evolution of the Carajás province (Pará, Brazil) (1996), 7, pp. 321-324. , [ext. abs.]: Congresso Brasileiro, de Geologia, XXXIX, Salvador, Sociedade Brasileira de Geologia, Extended Abstracts BulletinNelson, D.R., Compilation of SHRIMP U-Pb zircon geochronology data, 1996 (1997) Geological Survey of Western Australia Record 1997/2, p. 189Nogueira, A.C.R., Truckenbrod, W., Costa, J.B.S., Pinheiro, R.V.L., Análise faciológica e estrutural da Formação Águas Claras, Pré-Cambriano da Serra dos Carajás (1994) Simpósio De Geologia Da Amazônia, IV, pp. 363-364. , [ext. abs.]: Belém, Sociedade Brasileira de Geologia, Resumos ExpandidosNogueira, A.C.R., Truckenbrod, W., Pinheiro, R.V.L., Storm and tide-dominated siliciclastic deposits of the Archean Águas Claras Formation, Serra dos Carajás, Brazil (2000), [abs.]: International Geological Congress, 31st, Rio de Janeiro, Sociedade Brasileira de Geologia, Abstract volume (CD-ROM)Oliveira, C.G., Tazava, E., Tallarico, F.H.B., Santos, R.V., Gomes, C., Gênese do depósito de Au-Cu-(U-ETR) de Igarapé Bahia, Província Mineral de Carajás (1998), p. 137. , [abs.]: Congresso Brasileiro de Geologia, XL, Belo Horizonte, Sociedade Brasileira de Geologia, ProceedingsOlszewski, W.J., Wirth, K.R., Gibbs, A.K., Gaudette, H.E., The age, origin, and tectonics of the Grão Pará Group and associated rocks, Serra dos Carajás, Brazil: Archean continental vulcanism and rifting (1989) Precambrian Research, 42, pp. 229-254Oreskes, N., Einaudi, M.T., Origin of rare earth element-enriched hematite breccias at the Olympic Dam Cu-U-Au-Ag deposit, Roxby Downs, South Australia (1990) Economic Geology, 85, pp. 1-28Oreskes, N., Hitzman, M.W., A model for the origin of Olympic Dam-type deposits (1993) Geological Association of Canada Special Paper 40, pp. 615-633Pidgeon, R.T., Furfaro, D., Kennedy, A.K., Nemchin, A.A., Calibration of zircon standards for the Curtin SHRIMP II (1994) U.S. Geological Survey Circular 1107, p. 251. , [abs]Pidgeon, R.T., Macambira, M.J.B., Lafon, J.M., Th-U-Pb isotopic systems and internal structures of complex zircons from enderbite from the 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domains, Tapajós-Parima orogenic belt, Amazon craton, Brazil (2001) Mineralium Deposita, 36, pp. 278-299Silva, C.M.G., Villas, R.N., The Águas Claras Cu-sulfide ± Au deposit, Carajás region, Pará, Brazil: Geological setting, wall-rock alteration and mineralizing fluids (1998) Revista Brasileira De Geociências, 28, pp. 315-326Skirrow, R.G., Walshe, J.L., Reduced and oxidized Au-Cu-Bi iron oxide deposits of the Tennant Creek inlier, Australia: An integrated geologic and chemical model (2002) Economic Geology, 97, pp. 1167-1202Smith, J.B., Barley, M.E., Groves, D.I., Krapez, B., McNaughton, N.J., Bickle, N.J., Chapman, H.J., The Scholl shear zone, West Pilbara: Evidence for a domain boundary structure from integrated tectonostratigraphic analyses, SHRIMP U-Pb dating and isotopic and geochemical data of granitoids (1998) Precambrian Research, 88, pp. 143-171Soares, A.D.V., Santos, A.B., Vieira, E.A., Bella, V.M., Martins, L.P.B., Área Águas Claras: Contexto geológico e mineralizações 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Bornean orangutan Pongo pygmaeus pygmaeus population estimate within and around Danau Sentarum National Park, Kapuas Hulu, West Kalimantan

Of the three subspecies of Critically Endangered Bornean orangutans, Pongo pygmaeus pygmaeus has the smallest population size. One of its most important habitats is the tropical forest within and around Danau Sentarum National Park (DSNP). Research in the late 1990s estimated that ca. 1025 orangutans inhabited DSNP, while ca. 1717 orangutans inhabited the forest beyond DSNP's boundaries. However, concerns were later raised that incorrectly estimated nest decay rates (t values) may have led to the overestimation of the population size. Furthermore, the area experienced forest degradation and land use change between 2000 and 2013. Given these changing landscapes, updated population estimates were needed to inform policy makers and land-use planners on the implications of habitat loss for resident orangutans. We conducted this study to recalculate nest decay rates based on current recommended methods, and to update our knowledge on the orangutan population in the region. Our average nest decay rate was 288.3 days; applying this to the study in the late 1990s generated estimates of 807 individuals within DSNP and 1578 beyond DNSP's boundaries. New surveys of the transects undertaken between 2010 and 2014 revealed that the population size had declined substantially in these two areas, to 202 and 71 individuals respectively. Both declines are considerable, but larger losses occurred in logged-over and cleared forests outside the park. We discuss factors potentially driving these declines, emphasizing the need to improve habitat protection both inside and outside of DSNP, and make recommendations for improving the prospects for future orangutan conservation