io Geology of the Chang 7 Member oil shale of the Yanchang Formation of the Ordos Basin in central north China By pg.lyellcollection.org Published On :: 2020-05-01T00:30:41-07:00 We present a review of the Chang 7 Member oil shale, which occurs in the middle–late Triassic Yanchang Formation of the Ordos Basin in central north China. The oil shale has a thickness of 28 m (average), an area of around 30 000 km2 and a Ladinian age. It is mainly brown-black to black in colour with a laminar structure. It is characterized by average values of 18 wt% TOC (total organic carbon), 8 wt% oil yield, a 8.35 MJ kg–1 calorific value, 400 kg t–1 hydrocarbon productivity and kerogen of type I–II1, showing a medium quality. On average, it comprises 49% clay minerals, 29% quartz, 16% feldspar and some iron oxides, which is close to the average mineral composition of global shale. The total SiO2 and Al2O3 comprise 63.69 wt% of the whole rock, indicating a medium ash type. The Sr/Ba is 0.33, the V/Ni is 7.8, the U/Th is 4.8 and the FeO/Fe2O3 is 0.5, indicating formation in a strongly reducing, freshwater or low-salinity sedimentary environment. Multilayered intermediate-acid tuff is developed in the basin, which may have promoted the formation of the oil shale. The Ordos Basin was formed during the northwards subduction of the Qinling oceanic plate during the Ladinian–Norian in a back-arc basin context. The oil shale of the Ordos Basin has a large potential for hydrocarbon generation. Supplementary material: Tables of oil-shale geochemical composition, proximate and organic matter analyses from the Chang 7 Member oil shale, the Ordos Basin, Central north China are available at https://doi.org/10.6084/m9.figshare.c.4411703 Full Article
io Seismic pore pressure prediction at the Halten Terrace in the Norwegian Sea By pg.lyellcollection.org Published On :: 2020-05-01T00:30:41-07:00 Pre-drill pore pressure prediction is essential for safe and efficient drilling, and is a key element in the risk-reducing toolbox when designing a well. On the Norwegian Continental Shelf, pore pressure prediction commonly relies on traditional 1D offset well analysis, whereas velocity data from seismic surveys are often not considered. Our work with seismic interval velocities shows that the velocity field can provide an important basis for pressure prediction and enable the construction of regional 3D pressure cubes. This may increase the confidence in the pore pressure models and aid the pre-drill geohazard screening process. We demonstrate how a 3D velocity field can be converted to a 3D pore pressure cube using reported pressures in offset wells as calibration points. The method is applied to a regional dataset at the Halten Terrace in the Norwegian Sea; an area with a complex pattern of pore pressure anomalies which traditionally has been difficult to predict. The algorithm is searching for a velocity to pore pressure transform that best matches the reported pressures. The 3D velocity field is a proxy of rock velocity and is derived from seismic surveys, and is verified to checkshot velocities and sonic data in the offset wells. Full Article
io Lithological and chemostratigraphic discrimination of facies within the Bowland Shale Formation within the Craven and Edale basins, UK By pg.lyellcollection.org Published On :: 2020-05-01T00:30:41-07:00 The Carboniferous Bowland Shale Formation of the UK is a proven hydrocarbon source rock and currently a target for shale gas exploration. Most existing analysis details lithofacies and geochemical assessment of a small number of boreholes. Given a paucity of relevant borehole cores, surface samples provide a valuable contribution to the assessment of this unconventional gas source. This study reviews existing literature on the formation's hydrocarbon geochemistry and provides new lithological descriptions of seven lithofacies, XRD mineralogy and hydrocarbon-specific geochemical data for 32 outcrop localities within the Craven and Edale basins, respectively in the northern and southern parts of the resource area. Low oxygen indices suggest that the majority of samples are relatively unaltered (in terms of hydrocarbon geochemistry), and therefore suitable for the characterization of the shale organic character. Total organic carbon (TOC) ranges from 0.7 to 6.5 wt%, with highest values associated with maximum flooding surfaces. Mean Tmax values of 447 and 441°C for the Edale and Craven basins, respectively, suggest that nearly all the samples were too immature to have generated appreciable amounts of dry gas. The oil saturation index is consistently below the >100 mg g–1 TOC benchmark, suggesting that they are not prospective for shale oil. Supplementary material: A table summarizing the location, geological description and age of all of the samples in this paper is available at https://doi.org/10.6084/m9.figshare.c.4444589 Full Article
io Structural constraints on Lower Carboniferous shale gas exploration in the Craven Basin, NW England By pg.lyellcollection.org Published On :: 2020-05-01T00:30:41-07:00 Detailed interpretation of a 3D seismic data volume reveals the detrimental effect that post-depositional tectonic deformation has had on buried Lower Carboniferous (Dinantian–Namurian) shales and its consequences for shale gas exploration in the SW part (Fylde area) of the Craven Basin in NW England. The structural styles primarily result from Devono-Carboniferous (syn-sedimentary) extension, post-rift subsidence and Variscan inversion, a renewed phase of Permo-Triassic extension, and Cenozoic uplift and basin exhumation. In contrast to the shallow dips and bedding continuity that characterizes productive shale gas plays in other basins (e.g. in the USA and Argentina), our mapping shows that the area is affected by deformation that results in the Bowland Shale Formation targets being folded and dissected into fault-bound compartments defined by SW–NE striking (Lower Carboniferous and Variscan) reverse faults and SSW–NNE to N–S striking (Permo-Triassic) normal faults. The fault networks and the misalignment between the elongate compartments they contain and the present-day minimum horizontal stress orientation limit the length over which long lateral boreholes can remain in a productive horizon, placing an important constraint on optimal well positioning, reducing the size of the shale gas resource and affecting well productivity. Our subsurface mapping using this high-fidelity dataset provides an accurate picture of the Upper Palaeozoic structure and demonstrates that faulting is denser and more complex than apparent from geological mapping of the surface outcrop. That structural complexity has direct and significant consequences for: the location of well pads; the lateral continuity of target shale gas horizons; the evaluation of the risk of inducing seismicity on seismically resolvable (large displacement) fault planes prior to drilling; and the likelihood of faults with small throws (below seismic resolution) being present. Full Article
io UK Rockall prospectivity: re-awakening exploration in a frontier basin By pg.lyellcollection.org Published On :: 2020-05-01T00:30:41-07:00 The UK Rockall, located to the west of Scotland and the Hebrides, is a frontier petroleum-bearing basin. Exploratory drilling in the basin took place over a quarter of a century (1980–2006), during which time a total of 12 wells were drilled, leading to the discovery of a single, subcommercial gas accumulation. We argue that the basin, which has seen no drilling activity for more than a decade, has not been sufficiently tested by the existing well stock. We examine the reasons for the absence of key Jurassic source rocks in the UK Rockall wells, which are widely distributed elsewhere on the UK Continental Shelf (UKCS), and argue that their absence in the wells does not preclude their existence in the basin at large. An evaluation of the Permian–Early Eocene successions, based upon the seismic interpretation of new 2D seismic data, has been integrated with legacy data and regional evidence to establish the potential for source, reservoir and sealing elements within each interval. Finally, we look at the future for exploration in the UK Rockall and suggest a way forward in the drilling of a new joint governmental–industry test well that may help to unlock the exploration potential of this under-explored, yet prospective, basin. Thematic collection: This article is part of the Under-explored plays and frontier basins of the UK continental shelf collection available at: https://www.lyellcollection.org/cc/under-explored-plays-and-frontier-basins-of-the-uk-continental-shelf Full Article
io The role of relay ramp evolution in governing sediment dispersal and petroleum prospectivity of syn-rift stratigraphic plays in the Northern North Sea By pg.lyellcollection.org Published On :: 2020-05-01T00:30:41-07:00 Interpretation of a 3D seismic survey located on the western margin of the Northern North Sea Basin demonstrates how the propagation, overlap and linkage of two north–south-striking, en echelon normal fault segments exerted a powerful influence over prospective subtle stratigraphic traps. The relay ramp that formed between the segments appears to have focused sediment dispersal, controlled reservoir distribution and aided post-depositional petroleum migration. Integration of electrical well log data, root-mean-square (RMS)-amplitude analysis and biostratigraphy with seismic interpretation demonstrates that a series of elongate, linear, sand-prone (reservoir) channel complexes characterize the depositional slopes generated by fault growth. The combination of synsedimentary rotation of bedding due to fault propagation and associated footwall uplift led to erosion and truncation of a laterally extensive, older channelized system (Lower Sequence), the downdip parts of which extend beyond the relay ramp. Its subsequent drape by transgressive shales created the subtle stratigraphic trap that now hosts the Cladhan Field, with charge occurring because the sandstones belonging to the Lower Sequence extend as far as the active kitchen in the neighbouring (hanging-wall) depocentre situated downdip and to the east. In contrast, the exploration of a younger, Upper Sequence of sandstones has proven to be disappointing due to their more restricted distribution, lack of access to charge, and occurrence of faults that offset and breach the thin end of the stratigraphic wedge. The implication is that partially breached relay ramps not only provide a preferential site for syn-rift clastic reservoirs to develop but also form important migration pathways through which oil passed from a petroleum kitchen into a trap. Thematic collection: This article is part of the Under-explored plays and frontier basins of the UK continental shelf collection available at: http://www.lyellcollection.org/cc/under-explored-plays-and-frontier-basins-of-the-uk-continental-shelf Full Article
