REE minerals at the Songwe Hill carbonatite, Malawi: HREE-enrichment in late-stage apatite

Compared to all published data from carbonatites and granitoids, the fluorapatite compositions in the Songwe Hill carbonatite, determined by EPMA and LA ICP-MS, have the highest heavy (H)REE concentration of any carbonatite apatite described so far. A combination of this fluorapatite and the REE fluorocarbonates, synchysite-(Ce) and parisite-(Ce), which are the other principal REE bearing minerals at Songwe, gives a REE deposit with a high proportion of Nd and a higher proportion of HREE (Eu–Lu including Y) than most other carbonatites. Since Nd and HREE are currently the most sought REE for commercial applications, the conditions that give rise to this REE profile are particularly important to understand. Multiple apatite crystallisation stages have been differentiated texturally and geochemically at Songwe and fluorapatite is divided into five different types (Ap-0–4). While Ap-0 and Ap-1 are typical of apatite found in fenite and calcite-carbonatite, Ap-2, -3 and -4 are texturally atypical of apatite from carbonatite and are progressively HREE-enriched in later paragenetic stages. Ap-3 and Ap-4 exhibit anhedral, stringer-like textures and their REE distributions display an Y anomaly. These features attest to formation in a hydrothermal environment and fluid inclusion homogenisation temperatures indicate crystallisation occurred between 200–350 °C. Ap-3 crystallisation is succeeded by a light (L)REE mineral assemblage of synchysite-(Ce), strontianite and baryte. Finally, late-stage Ap-4 is associated with minor xenotime-(Y) mineralisation and HREE-enriched fluorite. Fluid inclusions in the fluorite constrain the minimum HREE mineralisation temperature to approximately 160 °C. A model is suggested where sub-solidus, carbonatite-derived, (carbo)-hydrothermal fluids remobilise and fractionate the REE. Chloride or fluoride complexes retain LREE in solution while rapid precipitation of apatite, owing to its low solubility, leads to destabilisation of HREE complexes and substitution into the apatite structure. The LREE are retained in solution, subsequently forming synchysite-(Ce). This model will be applicable to help guide exploration in other carbonatite complexes

Solving the initial conditions problem for modified gravity theories

Modified gravity theories such as Einstein scalar Gauss Bonnet (EsGB) contain higher derivative terms in the spacetime curvature in their action, which results in modifications to the Hamiltonian and momentum constraints of the theory. In principle, such modifications may affect the principal part of the operator in the resulting elliptic equations, and so further complicate the already highly non-linear, coupled constraints that apply to the initial data in numerical relativity simulations of curved spacetimes. However, since these are effective field theories, we expect the additional curvature terms to be small, which motivates treating them simply as an additional source in the constraints, and iterating to find a solution to the full problem. In this work we implement and test a modification to the CTT/CTTK methods of solving the constraints for the case of the most general four derivative, parity invariant scalar-tensor theory, and show that solutions can be found in both asymptotically flat/black hole and periodic/cosmological spacetimes, even up to couplings of order unity in the theory. Such methods will allow for numerical investigations of a much broader class of initial data than has previously been possible in these theories, and should be straightforward to extend to similar models in the Horndeski class.Comment: 9 pages, 4 figures, comments welcome

GRDzhadzha: A code for evolving relativistic matter on analytic metric backgrounds

GRDzhadzha is an open-source code for relativistic simulations of matter fields on curved spacetimes that admit an analytic description (e.g. stationary black holes). It is based on the publicly available 3+1D numerical relativity code GRChombo. Such a description is valid where the density of the matter is small compared to the curvature scale of the spacetime, which is the case for many physical scenarios - for example, dark matter environments. The approach offers significant savings on memory and speed compared to running full numerical relativity simulations, since the metric variables and their derivatives are calculated analytically, and therefore are not evolved or stored on the grid. This brief paper introduces the code and gives details of some applications for which it has already been used.Comment: Submitted for review in the Journal of Open Source Software; Comments welcome; The code can be found at https://github.com/GRChombo/GRDzhadzha.gi

