The Bero Volcanic Complex: extension of the Paraná-Etendeka Igneous Province into SW Angola
- Marsh, Julian S, Swart, Roger S
- Authors: Marsh, Julian S , Swart, Roger S
- Date: 2016
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/60763 , vital:27827 , https://www.sciencedirect.com/science/article/pii/S0377027316304176
- Description: An extension of the Etendeka-Paraná Igneous Province into SW Angola occurs as minor basalt lavas, intrusive gabbro sheets, minor mafic dykes and thick sheets and lava flows (with minor pyroclastics) of quartz latite composition This suite crops out along the eastern margin of the Cretaceous Namibe Basin in SW Angola. The quartz latites from one locality have been referred to informally as the Giraul volcanics but the name ‘Giraul’ has previously been used for Cretaceous conglomerates. We propose the name Bero Volcanic Complex for this suite of intrusive and extrusive rocks on the basis that the full compositional range of this diverse suite crops out along the Rio Bero. Major and trace element compositions and Sr-, Nd-, and Pb-isotopic compositions indicate that the basalts and gabbros are equivalent to the high-Ti Khumib/Urubici and Pitanga types from the Etendeka and Paraná. The basalts underlie the quartz latites which are cut by mafic dykes some of which are compositionally equivalent to the Paranapanema lavas in the Paraná. Five different geochemical types of high-Ti quartz latite are recognised amongst the silicic volcanics, 3 of which have very close geochemical affinities to the Ventura, Sarusas, and Khoraseb types of the northern Etendeka. Their relative stratigraphic position in the Bero volcanic sequence is the same as in the Etendeka sequence and extend significantly the area over which these types were erupted. The two remaining types, Chinguau and High-Nb are not known from either the Etendeka or the Paraná provinces.
- Full Text:
- Date Issued: 2016
- Authors: Marsh, Julian S , Swart, Roger S
- Date: 2016
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/60763 , vital:27827 , https://www.sciencedirect.com/science/article/pii/S0377027316304176
- Description: An extension of the Etendeka-Paraná Igneous Province into SW Angola occurs as minor basalt lavas, intrusive gabbro sheets, minor mafic dykes and thick sheets and lava flows (with minor pyroclastics) of quartz latite composition This suite crops out along the eastern margin of the Cretaceous Namibe Basin in SW Angola. The quartz latites from one locality have been referred to informally as the Giraul volcanics but the name ‘Giraul’ has previously been used for Cretaceous conglomerates. We propose the name Bero Volcanic Complex for this suite of intrusive and extrusive rocks on the basis that the full compositional range of this diverse suite crops out along the Rio Bero. Major and trace element compositions and Sr-, Nd-, and Pb-isotopic compositions indicate that the basalts and gabbros are equivalent to the high-Ti Khumib/Urubici and Pitanga types from the Etendeka and Paraná. The basalts underlie the quartz latites which are cut by mafic dykes some of which are compositionally equivalent to the Paranapanema lavas in the Paraná. Five different geochemical types of high-Ti quartz latite are recognised amongst the silicic volcanics, 3 of which have very close geochemical affinities to the Ventura, Sarusas, and Khoraseb types of the northern Etendeka. Their relative stratigraphic position in the Bero volcanic sequence is the same as in the Etendeka sequence and extend significantly the area over which these types were erupted. The two remaining types, Chinguau and High-Nb are not known from either the Etendeka or the Paraná provinces.
- Full Text:
- Date Issued: 2016
Transcription factor motif quality assessment requires systematic comparative analysis
- Kibet, Cabel K, Machanick, Philip
- Authors: Kibet, Cabel K , Machanick, Philip
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439366 , vital:73570 , https://f1000research.com/articles/4-1429
- Description: Transcription factor (TF) binding site prediction remains a challenge in gene regulatory research due to degeneracy and potential variability in binding sites in the genome. Dozens of algorithms designed to learn binding models (motifs) have generated many motifs available in research papers with a subset making it to databases like JASPAR, UniPROBE and Transfac. The presence of many versions of motifs from the various databases for a single TF and the lack of a standardized assessment technique makes it difficult for biologists to make an appropriate choice of binding model and for algorithm developers to benchmark, test and improve on their models. In this study, we review and evaluate the approaches in use, highlight differences and demonstrate the difficulty of defining a standardized motif assessment approach. We review scoring functions, motif length, test data and the type of performance metrics used in prior studies as some of the factors that influence the outcome of a motif assessment. We show that the scoring functions and statistics used in motif assessment influence ranking of motifs in a TF-specific manner. We also show that TF binding specificity can vary by source of genomic binding data. We also demonstrate that information content of a motif is not in isolation a measure of motif quality but is influenced by TF binding behaviour. We conclude that there is a need for an easy-to-use tool that presents all available evidence for a comparative analysis.
- Full Text:
- Date Issued: 2016
- Authors: Kibet, Cabel K , Machanick, Philip
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439366 , vital:73570 , https://f1000research.com/articles/4-1429
- Description: Transcription factor (TF) binding site prediction remains a challenge in gene regulatory research due to degeneracy and potential variability in binding sites in the genome. Dozens of algorithms designed to learn binding models (motifs) have generated many motifs available in research papers with a subset making it to databases like JASPAR, UniPROBE and Transfac. The presence of many versions of motifs from the various databases for a single TF and the lack of a standardized assessment technique makes it difficult for biologists to make an appropriate choice of binding model and for algorithm developers to benchmark, test and improve on their models. In this study, we review and evaluate the approaches in use, highlight differences and demonstrate the difficulty of defining a standardized motif assessment approach. We review scoring functions, motif length, test data and the type of performance metrics used in prior studies as some of the factors that influence the outcome of a motif assessment. We show that the scoring functions and statistics used in motif assessment influence ranking of motifs in a TF-specific manner. We also show that TF binding specificity can vary by source of genomic binding data. We also demonstrate that information content of a motif is not in isolation a measure of motif quality but is influenced by TF binding behaviour. We conclude that there is a need for an easy-to-use tool that presents all available evidence for a comparative analysis.
- Full Text:
- Date Issued: 2016
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