io Sedimentary and tectonic controls on Lower Carboniferous (Visean) mixed carbonate-siliciclastic deposition in NE England and the Southern North Sea: implications for reservoir architecture By pg.lyellcollection.org Published On :: 2020-05-01T00:30:41-07:00 Discovery of the Breagh gas field in the Southern North Sea (SNS) has demonstrated the potential that the Lower Carboniferous (Visean, 346.7–330.9 Ma) Farne Group reservoirs have to contribute to the UK's future energy mix. New biostratigraphic correlations provide a basis to compare Asbian and Brigantian sedimentary cores from the Breagh Field and age-equivalent sediments exposed on the Northumberland Coast, which has proved critical in gaining an understanding of exploration and development opportunities. Thirteen facies associations characterize the mixed carbonate–siliciclastic system, grouped into: marine, delta front, delta shoreface, lower delta plain and upper delta plain gross depositional environments. The facies associations are interpreted as depositing in a mixed carbonate and siliciclastic fluvio-deltaic environment, and are arranged into coarsening- and cleaning-upward cycles (parasequences) bounded by flooding surfaces. Most cycles are characterized by mouth bars, distributary channels, interdistributary bays and common braided rivers, interpreted as river-dominated deltaic deposits. Some cycles include rare shoreface and tidally-influenced deposits, interpreted as river-dominated and wave- or tide-influenced deltaic deposits. The depositional processes that formed each cycle have important implications for the reservoir net/gross ratio (where this ratio indicates the proportion of sandstone beds in a cycle), thickness and lateral extent. The deltaic deposits were controlled by a combination of tectonic and eustatic (allocyclic) events and delta avulsion (autocyclic) processes, and are likely to reflect a changing tectonic regime, from extension within elongate fault-bounded basins (synrift) to passive regional thermal subsidence (post-rift). Deep incision by the Base Permian Unconformity across the Breagh Field has removed the Westphalian, Namurian and upper Visean, to leave the more prospective thicker clastic reservoirs within closure. Thematic collection: This article is part of the Under-explored plays and frontier basins of the UK continental shelf collection available at: https://www.lyellcollection.org/cc/under-explored-plays-and-frontier-basins-of-the-uk-continental-shelf Full Article
io Structural evolution of the Breagh area: implications for carboniferous prospectivity of the Mid North Sea High, Southern North Sea By pg.lyellcollection.org Published On :: 2020-05-01T00:30:41-07:00 Exploration success at Breagh demonstrates that western parts of the Mid North Sea High area are prospective despite the absence of an Upper Permian (Rotliegend Group) Leman Sandstone Formation reservoir and source rocks belonging to the Upper Carboniferous Westphalian Coal Measures Group. Detailed seismic and well interpretation shows that the Breagh trap was a long-lived footwall high, the prospectivity of which was enhanced by Variscan folding and uplift, leading to the truncation (subcrop) of Lower Carboniferous reservoirs beneath the Base Permian Unconformity. Its drape (supra-crop) by Upper Permian (Zechstein Super Group) evaporites creates the seal. The complexity of its overburden means that an accurate picture of the Breagh structure only emerges after accurate depth-conversion that takes the effects of the Mesozoic graben into account. Pronounced easterly tilting during the Cenozoic affected the area and controlled gas migration into the structure from palaeostructures lying to the east. However, evidence that Breagh is not filled to spill point (underfill) suggests that charge limitation remained an issue. The study demonstrates that a poorly-documented and under-explored Lower Carboniferous play exists in Southern North Sea, which relies upon careful structural mapping and basin modelling to be undertaken for the play to be understood and its further potential to be realized. Thematic collection: This article is part of the Under-explored plays and frontier basins of the UK continental shelf collection available at: https://www.lyellcollection.org/cc/under-explored-plays-and-frontier-basins-of-the-uk-continental-shelf Full Article
io Structural and stratigraphic evolution of the Mid North Sea High region of the UK Continental Shelf By pg.lyellcollection.org Published On :: 2020-05-01T00:30:41-07:00 Interpretation of newly acquired seismic and legacy well data has led to a greater understanding of the Upper Paleozoic–Recent geological evolution of the Mid North Sea High (MNSH), an under-explored region of the North Sea. The position of granite-cored blocks controlled the distribution of Devono-Carboniferous highs and basins before Variscan uplift led to peneplanation and the creation of the Base Permian Unconformity. The MNSH became the dominant feature during the Permian when it formed a west–east-striking ridge between the Southern and Northern Permian basins. Following a period of non-deposition, sedimentation was renewed in the Late Permian–Triassic before Middle Jurassic doming caused uplift to the NE. Subsequent Late Jurassic North Sea rifting transected the MNSH to create the Western Platform between the Central Graben and Moray Firth rift arms. Following Cretaceous post-rift deposition, the area experienced a significant easterly tilt in the Cenozoic that led to the demise of the MNSH as a prominent topographical feature. The tectonic and stratigraphic evolution exerts a strong control over reservoir facies distribution, source-rock deposition and maturation. However, the area is not barren of petroleum potential. Despite the lack of Upper Carboniferous source rocks over large areas, hydrocarbon potential is evident through shows in legacy wells, indicating the Lower Carboniferous as a potential source rock. Cenozoic uplift to the west imparted a regional tilt, the effects of which remains key to unlocking the area's prospectivity since it reconfigured structures and formed remigration pathways from Lower Carboniferous and Jurassic source rocks. Thematic collection: This article is part of the Under-explored plays and frontier basins of the UK continental shelf collection available at: https://www.lyellcollection.org/cc/under-explored-plays-and-frontier-basins-of-the-uk-continental-shelf Full Article
io Reply to Discussion on 'Breakup continents at magma poor rifted margins: a seismic v. outcrop perspective. Journal of the Geological Society, London, 175, 875-882 By jgs.lyellcollection.org Published On :: 2020-05-04T02:10:48-07:00 Full Article
io Discussion on 'Breaking up continents at magma-poor rifted margins: a seismic v. outcrop perspective Journal of the Geological Society, London, 175, 875-882 By jgs.lyellcollection.org Published On :: 2020-05-04T02:10:48-07:00 Full Article
io Cyclical variations of fluid sources and stress state in a shallow megathrust-zone melange By jgs.lyellcollection.org Published On :: 2020-05-04T02:10:48-07:00 Differences in REE patterns of calcite from extensional and shear veins of the Sestola Vidiciatico Tectonic Unit in the Northern Apennines suggest variations in fluid source during the seismic cycle in an ancient analogue of a shallow megathrust (Tmax c. 100–150°C). In shear veins, a positive Eu anomaly suggests an exotic fluid source, probably hotter than the fault environment. Small-scale extensional veins were derived instead from a local fluid in equilibrium with the fault rocks. Mutually crosscutting relations between two extensional vein sets, parallel and perpendicular to the megathrust, suggest repeated shifting of the 1 and 3 stresses during the seismic cycle. This is consistent with: (1) a seismic phase, with brittle failure along the thrust, crystallization of shear veins from an exotic fluid, stress drop and stress rotation; (2) a post-seismic phase, with fault-normal compaction and formation of fault-normal extensional veins fed by local fluids; (3) a reloading phase, where shear stress and pore pressure are gradually restored and fault-parallel extensional veins form, until the thrust fails again. The combination of geochemical and structural analyses in veins from exhumed megathrust analogues represents a promising tool to better understand the interplay between stress state and fluids in modern subduction zones. Supplementary material: Cathodoluminescence microphotographs, methodological details of the microstructural analysis, microphotographs of the location of analysed spots and a geochemical data table are available at https://doi.org/10.6084/m9.figshare.c.4842165 Thematic collection: This article is part of the Polygenetic mélanges collection available at: https://www.lyellcollection.org/cc/polygenetic-melanges Full Article
io The progressive development of microfabrics from initial deposition to slump deformation: an example from a modern sedimenary melange on the Nankai Prism By jgs.lyellcollection.org Published On :: 2020-05-04T02:10:48-07:00 The progressive development of microfabrics from initial deposition to slump deformation and then a submarine slide was investigated in an active subduction zone using cores recovered during the Integrated Ocean Drilling Program Expedition 333. A Pleistocene–Holocene sequence was recovered at Site C0018A, which was located on a slope basin on the footwall of the megasplay fault in the Nankai Trough, SW Japan. Six mass-transport deposit units intercalated with coherent intervals were recovered from the upper 190 m of the drilled succession. The initial microfabrics in the undeformed hemipelagic sediments were characterized by random and porous fabrics composed predominantly of clay aggregations and connectors. The initial fabrics were cardhouse fabrics, which consist of clay flakes with edge-to-edge (E–E) and/or edge-to-face (E–F) contacts. These initial microfabrics developed into compacted microfabrics, which are random and consolidated fabrics (bookhouse fabrics) that consist of clay flakes with E–F and/or face-to-face (F–F) contacts and develop during burial as a pure shear deformation. During slumping, these fabrics were then deformed under simple shear to become predominantly F–F contacts and form clay chains. Thus, the microfabrics in these submarine slides are a sedimentary mélange that developed locally into a preferred clay orientation with F–F contacts. Supplementary material: A schematic illustration showing sedimentation processes and fabrics is available at https://doi.org/10.6084/m9.figshare.c.4483385 Thematic collection: This article is part of the Polygenetic mélanges collection available at: https://www.lyellcollection.org/cc/polygenetic-melanges Full Article
io Sedimentary and diapiric melanges in the Skrzydlna area (Outer Carpathians of Poland) as indicators of basinal and structural evolution By jgs.lyellcollection.org Published On :: 2020-05-04T02:10:48-07:00 The Dukla Nappe in the Skrzydlna area exposes two types of mélange reflecting two different phases of basinal and tectonic evolution of the Outer West Carpathian orogen in its Polish sector. The Oligocene-age sedimentary mélange (olistostrome) is related to growth of the accretionary wedge, whereas the Miocene-age diapiric mélange postdates the orogenic thrusting. Textural and structural features of the very coarse-grained sedimentary mélange suggest non-cohesive debris flows and high-density turbidity currents as predominant emplacement mechanisms. Growth strata, associated with progressive unconformities, and facies contrast between the underlying fine-grained unit and the overlying olistostrome reflect a considerable uplift of the source area and rotation of the adjacent part of the basin floor. The olistostrome and the overlying turbidite succession form a retrogressive sequence interpreted as a submarine canyon infill grading to a small submarine fan. The diapiric mélange, injected into the Oligocene-age succession of the Dukla Nappe, contains the Early and Late Cretaceous-age blocks and matrix derived from the underlying Silesian Nappe. The features reflecting diapiric emplacement include matrix proportion increase and block content decrease towards the mélange margins, scaly fabric and shear zones. Both mélanges, interpreted in the past as chaotic bodies, upon detailed examination reveal genesis-related subtle internal organization. Full Article
io Recycling of heterogeneous material in the subduction factory: evidence from the sedimentary melange of the Internal Ligurian Units, Italy By jgs.lyellcollection.org Published On :: 2020-05-04T02:10:48-07:00 In the Northern Apennine (Italy), the Internal Ligurian Units consist of Middle–Late Jurassic ophiolites covered by thick sedimentary deposits whose top is represented by the Early Paleocene Bocco Shale. This formation is characterized by mass-transport deposits interlayered with thin-bedded siliciclastic turbidites. The sedimentological and structural features of these mass-transport deposits reveal a long-lived history of recycling of heterogeneous material in a subduction setting. This history started with the frontal accretion of a fragment of oceanic crust into an accretionary prism whose lower slope was subsequently affected by tectonic erosion and consequent instability, leading to the production of mass-transport deposits and the transfer of material to the lower plate. These mass-transport deposits were subsequently underthrust and then again transferred to the base of the accretionary prism by coherent underplating, before their exhumation to the surface. The Bocco Shale is thus representative of a subduction setting where both accretionary and erosive events occurred, depending on changing boundary conditions. The reconstructed history for the Bocco Shale indicates that the sedimentary and gravitational processes both at the prism front and on the prism slope, possibly induced by alternating accretion and erosion events, are the most efficient mechanisms of lithological mixing and recycling in subduction margins. Full Article
io Mid-Eocene giant slope failure (sedimentary melanges) in the Ligurian accretionary wedge (NW Italy) and relationships with tectonics, global climate change and the dissociation of gas hydrates By jgs.lyellcollection.org Published On :: 2020-05-04T02:10:48-07:00 Upper Lutetian–Bartonian sedimentary mélanges, corresponding to ancient mud-rich submarine mass transport deposits, are widely distributed over an area c. 300 km long and tens of kilometres wide along the exhumed outer part of the External Ligurian accretionary wedge in the Northern Apennines. The occurrence of methane-derived carbonate concretions (septarians) in a specific tectonostratigraphic position below these sedimentary mélanges allows us to document the relationships among a significant period of regional-scale slope failure, climate change (the Early and Mid-Eocene Optimum stages), the dissociation of gas hydrates and accretionary tectonics during the Ligurian Tectonic Phase (early–mid-Lutetian). The distribution of septarians at the core of thrust-related anticlines suggests that the dissociation of gas hydrates was triggered by accretionary tectonics rather than climate change. The different ages of slope failure emplacement and the formation of the septarians support the view that the dissociation of gas hydrates was not the most important trigger for slope failure. The latter occurred during a tectonic quiescence stage associated with a regressive depositional trend, and probably minor residual tectonic pulses, which followed the Ligurian Tectonic Phase, favouring the dynamic re-equilibrium of the External Ligurian accretionary wedge. Our findings provide useful information for a better understanding of the factors controlling giant slope failure events in modern accretionary settings, where they may cause tsunamis. Full Article
io Redefinition of the Ligurian Units at the Alps-Apennines junction (NW Italy) and their role in the evolution of the Ligurian accretionary wedge: constraints from melanges and broken formations By jgs.lyellcollection.org Published On :: 2020-05-04T02:10:48-07:00 We document that the undifferentiated chaotic Ligurian Units of the Monferrato–Torino Hill sector (MO-TH) at the Alps–Apennines junction consist of three different units that are comparable with the Cassio, Caio and Sporno Units of the External Ligurian Units of the Northern Apennines. Their internal stratigraphy reflects the character of units deposited in an ocean–continent transition (OCT) zone between the northwestern termination of the Ligurian–Piedmont oceanic basin and the thinned passive margin of Adria microcontinent. The inherited wedge-shaped architecture of this OCT, which gradually closed toward the north in the present-day Canavese Zone, controlled the Late Cretaceous–early Eocene flysch deposition at the trench of the External Ligurian accretionary wedge during the oblique subduction. This favoured the formation of an accretionary wedge increasing in thickness and elevation toward the SE, from the MO-TH to the Emilia Northern Apennines. Our results therefore provide significant information on both the palaeogeographical reconstruction of the northwestern termination of the Ligurian–Piedmont oceanic basin and the role played by inherited along-strike variations (stratigraphy, structural architecture and morphology) of OCT zones in controlling subduction–accretionary processes. Supplementary material: A spreadsheet with X-ray fluorescence spectrometry and inductively coupled plasma mass spectrometry whole-rock major and trace element composition of mantle peridotites, and photomicrographs of mantle peridotites are available at https://doi.org/10.6084/m9.figshare.c.4519643 Full Article
io High-resolution carbon isotope stratigraphy of the Lower and Middle Ordovician succession of the Yangtze Platform, China: implications for global correlation By jgs.lyellcollection.org Published On :: 2020-05-04T02:10:48-07:00 The Lower and Middle Ordovician of the Yangtze Platform, China, is characterized by a sedimentary succession dominated by carbonate rocks. Three sections spanning the Nantsinkuan/Lunshan, Fenhsiang, Hunghuayuan, and Dawan/Zitai formations, corresponding to the Tremadocian–Dapingian in age, have been sampled for high-resolution 13C chemostratigraphy (542 samples in total). Our new 13C data reveal five tie-points with the potential for global correlation: (1) a positive 13C excursion in the lower Nantsinkuan Formation within the Tremadocian Rossodus manitouensis Zone; (2) an excursion with two peaks roughly within the late Tremadocian Paltodus ‘deltifer’ Zone; (3) a positive 13C shift in the lower Hunghuayuan Formation, within the early Floian Serratognathus diversus Zone; (4) a gradual positive 13C shift in the late Floian, ranging from the uppermost S. diversus Zone to the basal Oepikodus evae Zone; (5) a minor negative shift in the lower Dawan/Zitai Formation, within the early Dapingian Baltoniodus triangularis Zone. These excursions are herein used for correlation of the Yangtze Platform strata with successions from South China, North China, the Argentine Precordillera, North America and Baltica. From a palaeogeographical perspective the Gudongkou, Xiangshuidong and Daling sections represent depositional environments along an inner to outer ramp profile. 13C data from these sections show successively heavier (higher) 13C values with increasing depositional depth. This is interpreted as due to remineralization of organic carbon within the carbonate rocks. Supplementary material: Carbon and oxygen isotope data are available at: https://doi.org/10.6084/m9.figshare.c.4767080 Full Article
io Weathering history and landscape evolution of Western Ghats (India) from 40Ar/39Ar dating of supergene K-Mn oxides By jgs.lyellcollection.org Published On :: 2020-05-04T02:10:48-07:00 Laterites preserved on both sides of the Western Ghats Escarpment of Peninsular India have formed by long-term lateritic weathering essentially after India–Seychelles continental break-up following Deccan Traps emplacement (c. 63 myr ago). Supergene manganese ores of the Western Ghats were formed on Late Archean manganese protores. Among Mn oxides composing the ores, cryptomelane (K-rich Mn oxide) was characterized and dated by 40Ar/39Ar geochronology. Measured ages complement those previously obtained in other South Indian manganese ores from the hinterland plateau and further document three major weathering periods, c. 53–44, c. 39–22 and c. 14–10 Ma, the last being documented for the first time in India. These periods coincide with global palaeoclimatic proxies and date the lateritic weathering of three successive palaeolandscapes of the Western Ghats that evolved under slow denudation (c. 8 m Ma–1) over the last 44 myr and were mostly incised during the Neogene (<22 Ma). This indicates that the Western Ghats are a relict of a South Indian plateau preserved at the headwaters of very long east-flowing river systems and above the Western Ghats Escarpment. Topography and denudation history of this landscape do not require Neogene tilt of the Peninsula as recently proposed. Supplementary material: Full details of field and sample description, methods and analytical data including electron probe microanalyses of cryptomelane, and isotopic analyses and degassing spectra of irradiated cryptomelane grains are available at https://doi.org/10.6084/m9.figshare.c.4726661 Full Article
io Paleomagnetic and magnetic fabric data from Lower Triassic redbeds of the Central Western Carpathians: new constraints on the paleogeographic and tectonic evolution of the Carpathian region By jgs.lyellcollection.org Published On :: 2020-05-04T02:10:48-07:00 In the Central Western Carpathians (CWC), most published paleomagnetic results from Permo-Mesozoic rocks document extensive remagnetizations and come from thin-skinned thrust units that have undergone multistage deformation. We present results from lower Triassic redbeds from the autochthonous cover overlying the basement that carry a primary magnetization. Petromagnetic results indicate that the dominant ferromagnetic carrier is hematite, while magnetic susceptibility and its anisotropy are controlled by both ferromagnetic and paramagnetic minerals. Magnetic fabrics document weak deformation related to Late Cretaceous shortening. The directions of the high unblocking temperature remanence components pass both reversal and fold tests, attesting to their primary nature. Paleomagnetic inclinations are flatter than expected from reference datasets, suggesting small latitudinal separation between the CWC and stable Europe. Paleomagnetic declinations are mostly clustered within individual mountain massifs, implying their tectonic coherence. They show only minor differences between the massifs, indicating a lack of significant vertical-axis tectonic rotations within the studied central parts of the CWC. The paleomagnetic declinations are therefore representative of the whole of the CWC in terms of regional paleogeographic interpretations, and imply moderate counterclockwise rotations (c. 26°) of the region with respect to stable Europe since the Early Triassic. Full Article
io Layering and structural inheritance controls on fault zone structure in three dimensions: a case study from the northern Molasse Basin, Switzerland By jgs.lyellcollection.org Published On :: 2020-05-04T02:10:48-07:00 Mechanical heterogeneity of a sedimentary sequence exerts a primary control on the geometry of fault zones and the proportion of offset accommodated by folding. The Wildensbuch Fault Zone in the Swiss Molasse Basin, with a maximum throw of 40 m, intersects a Mesozoic section containing a thick (120 m) clay-dominated unit (Opalinus Clay) over- and underlain by more competent limestone units. Interpretation of a 3D seismic reflection survey indicates that the fault zone formed by upward propagation of an east–west-trending basement structure, through the Mesozoic section, in response to NE–SW Miocene extension. This configuration formed an array of left-stepping normal fault segments above and below the Opalinus Clay. In cross-section a broad monoclinal fold is observed in the Opalinus Clay. Folding, however, is not ubiquitous and occurs in the Opalinus Clay where fault segments above and below are oblique to one another; where they are parallel the fault passes through the Opalinus Clay with little folding. These observations demonstrate that, even in strongly heterogeneous sequences, here a four-fold difference in both Young's modulus and cohesion between layers, the occurrence of folding may depend on the local relationship between fault geometry and applied stress field rather than rheological properties alone. Full Article
io Basement-cover relationships and deformation in the Northern Paraguai Belt, central Brazil: implications for the Neoproterozoic-early Paleozoic history of western Gondwana By jgs.lyellcollection.org Published On :: 2020-05-04T02:10:48-07:00 The Northern Paraguai Belt, at the SE border of the Amazonian Craton, central Brazil, has been interpreted as a Brasiliano–Pan-African (c. 650–600 Ma) belt with a foreland basin, recording collisional polyphase tectonism and greenschist-facies metamorphism extending from the late Precambrian to the Cambrian–Ordovician. New structural investigations indicate that the older metasedimentary rocks of the Cuiabá Group represent a Tonian–Cryogenian basement assemblage deformed in two contemporaneous fault-bounded structural sub-domains of wrench-dominated (rake <10°) and contraction-dominated (rake ~30–40°) sinistral transpression, with tectonic vergence towards the SE. The younger late Cryogenian to early Cambrian sedimentary rocks lying to the NW of the Cuiabá Group are non-metamorphic and display only pervasive brittle transtension characterized by normal-oblique faults, fractures and forced drag folds with no consistent vergence pattern. Our analyses suggest that an unconformity separates the metasedimentary Cuiabá Group basement of the Northern Paraguai Belt from the unmetamorphosed sedimentary cover. It is proposed that the latter units were deposited during a post-glacial marine transgression (after c. 635 Ma) in a post-collisional basin. The Paraguai Belt basement and its post-collisional sedimentary cover share a number of significant geological similarities with sequences in the Bassarides Belt and Taoudéni Basin in the SW portion of the West African Craton. Full Article
io Geochronology and geochemistry of the Tabaquito batholith (Frontal Cordillera, Argentina): geodynamic implications and temporal correlations in the SW Gondwana margin By jgs.lyellcollection.org Published On :: 2020-05-04T02:10:48-07:00 The Tabaquito batholith (Frontal Cordillera, western Argentina), is mainly composed of shallowly emplaced granodiorite to minor monzogranite with abundant mafic microgranular enclaves. New sensitive high-resolution ion microprobe U–Pb zircon ages of c. 337 Ma (biotite granodiorite) and c. 284 Ma (mafic dyke) along with previously published geochronological data suggest that a long-lived magmatic system formed through at least two magmatic pulses at c. 337 and c. 322 Ma with later superimposition of Permian magmatism. The Tabaquito granitoids are metaluminous, calc-alkalic and magnesian with I-type affinity. Elevated Th/Nb, Y/Nb and La/Nb ratios along with negative Nb–Ta and positive Pb anomalies are consistent with a continental arc setting. Hf, Nd and Sr isotopic composition of the Tabaquito granitoids suggests that their source could result from mixing of an old felsic crustal component and a juvenile mafic to intermediate component. New geochronological and geochemical data together with published data reveal a continuous arc setting from the Carboniferous to the Permian in Argentina, and important magmatic compositional variations through time and space controlled by episodic fluctuations in the subduction angle of the oceanic plate. Reported and compiled data allow us to infer the continuity of the Carboniferous magmatic arc along the west margin of Gondwana. Supplementary material: Detailed petrography, analytical methods and data, zircon cathodoluminescence images and supplementary figures are available at https://doi.org/10.6084/m9.figshare.c.4763993 Full Article
io Protein Structure Facilitates High-Resolution Immunological Mapping [Commentary] By cvi.asm.org Published On :: 2017-12-05T08:00:30-08:00 Select agents (SA) pose unique challenges for licensing vaccines and therapies. In the case of toxin-mediated diseases, HHS assigns guidelines for SA use, oversees vaccine and therapy development, and approves animal models and approaches to identify mechanisms for toxin neutralization. In this commentary, we discuss next-generation vaccines and therapies against ricin toxin and botulinum toxin, which are regulated SA toxins that utilize structure-based approaches for countermeasures to guide rapid response to future biothreats. Full Article
io Progress toward Development of a Vaccine against Congenital Cytomegalovirus Infection [Minireviews] By cvi.asm.org Published On :: 2017-12-05T08:00:30-08:00 A vaccine against congenital human cytomegalovirus (CMV) infection is a major public health priority. Congenital CMV causes substantial long-term morbidity, particularly sensorineural hearing loss (SNHL), in newborns, and the public health impact of this infection on maternal and child health is underrecognized. Although progress toward development of a vaccine has been limited by an incomplete understanding of the correlates of protective immunity for the fetus, knowledge about some of the key components of the maternal immune response necessary for preventing transplacental transmission is accumulating. Moreover, although there have been concerns raised about observations indicating that maternal seropositivity does not fully prevent recurrent maternal CMV infections during pregnancy, it is becoming increasing clear that preconception immunity does confer some measure of protection against both CMV transmission and CMV disease (if transmission occurs) in the newborn infant. Although the immunity to CMV conferred by both infection and vaccination is imperfect, there are encouraging data emerging from clinical trials demonstrating the immunogenicity and potential efficacy of candidate CMV vaccines. In the face of the knowledge that between 20,000 and 30,000 infants are born with congenital CMV in the United States every year, there is an urgent and compelling need to accelerate the pace of vaccine trials. In this minireview, we summarize the status of CMV vaccines in clinical trials and provide a perspective on what would be required for a CMV immunization program to become incorporated into clinical practice. Full Article
io Development of an Extended-Specificity Multiplex Immunoassay for Detection of Streptococcus pneumoniae Serotype-Specific Antigen in Urine by Use of Human Monoclonal Antibodies [Diagnostic Laboratory Immunology] By cvi.asm.org Published On :: 2017-12-05T08:00:30-08:00 Current pneumococcal vaccines cover the 10 to 23 most common serotypes of the 92 presently described. However, with the increased usage of pneumococcal-serotype-based vaccines, the risk of serotype replacement and an increase in disease caused by nonvaccine serotypes remains. Serotype surveillance of pneumococcal infections relies heavily on culture techniques, which are known to be insensitive, particularly in cases of noninvasive disease. Pneumococcal-serotype-specific urine assays offer an alternative method of serotyping for both invasive and noninvasive disease. However, the assays described previously cover mainly conjugate vaccine serotypes, give little information about circulating nonvaccine serotypes, and are currently available only in one or two specialist laboratories. Our laboratory has developed a Luminex-based extended-range antigen capture assay to detect pneumococcal-serotype-specific antigens in urine samples. The assay targets 24 distinct serotypes/serogroups plus the cell wall polysaccharide (CWP) and some cross-reactive serotypes. We report that the assay is capable of detecting all the targeted serotypes and the CWP at 0.1 ng/ml, while some serotypes are detected at concentrations as low as 0.3 pg/ml. The analytical serotype specificity was determined to be 98.4% using a panel of polysaccharide-negative urine specimens spiked with nonpneumococcal bacterial antigens. We also report clinical sensitivities of 96.2% and specificities of 89.9% established using a panel of urine specimens from patients diagnosed with community-acquired pneumonia or pneumococcal disease. This assay can be extended for testing other clinical samples and has the potential to greatly improve serotype-specific surveillance in the many cases of pneumococcal disease in which a culture is never obtained. Full Article
io Identification of Novel Antigens Recognized by Serum Antibodies in Bovine Tuberculosis [Diagnostic Laboratory Immunology] By cvi.asm.org Published On :: 2017-12-05T08:00:30-08:00 Bovine tuberculosis (TB), caused by Mycobacterium bovis, remains an important zoonotic disease posing a serious threat to livestock and wildlife. The current TB tests relying on cell-mediated and humoral immune responses in cattle have performance limitations. To identify new serodiagnostic markers of bovine TB, we screened a panel of 101 recombinant proteins, including 10 polyepitope fusions, by a multiantigen print immunoassay (MAPIA) with well-characterized serum samples serially collected from cattle with experimental or naturally acquired M. bovis infection. A novel set of 12 seroreactive antigens was established. Evaluation of selected proteins in the dual-path platform (DPP) assay showed that the highest diagnostic accuracy (~95%) was achieved with a cocktail of five best-performing antigens, thus demonstrating the potential for development of an improved and more practical serodiagnostic test for bovine TB. Full Article
io Kinetics, Longevity, and Cross-Reactivity of Antineuraminidase Antibody after Natural Infection with Influenza A Viruses [Clinical Immunology] By cvi.asm.org Published On :: 2017-12-05T08:00:30-08:00 The kinetics, longevity, and breadth of antibodies to influenza virus neuraminidase (NA) in archival, sequential serum/plasma samples from influenza A virus (IAV) H5N1 infection survivors and from patients infected with the 2009 pandemic IAV (H1N1) virus were determined using an enzyme-linked lectin-based assay. The reverse-genetics-derived H4N1 viruses harboring a hemagglutinin (HA) segment from A/duck/Shan Tou/461/2000 (H4N9) and an NA segment derived from either IAV H5N1 clade 1, IAV H5N1 clade 2.3.4, the 2009 pandemic IAV (H1N1) (H1N1pdm), or A/Puerto Rico/8/1934 (H1N1) virus were used as the test antigens. These serum/plasma samples were also investigated by microneutralization (MN) and/or hemagglutination inhibition (HI) assays. Neuraminidase-inhibiting (NI) antibodies against N1 NA of both homologous and heterologous viruses were observed in H5N1 survivors and H1N1pdm patients. H5N1 survivors who were never exposed to H1N1pdm virus developed NI antibodies to H1N1pdm NA. Seroconversion of NI antibodies was observed in 65% of the H1N1pdm patients at day 7 after disease onset, but an increase in titer was not observed in serum samples obtained late in infection. On the other hand, an increase in seroconversion rate with the HI assay was observed in the follow-up series of sera obtained on days 7, 14, 28, and 90 after infection. The study also showed that NI antibodies are broadly reactive, while MN and HI antibodies are more strain specific. Full Article
io High-Definition Mapping of Four Spatially Distinct Neutralizing Epitope Clusters on RiVax, a Candidate Ricin Toxin Subunit Vaccine [Vaccines] By cvi.asm.org Published On :: 2017-12-05T08:00:29-08:00 RiVax is a promising recombinant ricin toxin A subunit (RTA) vaccine antigen that has been shown to be safe and immunogenic in humans and effective at protecting rhesus macaques against lethal-dose aerosolized toxin exposure. We previously used a panel of RTA-specific monoclonal antibodies (MAbs) to demonstrate, by competition enzyme-linked immunosorbent assay (ELISA), that RiVax elicits similar serum antibody profiles in humans and macaques. However, the MAb binding sites on RiVax have yet to be defined. In this study, we employed hydrogen exchange-mass spectrometry (HX-MS) to localize the epitopes on RiVax recognized by nine toxin-neutralizing MAbs and one nonneutralizing MAb. Based on strong protection from hydrogen exchange, the nine MAbs grouped into four spatially distinct epitope clusters (namely, clusters I to IV). Cluster I MAbs protected RiVax's α-helix B (residues 94 to 107), a protruding immunodominant secondary structure element known to be a target of potent toxin-neutralizing antibodies. Cluster II consisted of two subclusters located on the "back side" (relative to the active site pocket) of RiVax. One subcluster involved α-helix A (residues 14 to 24) and α-helices F-G (residues 184 to 207); the other encompassed β-strand d (residues 62 to 69) and parts of α-helices D-E (154 to 164) and the intervening loop. Cluster III involved α-helices C and G on the front side of RiVax, while cluster IV formed a sash from the front to back of RiVax, spanning strands b, c, and d (residues 35 to 59). Having a high-resolution B cell epitope map of RiVax will enable the development and optimization of competitive serum profiling assays to examine vaccine-induced antibody responses across species. Full Article
io High-Resolution Epitope Positioning of a Large Collection of Neutralizing and Nonneutralizing Single-Domain Antibodies on the Enzymatic and Binding Subunits of Ricin Toxin [Clinical Immunology] By cvi.asm.org Published On :: 2017-12-05T08:00:29-08:00 We previously produced a heavy-chain-only antibody (Ab) VH domain (VHH)-displayed phage library from two alpacas that had been immunized with ricin toxoid and nontoxic mixtures of the enzymatic ricin toxin A subunit (RTA) and binding ricin toxin B subunit (RTB) (D. J. Vance, J. M. Tremblay, N. J. Mantis, and C. B. Shoemaker, J Biol Chem 288:36538–36547, 2013, https://doi.org/10.1074/jbc.M113.519207). Initial and subsequent screens of that library by direct enzyme-linked immunosorbent assay (ELISA) yielded more than two dozen unique RTA- and RTB-specific VHHs, including 10 whose structures were subsequently solved in complex with RTA. To generate a more complete antigenic map of ricin toxin and to define the epitopes associated with toxin-neutralizing activity, we subjected the VHH-displayed phage library to additional "pannings" on both receptor-bound ricin and antibody-captured ricin. We now report the full-length DNA sequences, binding affinities, and neutralizing activities of 68 unique VHHs: 31 against RTA, 33 against RTB, and 4 against ricin holotoxin. Epitope positioning was achieved through cross-competition ELISAs performed with a panel of monoclonal antibodies (MAbs) and verified, in some instances, with hydrogen-deuterium exchange mass spectrometry. The 68 VHHs grouped into more than 20 different competition bins. The RTA-specific VHHs with strong toxin-neutralizing activities were confined to bins that overlapped two previously identified neutralizing hot spots, termed clusters I and II. The four RTB-specific VHHs with potent toxin-neutralizing activity grouped within three adjacent bins situated at the RTA-RTB interface near cluster II. These results provide important insights into epitope interrelationships on the surface of ricin and delineate regions of vulnerability that can be exploited for the purpose of vaccine and therapeutic development. Full Article
io Development of a High-Throughput Respiratory Syncytial Virus Fluorescent Focus-Based Microneutralization Assay [Diagnostic Laboratory Immunology] By cvi.asm.org Published On :: 2017-12-05T08:00:29-08:00 Neutralizing antibodies specific for respiratory syncytial virus (RSV) represent a major protective mechanism against RSV infection, as demonstrated by the efficacy of the immune-prophylactic monoclonal antibody palivizumab in preventing RSV-associated lower respiratory tract infections in premature infants. Accordingly, the RSV neutralization assay has become a key functional method to assess the neutralizing activity of serum antibodies in preclinical animal models, epidemiology studies, and clinical trials. In this study, we qualified a 24-h, fluorescent focus-based microneutralization (RSVA FFA-MN) method that requires no medium exchange or pre- or postinfection processing to detect green fluorescent protein-expressing RSV strain A2 (RSVA-GFP)-infected cells, using a high-content imaging system for automated image acquisition and focus enumeration. The RSVA FFA-MN method was shown to be sensitive, with a limit of detection (LOD) and limit of quantitation (LOQ) of 1:10, or 3.32 log2; linear over a range of 4.27 to 9.65 log2 50% inhibitory concentration (IC50); and precise, with intra- and interassay coefficients of variation of <21%. This precision allowed the choice of a statistically justified 3-fold-rise seroresponse cutoff criterion. The repeatability and robustness of this method were demonstrated by including a pooled human serum sample in every assay as a positive control (PC). Over 3 years of testing between two laboratories, this PC generated data falling within 2.5 standard deviations of the mean 98.7% of the time (n = 1,720). This high-throughput and reliable RSV microneutralization assay has proven useful for testing sera from preclinical vaccine candidate evaluation studies, epidemiology studies, and both pediatric and adult vaccine clinical trials. Full Article
io Stable Chromosomal Expression of Shigella flexneri 2a and 3a O-Antigens in the Live Salmonella Oral Vaccine Vector Ty21a [Vaccines] By cvi.asm.org Published On :: 2017-12-05T08:00:29-08:00 We have been exploring the use of the live attenuated Salmonella enterica serovar Typhi Ty21a vaccine strain as a versatile oral vaccine vector for the expression and delivery of multiple foreign antigens, including Shigella O-antigens. In this study, we separately cloned genes necessary for the biosynthesis of the Shigella flexneri serotype 2a and 3a O-antigens, which have been shown to provide broad cross-protection to multiple disease-predominant S. flexneri serotypes. The cloned S. flexneri 2a rfb operon, along with bgt and gtrII, contained on the SfII bacteriophage, was sufficient in Ty21a to express the heterologous S. flexneri 2a O-antigen containing the 3,4 antigenic determinants. Further, this rfb operon, along with gtrA, gtrB, and gtrX contained on the Sfx bacteriophage and oac contained on the Sf6 bacteriophage, was sufficient to express S. flexneri 3a O-antigen containing the 6, 7, and 8 antigenic determinants. Ty21a, with these plasmid-carried or chromosomally inserted genes, demonstrated simultaneous and stable expression of homologous S. Typhi O-antigen plus the heterologous S. flexneri O-antigen. Candidate Ty21a vaccine strains expressing heterologous S. flexneri 2a or 3a lipopolysaccharide (LPS) elicited significant serum antibody responses against both homologous S. Typhi and heterologous Shigella LPS and protected mice against virulent S. flexneri 2a or 3a challenges. These new S. flexneri 2a and 3a O-antigen-expressing Ty21a vaccine strains, together with our previously constructed Ty21a strains expressing Shigella sonnei or Shigella dysenteriae 1 O-antigens, have the potential to be used together for simultaneous protection against the predominant causes of shigellosis worldwide as well as against typhoid fever. Full Article
io Development and Qualification of an Opsonophagocytic Killing Assay To Assess Immunogenicity of a Bioconjugated Escherichia coli Vaccine [Vaccines] By cvi.asm.org Published On :: 2017-12-05T08:00:29-08:00 The global burden of disease caused by extraintestinal pathogenic Escherichia coli (ExPEC) is increasing as the prevalence of multidrug-resistant strains rises. A multivalent ExPEC O-antigen bioconjugate vaccine could have a substantial impact in preventing bacteremia and urinary tract infections. Development of an ExPEC vaccine requires a readout to assess the functionality of antibodies. We developed an opsonophagocytic killing assay (OPA) for four ExPEC serotypes (serotypes O1A, O2, O6A, and O25B) based on methods established for pneumococcal conjugate vaccines. The performance of the assay was assessed with human serum by computing the precision, linearity, trueness, total error, working range, and specificity. Serotypes O1A and O6A met the acceptance criteria for precision (coefficient of variation for repeatability and intermediate precision, ≤50%), linearity (90% confidence interval of the slope of each strain, 0.80, 1.25), trueness (relative bias range, –30% to 30%), and total error (total error range, –65% to 183%) at five serum concentrations and serotypes O2 and O25B met the acceptance criteria at four concentrations (the lowest concentration for serotypes O2 and O25B did not meet the system suitability test of maximum killing of ≥85% of E. coli cells). All serotypes met the acceptance criteria for specificity (opsonization index value reductions of ≤20% for heterologous serum preadsorption and ≥70% for homologous serum preadsorption). The assay working range was defined on the basis of the lowest and highest concentrations at which the assay jointly fulfilled the target acceptance criteria for linearity, precision, and accuracy. An OPA suitable for multiple E. coli serotypes has been developed, qualified, and used to assess the immunogenicity of a 4-valent E. coli bioconjugate vaccine (ExPEC4V) administered to humans. Full Article
io COVID-19 infection in a patient with multiple sclerosis treated with fingolimod By nn.neurology.org Published On :: 2020-05-05T12:45:12-07:00 In December 2019, a novel coronavirus causing an infectious respiratory disease (COVID-19) was identified, which since then has developed into a pandemic with higher rates of mortality in older individuals and those with underlying medical conditions.1 Multiple sclerosis (MS) is an immune-mediated neurologic disease which requires long-term treatment with immunotherapies that have been shown to increase the risk of infections.2 As a result, there is significant anxiety among patients and neurologists during the pandemic regarding the infection outcome in this patient population. We present a patient with MS treated with fingolimod who was diagnosed with COVID-19 and had a favorable outcome. Full Article
io Guillain-Barre syndrome related to COVID-19 infection By nn.neurology.org Published On :: 2020-04-29T12:45:09-07:00 At the time of this writing, healthcare systems are facing worldwide the pandemic of the coronavirus severe acute respiratory coronavirus 2 (SARS-COV-2) and its associated disease, named cronavirus disease 19 (COVID-19). This virus is a new human pathogen, and currently, there are no specific treatment options.1 COVID-19 mostly affects the respiratory system, ranging from mild flu-like symptoms to severe pneumonia, but extrarespiratory multisystemic involvement has also been reported.2 Li et al.3 recently described the neuroinvasive potential of COVID-19, but, to our knowledge, no case of acute dysimmune neuropathy has been described so far. Here, the authors report the case of an acute and severe peripheral nervous system disorder possibly related to COVID-19 infection. Full Article
io Single-cell RNA-seq analysis of human CSF microglia and myeloid cells in neuroinflammation By nn.neurology.org Published On :: 2020-05-05T12:45:12-07:00 Objective To identify and characterize myeloid cell populations within the CSF of patients with MS and anti-myelin oligodendrocyte glycoprotein (MOG) disorder by high-resolution single-cell gene expression analysis. Methods Single-cell RNA sequencing (scRNA-seq) was used to profile individual cells of CSF and blood from 2 subjects with relapsing-remitting MS (RRMS) and one with anti-MOG disorder. Publicly available scRNA-seq data from the blood and CSF of 2 subjects with HIV were also analyzed. An informatics pipeline was used to cluster cell populations by transcriptomic profiling. Based on gene expression by CSF myeloid cells, a flow cytometry panel was devised to examine myeloid cell populations from the CSF of 11 additional subjects, including individuals with RRMS, anti-MOG disorder, and control subjects without inflammatory demyelination. Results Common myeloid populations were identified within the CSF of subjects with RRMS, anti-MOG disorder, and HIV. These included monocytes, conventional and plasmacytoid dendritic cells, and cells with a transcriptomic signature matching microglia. Microglia could be discriminated from other myeloid cell populations in the CSF by flow cytometry. Conclusions High-resolution single-cell gene expression analysis clearly distinguishes distinct myeloid cell types present within the CSF of subjects with neuroinflammation. A population of microglia exists within the human CSF, which is detectable by surface protein expression. The function of these cells during immunity and disease requires further investigation. Full Article
io Dimethyl fumarate suppresses granulocyte macrophage colony-stimulating factor-producing Th1 cells in CNS neuroinflammation By nn.neurology.org Published On :: 2020-05-05T12:45:12-07:00 Objective To study the immunomodulatory effect of dimethyl fumarate (DF) on granulocyte macrophage colony-stimulating factor (GM-CSF) production in CD4+ T cells in experimental autoimmune encephalomyelitis (EAE) and human peripheral blood mononuclear cells (PBMCs). Methods We collected splenocytes and CD4+ T cells from C57BL/6 wild-type and interferon (IFN)-–deficient mice. For human PBMCs, venous blood was collected from healthy donors, and PBMCs were collected using the Percoll gradient method. Cells were cultured with anti-CD3/28 in the presence/absence of DF for 3 to 5 days. Cells were stained and analyzed by flow cytometry. Cytokines were measured by ELISA in cell supernatants. For in vivo experiments, EAE was induced by myelin oligodendrocyte glycoprotein35–55 and mice were treated with oral DF or vehicle daily. Results DF acts directly on CD4+ T cells and suppresses GM-CSF–producing Th1 not Th17 or single GM-CSF+ T cells in EAE. In addition, GM-CSF suppression depends on the IFN- pathway. We also show that DF specifically suppresses Th1 and GM-CSF–producing Th1 cells in PBMCs from healthy donors. Conclusions We suggest that DF exclusively suppresses GM-CSF–producing Th1 cells in both animal and human CD4+ T cells through an IFN-–dependent pathway. These findings indicate that DF has a better therapeutic effect on patients with Th1-dominant immunophenotype. However, future longitudinal study to validate this finding in MS is needed. Full Article
io Risk of MS relapse after yellow fever vaccination: A self-controlled case series By nn.neurology.org Published On :: 2020-05-01T12:45:10-07:00 Objective To determine whether live-attenuated yellow fever vaccine (YFV) was associated with MS relapse, we evaluated the clinical courses of 23 patients in the year before and the year after immunization at the university hospital of Geneva, Switzerland. Methods This self-controlled retrospective cohort included adult patients with MS receiving YFV between 2014 and 2018 and defined the year before vaccination, the 3 months thereafter, and the 9 months following as the pre-exposure (PEP), exposure-risk (ERP), and postrisk (PRP) periods, respectively. The primary outcome was the relative incidence of relapse in the ERP vs the PEP. Secondary end points included the presence of new T2-weighted (T2) or T1-weighted gadolinium-positive (T1Gd+) MRI lesions. Results Of 23 patients with MS receiving YFV (20 relapsing MS and 3 primary progressive MS), 17 (74%) were women; mean age was 34 years (SD ±10); and 10 of 23 (40%) were treated with disease-modifying therapies (DMTs). Although 9 patients experienced 12 relapses in the PEP, only one experienced a relapse in the ERP; 3 other patients experienced one relapse each in the PRP. None of the 8 patients receiving natalizumab at the time of vaccination experienced relapse thereafter. In the PEP, ERP, and PRP, 18, 2, and 9 patients had new brain and/or spinal cord lesions on T2 or T1Gd + MRI, respectively. Conclusions In this cohort, YF vaccination was associated with neither an increase in MS relapse nor emergence of brain and/or spinal lesions. Further studies are warranted to confirm these findings. Classification of evidence This study provides Class IV evidence that for persons with MS, YFV may not increase relapse risk. Full Article
io Monoclonal antibody treatment during pregnancy and/or lactation in women with MS or neuromyelitis optica spectrum disorder By nn.neurology.org Published On :: 2020-04-23T12:45:10-07:00 Objective To assess possible adverse effects on breastfed infants of mothers receiving monoclonal antibodies (MAbs) during pregnancy and/or lactation. Methods We identified 23 patients from the German Multiple Sclerosis and Pregnancy Registry (DMSKW) who received MAbs (17 natalizumab and 6 anti-CD20) during lactation. Thirteen were already exposed to natalizumab during the third trimester of pregnancy, and 1 received ocrelizumab during pregnancy. Data were obtained from standardized, telephone-administered questionnaires completed by the mother during pregnancy and at 1, 3, 6, and 12 months postpartum. Natalizumab concentration in mother’s milk was analyzed in 3 patients and natalizumab serum concentration in 2 of these patients and their breastfed infants. Results We did not observe a negative impact on infant health and development attributable to breast milk exposure after a median follow-up of 1 year. Infants exposed to natalizumab during the third trimester had a lower birth weight and more hospitalizations in the first year of life. The concentration of natalizumab in breast milk and serum of infants was low; B cells normal in infants breastfed under anti-CD20. Conclusion More data on the effect of Mab exposure during pregnancy are needed. Otherwise, our data suggest that treatment with natalizumab, ocrelizumab, or rituximab during lactation might be safe for breastfed infants. Full Article
io Ocrelizumab initiation in patients with MS: A multicenter observational study By nn.neurology.org Published On :: 2020-04-09T14:01:03-07:00 Objective To provide first real-world experience on patients with MS treated with the B cell–depleting antibody ocrelizumab. Methods We retrospectively collected data of patients who had received at least 1 treatment cycle (2 infusions) of ocrelizumab at 3 large neurology centers. Patients' characteristics including premedication, clinical disease course, and documented side effects were analyzed. Results We could identify 210 patients (125 women, mean age ± SD, 42.1 ± 11.4 years) who had received ocrelizumab with a mean disease duration of 7.3 years and a median Expanded Disability Status Scale score of 3.75 (interquartile range 2.5–5.5; range 0–8). Twenty-six percent of these patients had a primary progressive MS (PPMS), whereas 74% had a relapsing-remitting (RRMS) or active secondary progressive (aSPMS) disease course. Twenty-four percent of all patients were treatment naive, whereas 76% had received immune therapies before. After ocrelizumab initiation (median follow-up was 200 days, range 30–1,674 days), 13% of patients with RRMS/aSPMS experienced a relapse (accounting for an annualized relapse rate of 0.17, 95% CI 0.10–0.24), and 5% of all patients with MS experienced a 12-week confirmed disability progression. Treatment was generally well tolerated, albeit only short-term side effects were recorded, including direct infusion-related reactions and mild infections. Conclusions We provide class IV evidence that treatment with ocrelizumab can stabilize naive and pretreated patients, indicating that ocrelizumab is an option following potent MS drugs such as natalizumab and fingolimod. Further studies are warranted to confirm these findings and to reveal safety concerns in the longer-term follow-up. Classification of evidence This study provides Class IV evidence that for patients with MS, ocrelizumab can stabilize both treatment-naive and previously treated patients. Full Article
io Monitoring of radiologic disease activity by serum neurofilaments in MS By nn.neurology.org Published On :: 2020-04-09T14:01:03-07:00 Objective To determine whether serum neurofilament light chain (sNfL) levels are associated with recent MRI activity in patients with relapsing-remitting MS (RRMS). Methods This observational study included 163 patients (405 samples) with early RRMS from the Study of Early interferon-beta1a (IFN-β1a) Treatment (SET) cohort and 179 patients (664 samples) with more advanced RRMS from the Genome-Wide Association Study of Multiple Sclerosis (GeneMSA) cohort. Based on annual brain MRI, we assessed the ability of sNfL cutoffs to reflect the presence of combined unique active lesions, defined as new/enlarging lesion compared with MRI in the preceding year or contrast-enhancing lesion. The probability of active MRI lesions among patients with different sNfL levels was estimated with generalized estimating equations models. Results From the sNfL samples ≥90th percentile, 81.6% of the SET (OR = 3.4, 95% CI = 1.8-6.4) and 48.9% of the GeneMSA cohort samples (OR = 2.6, 95% CI = 1.7-3.9) was associated with radiological disease activity on MRI. The sNfL level between the 10th and 30th percentile was reflective of negligible MRI activity: 1.4% (SET) and 6.5% (GeneMSA) of patients developed ≥3 active lesions, 5.8% (SET) and 6.5% (GeneMSA) developed ≥2 active lesions, and 34.8% (SET) and 11.8% (GeneMSA) showed ≥1 active lesion on brain MRI. The sNfL level <10th percentile was associated with even lower MRI activity. Similar results were found in a subgroup of clinically stable patients. Conclusions Low sNfL levels (≤30th percentile) help identify patients with MS with very low probability of recent radiologic disease activity during the preceding year. This result suggests that in future, sNfL assessment may substitute the need for annual brain MRI monitoring in considerable number (23.1%–36.4%) of visits in clinically stable patients. Full Article
io The identification and mitigation of geohazards using shallow airborne engineering geophysics and land-based geophysics for brown- and greenfield road investigations By qjegh.lyellcollection.org Published On :: 2020-05-01T00:46:18-07:00 South Africa is a mineral-rich country with a diverse geology and a long history of mining. The rich history of mining activities includes the extraction of coal from the Ecca Group Sediments of the Karoo Supergroup (250 Ma), gold and uranium from the Witwatersrand Supergroup (2900 Ma), as well as platinum, uranium, tin and lead from the layered Bushveld Igneous Complex (BIC) (2150 Ma). The extraction of gold, copper, tin, lead and rare earth minerals also took place in the Archean rocks of Swazium age (3500–3000 Ma). The historical mining records have either not been accurately recorded or have been lost over time. This has resulted in significant geohazard risk during infrastructure development, especially in and around historical mining towns, such as Johannesburg and Ermelo. These geohazard risks require careful appraisal and quantification prior to any infrastructure design or construction. This case study aims to set out the development aspects of the Multi-Faceted Geophysical Modelling Systems approach, which was used by the South African National Roads Agency SOC Ltd (SANRAL) during an investigation of undermined ground for the historical coal-mining town of Ermelo in South Africa. The N11/N2 ring road was planned to go around Ermelo to ensure mobility between major routes, whilst still maintaining town access. The systems approach used a combination of airborne geophysics (Versatile Time Domain Electromagnetic System (VTEMTM) and magnetics), generally used in mining exploration, land-based and borehole geophysics, borehole water testing, and ground-truthing. The approach was continuous and iterative, building on the data at hand and reducing unnecessary investigations while eliminating the possibility of anomalies being missed, as in the case of conventional discrete drilling. The investigation ensured that 100% of the route was comprehensively investigated with a high confidence in the geological and geophysical data, and concomitant mitigation of infrastructure risk. The Multi-Faceted Geophysical Modelling Systems approach was successfully used to identify a previously unknown 1 x 1 m mining stope cavity at 90 m depth and a 3 x 5 m access tunnel at 24 m depth in a timely and cost-effective manner. Seven reverse-circulation percussion boreholes confirmed the structural integrity of these underground cavities, as well as the structural geology along the centreline. Based on the great success achieved in identifying shallow anomalies, this Multi-Faceted Geophysical Modelling Systems approach is now being considered for field trails on the dolomitic formations and the Wild Coast greenfields road project where there are large historical slumps and many fault lines. Thematic collection: This article is part of the Ground-related risk to transportation infrastructure collection available at https://www.lyellcollection.org/cc/Ground-related-risk-to-transportation-infrastructure Full Article
io Void ratio-permeability relations for clays By qjegh.lyellcollection.org Published On :: 2020-05-01T00:46:18-07:00 In spite of the Kozeny–Carman formula having been applied effectively to sands, there is at present no generally accepted explanation for why it is inadequate for clays. The impermeable adsorbed water layer surrounding the soil particles throws further light on the issue. By introducing the pervious void ratio, which accounts for the effective voids that a fluid flows through, a modified Kozeny–Carman formula is presented. The results presented here show that the modified Kozeny–Carman formula predicts fairly well the hydraulic conductivity of clays, especially for fine-grained soils. Full Article
io A large palaeo-landslide reactivated by high-speed railway construction works (northern Spain) By qjegh.lyellcollection.org Published On :: 2020-05-01T00:46:18-07:00 The presence of large palaeo-landslides can hinder the construction of railway lines if they cause an alteration of the natural balance of the slope, significantly increasing the cost of the project. During the construction works in a section of the Madrid–Asturias high-speed railway line (Spain), a large-scale hillside instability affected 460 m of the section. The ground movement began 10 months after the start of the excavations and remained active throughout the observation period (2008–2010). Data provided by fieldwork, boreholes and instrumental monitoring have allowed the investigation of the geological units involved, together with the geometry and the kinematics of the mass movement. This landslide involves a Paleozoic basement with an estimated volume of 4 400 000 m3. It shows low displacement rates (<45 mm a–1) and was accommodated on a single surface of rupture, which reaches more than 60 m depth. The kinematics is favoured by structural and lithological conditions, there being a strong rheological contrast in the lower part of the mobilized ground. This movement is linked to a large palaeo-landslide that was partially reactivated when excavations undermined the lower slopes of the hillside. Technical solutions for the stabilization have already caused an additional cost of 17% over the initial budget. Full Article
io Effect of depositional water content on the collapsibility of a reconstituted loess By qjegh.lyellcollection.org Published On :: 2020-05-01T00:46:18-07:00 Loess, a wind-blown silty soil, can be deposited under a variety of moisture conditions, including dry deposition, wet deposition and gravitational settling of aggregations formed in moist air by capillary forces at grain contacts. This experimental study uses single and double oedometer tests to assess the effect of depositional water content on the collapse potential of reconstituted samples of the Langley Silt Member, known as Brickearth, a natural loessic soil. A freefall sample preparation technique was used to mimic loess formation and environmental scanning electron microscopy was used to relate the observed behaviour to sample fabric. The results show that loess deposited at higher water contents has a greater collapse potential, which is shown to be related to its looser, more granular fabric. Full Article
io A case study for identification of organic-silt bottom sediments in an artificial lake formed in gravel alluvium in the geotourism locality of Slnecne Jazera in Senec (Bratislava, Slovakia) By qjegh.lyellcollection.org Published On :: 2020-05-01T00:46:18-07:00 This case study aims to identify the cubic capacity and geometry of the geological body of silt–organic sediments in the environment of a former gravel pit situated in a drainless depression of the alluvium of the Čierna voda River. It is located in the well-known geotourism locality of Slnečné Jazera in Senec, in the SW of Slovakia. To identify the body, electrical resistivity tomography was combined with the use of sonar. The research shows that this approach is appropriate for a number of activities that are subjects of engineering-geological investigations. The cubic capacity and geometry of specific aqueous engineering-geological environments must be determined in connection with the need for the management, control, quantification and extraction of selected sedimentary bodies. In addition, the management of sustainable development of reservoirs, sedimentation basins, industrial ponds, settling pits and natural pools for recreation (the subject of the case study) is important to control the limit amounts of sediments in such environments. The results of this study may be applied in analogous engineering-geological conditions. The drainless depression Slnečné Jazera contained a body of silt–organic sediments amounting to 23 000 m3 (41 Olympic-size pools of 25 m x 12.5 m x 1.8 m). The maximum thickness of the bottom sediments was about 6.3 m on the alluvium with an articulated morphology owing to the submerged digging of gravel. The proposed approach improved the control of extraction of the sedimentary body and optimized the engineering-geological conditions in this geotourism locality. Full Article
io The shear stiffness criterion for rock joints considering rock wear behaviour By qjegh.lyellcollection.org Published On :: 2020-05-01T00:46:18-07:00 Rock is a material that is affected by wear, and the curvature of the asperities on a rock joint surface increases with the degree of wear after shearing. Based on the Greenwood and Williamson (GW) model, a new model considering the change of asperity curvature is proposed to explain the wear behaviour of rock joints. First, the shear stiffness formula for a joint surface is derived when the asperity curvature is constant, which shows that the shear stiffness increases with increase of asperity curvature. According to the Mohr–Coulomb criterion, the yield position of a single asperity under normal force and tangential friction force is discussed. Then, the critical normal force for a single asperity at a specific friction coefficient is obtained, which shows that the normal force corresponds to the curvature radius of the asperity. A rough surface model with multi-level curvature radius is proposed. With increase of normal force, the higher-order asperities gradually fail and the curvature radius become larger. A specific pressure value excites a specific radius of curvature, and the larger the pressure, the larger the radius of curvature. The relation between the normal force and the curvature radius is proposed and a shear stiffness formula considering the change of curvature radius of the asperity is derived. The proposed model is verified on the basis of the published experimental results. The calculation results of the proposed model can reflect the test results well: for a given joint surface, with increase in normal force the joint surface gradually becomes smooth; for different joint surfaces, with increase in roughness, the joint surface is more easily smoothed. Full Article
io Prediction of tunnelling impact on flow rates of adjacent extraction water wells By qjegh.lyellcollection.org Published On :: 2020-05-01T00:46:18-07:00 The decline or drying up of groundwater sources near a tunnel route is damaging to groundwater users. Therefore, forecasting the impact of a tunnel on nearby groundwater sources is a challenging task in tunnel design. In this study, numerical and analytical approaches were applied to the Qomroud water conveyance tunnel (located in Lorestan province, Iran) to assess the impact of tunnelling on the nearby extraction water wells. Using simulation of groundwater-level fluctuation owing to tunnelling, the drawdown at the well locations was determined. From the drawdowns and using Dupuit's equation, the depletion of well flow rates after tunnelling was estimated. To evaluate the results, observed well flow rates before and after tunnelling were compared with the predicted flow rates. The observed and estimated water well flows (before and after tunnelling) showed a regression factor of 0.64, pointing to satisfactory results Full Article
io Groundwater chemical characteristics and circulation mode in the Suixiao coal-mining district By qjegh.lyellcollection.org Published On :: 2020-05-01T00:46:18-07:00 Groundwater recharge and runoff conditions are ascertained in the Suixiao coal-mining district using the hydrogen and oxygen isotopes and the trace elements in the unconsolidated pore aquifer of the Cenozoic group, the fissured sandstone aquifer of the Permian system, and the karst fissured limestone aquifer of the Carboniferous Taiyuan Formation and the Ordovician system, which are the main recharge aquifers during coal mining. The main water–rock interactions are pyrite oxidation, cation exchange and adsorption, and carbonate acidification, which are educed by principal component analysis of conventional ions. These results combined with geological conditions prove that hydraulic connection exists generally between the main recharge aquifers, and the groundwater circulation is controlled by faults in the sandstone and limestone aquifers. The water–rock interaction is very weak in the east of the district, which is proved to be a recharge area by Fisher discriminant analysis. This study provides the theoretical basis for the hydrochemistry exploration and the establishment of a water-inrush warning system in a concealed coalfield. Full Article
io The origin and pedogenesis of the Clay-with-flints Formation By qjegh.lyellcollection.org Published On :: 2020-05-01T00:46:18-07:00 The Clay-with-flints Formation outcrops on the high chalk plateaux and interfluves of the chalk downs in southern England. Both current and historical definitions of the Clay-with-flints are detailed and important distinctions are identified with other deposits that appear identical but are formed in different ways. Historically pedological or geomorphological studies have been carried out on the deposit. Engineering studies are only carried out where the deposit is crossed by infrastructure. The physical and chemical processes acting on the deposit and the resulting effects on the physical properties are discussed. Full Article