Geology, geochemistry and geochronology of the Songwe Hill carbonatite, Malawi

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record.Songwe Hill, Malawi, is one of the least studied carbonatites but has now become particularly important as it hosts a relatively large rare earth deposit. The results of new mapping, petrography, geochemistry and geochronology indicate that the 0.8 km diameter Songwe Hill is distinct from the other Chilwa Alkaline Province carbonatites in that it intruded the side of the much larger (4 x 6 km) and slightly older (134.6 ± 4.4 Ma) Mauze nepheline syenite and then evolved through three different carbonatite compositions (C1–C3). Early C1 carbonatite is scarce and is composed of medium–coarse-grained calcite carbonatite containing zircons with a U–Pb age of 132.9 ± 6.7 Ma. It is similar to magmatic carbonatite in other carbonatite complexes at Chilwa Island and Tundulu in the Chilwa Alkaline Province and others worldwide. The fine-grained calcite carbonatite (C2) is the most abundant stage at Songwe Hill, followed by a more REE- and Sr-rich ferroan calcite carbonatite (C3). Both stages C2 and C3 display evidence of extensive (carbo)-hydrothermal overprinting that has produced apatite enriched in HREE (<2000 ppm Y) and, in C3, synchysite-(Ce). The final stages comprise HREE-rich apatite fluorite veins and Mn-Fe-rich veins. Widespread brecciation and incorporation of fenite into carbonatite, brittle fracturing, rounded clasts and a fenite carapace at the top of the hill indicate a shallow level of emplacement into the crust. This shallow intrusion level acted as a reservoir for multiple stages of carbonatite-derived fluid and HREE-enriched apatite mineralisation as well as LREE-enriched synchysite-(Ce). The close proximity and similar age of the large Mauze nepheline syenite suggests it may have acted as a heat source driving a hydrothermal system that has differentiated Songwe Hill from other Chilwa carbonatites.Thanks are due to A. Lemon, A. Zabula, C. Mcheka, I. Nkukumila (Mkango Resources Ltd.), É. Deady (BGS) and P. Armitage (Paul Armitage Consulting Ltd.) for logistical support and enthusiastic discussions in the field. This contribution benefitted from reviews by Jindřich Kynický and Ray Macdonald, as well as anonymous reviewers, who we thank for their time and insightful comments. This work was funded by a NERC BGS studentship to SBF (NEE/J50318/1; S208), the NERC SoS RARE consortium (NE/M011429/1) and by Mkango Resources Ltd. AGG publishes with the permission of the Executive Director of the British Geological Survey (NERC)

Geology, geochemistry and geochronology of the Songwe Hill carbonatite, Malawi

Songwe Hill, Malawi, is one of the least studied carbonatites but has now become particularly important as it hosts a relatively large rare earth deposit. The results of new mapping, petrography, geochemistry and geochronology indicate that the 0.8 km diameter Songwe Hill is distinct from the other Chilwa Alkaline Province carbonatites in that it intruded the side of the much larger (4 × 6 km) and slightly older (134.6 ± 4.4 Ma) Mauze nepheline syenite and then evolved through three different carbonatite compositions (C1–C3). Early C1 carbonatite is scarce and is composed of medium–coarse-grained calcite carbonatite containing zircons with a U–Pb age of 132.9 ± 6.7 Ma. It is similar to magmatic carbonatite in other carbonatite complexes at Chilwa Island and Tundulu in the Chilwa Alkaline Province and others worldwide. The fine-grained calcite carbonatite (C2) is the most abundant stage at Songwe Hill, followed by a more REE- and Sr-rich ferroan calcite carbonatite (C3). Both stages C2 and C3 display evidence of extensive (carbo)-hydrothermal overprinting that has produced apatite enriched in HREE (<2000 ppm Y) and, in C3, synchysite-(Ce). The final stages comprise HREE-rich apatite fluorite veins and Mn-Fe-rich veins. Widespread brecciation and incorporation of fenite into carbonatite, brittle fracturing, rounded clasts and a fenite carapace at the top of the hill indicate a shallow level of emplacement into the crust. This shallow intrusion level acted as a reservoir for multiple stages of carbonatite-derived fluid and HREE-enriched apatite mineralisation as well as LREE-enriched synchysite-(Ce). The close proximity and similar age of the large Mauze nepheline syenite suggests it may have acted as a heat source driving a hydrothermal system that has differentiated Songwe Hill from other Chilwa carbonatites

GRFolres: A code for modified gravity simulations in strong gravity

GRFolres is an open-source code for performing simulations in modified theories of gravity, based on the publicly available 3+1D numerical relativity code GRChombo. Note: Submitted for review in the Journal of Open Source Software; Comments welcome; The code can be found at https://github.com/GRChombo/GRFolre

A General Modeling Framework for Describing Spatially Structured Population Dynamics

Variation in movement across time and space fundamentally shapes the abundance and distribution of populations. Although a variety of approaches model structured population dynamics, they are limited to specific types of spatially structured populations and lack a unifying framework. Here, we propose a unified network‐based framework sufficiently novel in its flexibility to capture a wide variety of spatiotemporal processes including metapopulations and a range of migratory patterns. It can accommodate different kinds of age structures, forms of population growth, dispersal, nomadism and migration, and alternative life‐history strategies. Our objective was to link three general elements common to all spatially structured populations (space, time and movement) under a single mathematical framework. To do this, we adopt a network modeling approach. The spatial structure of a population is represented by a weighted and directed network. Each node and each edge has a set of attributes which vary through time. The dynamics of our network‐based population is modeled with discrete time steps. Using both theoretical and real‐world examples, we show how common elements recur across species with disparate movement strategies and how they can be combined under a unified mathematical framework. We illustrate how metapopulations, various migratory patterns, and nomadism can be represented with this modeling approach. We also apply our network‐based framework to four organisms spanning a wide range of life histories, movement patterns, and carrying capacities. General computer code to implement our framework is provided, which can be applied to almost any spatially structured population. This framework contributes to our theoretical understanding of population dynamics and has practical management applications, including understanding the impact of perturbations on population size, distribution, and movement patterns. By working within a common framework, there is less chance that comparative analyses are colored by model details rather than general principles

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin