The sedimentology of the Zerrissene turbidite system, Damara Orogen, Namibia

The Zerrissene turbidite system of central-western Namibia is a late Proterozoic sequence which consists of dominantly siliciclastic turbidites interbedded with minor turbiditic and hemipelagic marbles. The basin in which these sediments were deposited is located at the junction of the coastal and intra-cratonic arms of the Pan-African Damara Orogen, and an understanding of the sedimentary evolution of this basin is therefore important to the understanding of the development of the orogen as a whole. One major and two minor phases of folding have deformed the sediments, but the grade of metamorphism is low and sedimentary structures are often well preserved. Further, the area lies entirely within the Namib Desert and the lack of vegetation cover results in good outcrops providing an unusual opportunity for examining a large Precambrian turbidite system. The system consists of five formations: three siliciclastic and two mixed carbonatesiliciclastic units. The floor of the system is not exposed, and the oldest sedimentary rocks which outcrop are siliciclastics of the Zebrapiits Formation. This is overlain successively by the Brandberg West Formation (dominantly calcareous), the Brak River Formation (siliciclastic), the Gemsbok River Formation (calcareous) and the Amis River Formation (siliciclastic). Nine silicilastic turbidite facies have been recognised in the basin. These are facies A₂ (disorganised onglomerates), B₁ (horizontally laminated to massive greyackes), C₂ ("classical" turbidites), Dl (sandstone-shale couplets with base cut-out Bouma sequences), D₂ (sandstone-shale couplets with less sand than shale and base cut-out Bouma sequences), E (coarse, discontinuous sandstone-shale couplets), F (slumped units), G (shale) and H (glacial dropstones). Four facies are associated with the carbonate horizons, and these carbonate facies are given the suffix c to distinguish them from similar siliciclastic facies. These are facies Ac (disorganised and graded marble breccias), facies Cc (graded carbonates), facies Gc (hemi-pelagic marbles) and facies G (pelagic shales). The basal Zebrapiits Formation is made up of relatively thin packages of thin- to thickbedded, laterally continuous facies D₁, D₂ and B₁ beds encased in thick envelopes of shale. This type of sequence is typical of a distal lobe-fringe, and requires an unconfined basin-floor on which it can develop. The overlying Brandberg West Formation consists of a basal portion of interbedded facies Cc and G, followed by a sequence dominanted by facies Gc. This sequence is interpreted as representing outer-apron carbonate turbidites, derived from multiple point sources (facies Cc), with background pelagic settling (facies G) overlain by hemi-pelagic deposits (facies Gc). A reversal back to siliciclastic turbidites followed with deposition of the Brak River Formation. This sequence comprises relatively thick packages of laterally continuous facies B₁, D₁, and D₂ beds sandwiched between facies G shales, a succession characteristic of a lobe to lobe-fringe environment with intermittent abandonment of lobes. An unconfined basin floor adjacent to a passive margin is required for the development of this type of sequence. Glacial dropstones (facies H) are found in the upper portions of this formation, and slumped beds are also present (facies F), but are uncommon. The facies F beds are only found in association with facies H and are therefore considered to be genetically related. Slumping of beds was possibly caused by an oversupply of sediment from ice-rafting which caused instability. The overlying Gemsbok River Formation has a sequence similar to the Brandberg West Formation in that the basal portion consists of interbedded facies Cc and G, which is overlain by a thick sequence of largely facies Gc beds. Minor facies Ac beds occur near the top of the overall sequence. This formation is interpreted as an outer-apron succession with the facies Ac beds representing distal inner-apron deposits, indicating progradation of the system. The youngest unit in the basin, the Amis River Formation, shows strong lateral variation from west to east. In the west the sequence comprises laterally continuous facies B₁, C₂, D₁ and D₂ with rare, discontinuous facies E beds. Facies G is relatively minor in the sequence. In the east the succession is dominated by facies D₁, D₂ and G, and this succession is interpreted as a sequence of distal turbidites which were deposited on a basin-plain. The system developed by aggradation rather than progradation as only minor cycles are developed. Geochemical and petrological features indicate that the entire siliciclastic system was derived from a granite-recycled orogen terrane. Palaeocurrent data are unreliable because of the deformation, but transport was initially from the south-west, moving later to the west and north-west. The provenance of the carbonates is uncertain as reliable palaeocurrent indicators are rare, but they could have been derived either from South America or from the extensive carbonate deposits developed on the north-western margins of the basin. The Zenissene siliciclastic turbidite system represents the distal portion of a major submarine turbidite system, the more proximal parts of which now lie west of the exposed basin, either under the Atlantic Ocean or in eastern South America. The calcareous deposits developed as an apron adjacent to a multiple point source, the position of which is at present unknown

The stratigraphy and structure of the Kommadagga subgroup and contiguous rocks|

The Lake Mentz and Kommadagga Subgroups were deposited in a marine environment and are characterised by a heterogeneous sequence of sediments, which range in grain size from clays to grits. During the first phase of deposition the Kweekvlei Shale and Floriskraal Formations were deposited in a prograding shoreline environment, whereas the succeeding Waaipoort Shale Formation is interpreted as represnting a reworked shoreline . The final phase of deposition of the Cape Supergroup was a regressive one in which the Kommadagga Subgroup was formed. The coarsening upward cycle of this subgroup represents a deltaic deposit. A significant time gap appears to exist before the deposition of the glacial-marine Dwyka Tillite Formation. Structurally, the area was subjected to deformation by buckle folding at about 250 Ma into a series of folds with southward dipping axial planes. Only one phase of deformation is recognised in the study area . A decrease in pore space, mineral overgrowths,formation of silica and calcite cements and development of autigenic minerals such as opal, stilpnomelane, analcite, prehnite, muscovite and various clay minerals are the characteristic diagenetic features of the sediments. The mineralogical evidence suggests that the maximum temperature and pressure of burial was 150 C and 4 to 5 Kbar respectively

Cancer diagnoses profile of bone marrow specimens from November 2012 to December 2015 in a tertiary academic setting

This study aimed to examine the number and type of cancer diagnoses made based on bone marrow aspirates (BMA) using morphology and/or histology, over a three year period. All the data collected (2012-2015) was obtained using the Trak-Care laboratory information system (LIS) of the National Health Laboratory Service (NHLS). Data was categorised into four categories including acute leukaemias (ALs), chronic leukaemias (CLs), Hodgkin’s lymphoma (HL), Non-Hodgkin’s lymphoma (NHL) and a miscellaneous group. The laboratory test most frequently used to make diagnoses was bone marrow aspiration (BMA) morphology (199), followed by flow cytometry (138), histology (113), fluorescent in situ hybridisation (FISH) (54) and polymerase chain reaction (PCR) (9). In total, the top three conditions diagnosed were acute myeloid leukaemias (AMLs), chronic myeloid leukaemia (CML) and B-cell acute lymphoblastic leukaemia (B-ALL). There was good agreement between the diagnoses made by BMA morphology, BMT histology and flow cytometry. Results showed that BMA morphology was the most popular diagnostic test used and that this test had excellent agreement with BMT histology and flow cytometry diagnoses. The most frequently diagnosed conditions were the AMLs.http://www.smltsa.org.za/publications.htmlam2018Haematolog

Variants in the CYP2B6 3′UTR Alter In Vitro and In Vivo CYP2B6 Activity: Potential Role of MicroRNAs

CYP2B6*6 and CYP2B6*18 are the most clinically important variants causing reduced CYP2B6 protein expression and activity. However, these variants do not account for all variability in CYP2B6 activity. Emerging evidence has shown that genetic variants in the 3′UTR may explain variable drug response by altering microRNA regulation. Five 3′UTR variants were associated with significantly altered efavirenz AUC0-48 (8-OH-EFV/EFV) ratios in healthy human volunteers. The rs70950385 (AG>CA) variant, predicted to create a microRNA binding site for miR-1275, was associated with a 33% decreased CYP2B6 activity among normal metabolizers (AG/AG vs. CA/CA (P < 0.05)). In vitro luciferase assays were used to confirm that the CA on the variant allele created a microRNA binding site causing an 11.3% decrease in activity compared to the AG allele when treated with miR-1275 (P = 0.0035). Our results show that a 3′UTR variant contributes to variability in CYP2B6 activity

Paleoenvironmental and diagenetic evolution of the Aptian Pre-Salt succession in Namibe Basin (Onshore Angola)

The Aptian Pre-Salt sedimentary succession cropping out in Cangulo palaeovalley onshore Namibe Basin (Angola) was studied by a combination of field and analytical techniques to constrain the sedimentary and diagenetic evolution of the uppermost sag sequence of the South Atlantic passive margin. Field observations allows definition of four transgressive-regressive cycles characterised by fluvial to tidal-influenced mixed clastic-carbonate and carbonate-dominated deposits, that locally show evidence of evaporite dissolution; highlighting that evaporite deposition started earlier than deposition of the regional South Atlantic Loeme-Bambata evaporite formations. Two separate pre-salt carbonate units have been differentiated within the Cangulo Fm; i) a lower transitional to marginal marine, and ii) a younger upper non-marine freshwater travertine system, that is documented for the first time in the west African margin. Transgressive-regressive cycles control the early diagenesis of the tidal carbonates that include dolomitization due to mixing fluids during transgressions, and karstification due to evaporite dissolution by meteoric water circulation during regressive events. Clastic supply appears to have been completely shut down during carbonate deposition, suggesting major climatic change associated with carbonate deposition. During the lowstand between the two carbonate units, fluid flow through Cangulo palaeovalley was re-established resulting in extensive karstification and formation of a large-scale erosional unconformity that is interpreted to be time equivalent to an intra Chela-Cuvo Fm. event. The top of the studied succession corresponds to the transgressive deposits of the Bambata evaporites that are not preserved in the Cangulo palaeovalley due to its erosion but are regionally developed. The results of this study can be directly linked to along strike age equivalent Pre-Salt successions cropping out in the Namibe, Benguela and Kwanza basins, and directly offshore Angola and Brazil using well and seismic data. These new data shed important new light and constraints on the depositional and diagenetic evolution of the complex Pre-Salt reservoir systems of the South Atlantic, and the depositional and bathymetric setting at the time of onset of the main south Atlantic evaporite deposition.publishedVersio

Fungal Planet description sheets: 1042-1111

Novel species of fungi described in this study include those from various countries as follows: Antarctica, Cladosporium arenosum from marine sediment sand. Argentina, Kosmimatamyces alatophylus (incl. Kosmimatamyces gen. nov.) from soil. Australia, Aspergillus banksianus, Aspergillus kumbius, Aspergillus luteorubrus, Aspergillus malvicolor and Aspergillus nanangensis from soil, Erysiphe medicaginis from leaves of Medicago polymorpha, Hymenotorrendiella communis on leaf litter of Eucalyptus bicostata, Lactifluus albopicri and Lactifluus austropiperatus on soil, Macalpinomyces collinsiae on Eriachne benthamii, Marasmius vagus on soil, Microdochium dawsoniorum from leaves of Sporobolus natalensis, Neopestalotiopsis nebuloides from leaves of Sporobolus elongatus, Pestalotiopsis etonensis from leaves of Sporobolus jacquemontii, Phytophthora personensis from soil associated with dying Grevillea mccutcheonii. Brazil, Aspergillus oxumiae from soil, Calvatia baixaverdensis on soil, Geastrum calycicoriaceum on leaf litter, Greeneria kielmeyerae on leaf spots of Kielmeyera coriacea. Chile, Phytophthora aysenensis on collar rot and stem of Aristotelia chilensis. Croatia, Mollisia gibbospora on fallen branch of Fagus sylvatica. Czech Republic, Neosetophoma hnaniceana from Buxus sempervirens. Ecuador, Exophiala frigidotolerans from soil. Estonia, Elaphomyces bucholtzii in soil. France, Venturia paralias from leaves of Euphorbia paralias. India, Cortinarius balteatoindicus and Cortinarius ulkhagarhiensis on leaf litter. Indonesia, Hymenotorrendiella indonesiana on Eucalyptus urophylla leaf litter. Italy, Penicillium taurinense from indoor chestnut mill. Malaysia, Hemileucoglossum kelabitense on soil, Satchmopsis pini on dead needles of Pinus tecunumanii. Poland, Lecanicillium praecognitum on insects' frass. Portugal, Neodevriesia aestuarina from saline water. Republic of Korea, Gongronella namwonensis from freshwater. Russia, Candida pellucida from Exomias pellucidus, Heterocephalacria septentrionalis as endophyte from Cladonia rangiferina, Vishniacozyma phoenicis from dates fruit, Volvariella paludosa from swamp. Slovenia, Mallocybe crassivelata on soil. South Africa, Beltraniella podocarpi, Hamatocanthoscypha podocarpi, Coleophoma podocarpi and Nothoseiridium podocarpi (incl. Nothoseiridium gen. nov.)from leaves of Podocarpus latifolius, Gyrothrix encephalarti from leaves of Encephalartos sp., Paraphyton cutaneum from skin of human patient, Phacidiella alsophilae from leaves of Alsophila capensis, and Satchmopsis metrosideri on leaf litter of Metrosideros excelsa. Spain, Cladophialophora cabanerensis from soil, Cortinarius paezii on soil, Cylindrium magnoliae from leaves of Magnolia grandiflora, Trichophoma cylindrospora (incl. Trichophoma gen. nov.) from plant debris, Tuber alcaracense in calcareus soil, Tuber buendiae in calcareus soil. Thailand, Annulohypoxylon spougei on corticated wood, Poaceascoma filiforme from leaves of unknown Poaceae. UK, Dendrostoma luteum on branch lesions of Castanea sativa, Ypsilina buttingtonensis from heartwood of Quercus sp. Ukraine, Myrmecridium phragmiticola from leaves of Phragmites australis. USA, Absidia pararepens from air, Juncomyces californiensis (incl. Juncomyces gen. nov.) from leaves of Juncus effusus, Montagnula cylindrospora from a human skin sample, Muriphila oklahomaensis (incl. Muriphila gen. nov.)on outside wall of alcohol distillery, Neofabraea eucalyptorum from leaves of Eucalyptus macrandra, Diabolocovidia claustri (incl. Diabolocovidia gen. nov.)from leaves of Serenoa repens, Paecilomyces penicilliformis from air, Pseudopezicula betulae from leaves of leaf spots of Populus tremuloides. Vietnam, Diaporthe durionigena on branches of Durio zibethinus and Roridomyces pseudoirritans on rotten wood. Morphological and culture characteristics are supported by DNA barcodes

Modeling the measles paradox reveals the importance of cellular immunity in regulating viral clearance

Measles virus (MV) is a highly contagious member of the Morbillivirus genus that remains a major cause of childhood mortality worldwide. Although infection induces a strong MV-specific immune response that clears viral load and confers lifelong immunity, transient immunosuppression can also occur, leaving the host vulnerable to colonization from secondary pathogens. This apparent contradiction of viral clearance in the face of immunosuppression underlies what is often referred to as the ‘measles paradox’, and remains poorly understood. To explore the mechanistic basis underlying the measles paradox, and identify key factors driving viral clearance, we return to a previously published dataset of MV infection in rhesus macaques. These data include virological and immunological information that enable us to fit a mathematical model describing how the virus interacts with the host immune system. In particular, our model incorporates target cell depletion through infection of host immune cells—a hallmark of MV pathology that has been neglected from previous models. We find the model captures the data well, and that both target cell depletion and immune activation are required to explain the overall dynamics. Furthermore, by simulating conditions of increased target cell availability and suppressed cellular immunity, we show that the latter causes greater increases in viral load and delays to MV clearance. Overall, this signals a more dominant role for cellular immunity in resolving acute MV infection. Interestingly, we find contrasting dynamics dominated by target cell depletion when viral fitness is increased. This may have wider implications for animal morbilliviruses, such as canine distemper virus (CDV), that cause fatal target cell depletion in their natural hosts. To our knowledge this work represents the first fully calibrated within-host model of MV dynamics and, more broadly, provides a new platform from which to explore the complex mechanisms underlying Morbillivirus infection

Ska telescope manager (tm): status and architecture overview

The SKA radio telescope project is building two telescopes, SKA-Low in Australia and SKA-Mid in South Africa respectively. The Telescope Manager is responsible for the observations lifecycle and for monitoring and control of each instrument, and is being developed by an international consortium. The project is currently in the design phase, with the Preliminary Design Review having been successfully completed, along with re-baselining to match project scope to available budget. This report presents the status of the Telescope Manager work, key architectural challenges and our approach to addressing them

Correction:How the COVID-19 pandemic highlights the necessity of animal research (vol 30, pg R1014, 2020)

(Current Biology 30, R1014–R1018; September 21, 2020) As a result of an author oversight in the originally published version of this article, a number of errors were introduced in the author list and affiliations. First, the middle initials were omitted from the names of several authors. Second, the surname of Dr. van Dam was mistakenly written as “Dam.” Third, the first name of author Bernhard Englitz was misspelled as “Bernard” and the surname of author B.J.A. Pollux was misspelled as “Pullox.” Finally, Dr. Keijer's first name was abbreviated rather than written in full. These errors, as well as various errors in the author affiliations, have now been corrected online