Deep to shallow-marine sedimentology and impact of volcanism within the Middle Triassic Palaeo-Tethyan Semantan Basin, Singapore

The Middle Triassic Pulau Ayer Chawan Formation is a predominantly deep-marine, occasionally shallow-marine sedimentary succession, deposited in the Singapore sector of the Palaeo-Tethyan Semantan Basin. The formation provides an important record of the dynamic interplay between a siliciclastic sedimentary system and the products of an adjacent active volcanic arc. It is characterised by six sub-environments, including: deep-marine turbidite fan, deep-marine background sedimentation, subaqueous debris cone, shallow-marine, volcanically-sourced turbidite fan, and hyaloclastite mound or ridge. Turbidite fan deposits preserve the input of both siliciclastic and volcaniclastic sediments from the shelf, transported into the deep-marine environment by a suite of subaqueous sediment gravity flow processes, including: turbidity currents; mixed flow types (hybrid event beds); concentrated and hyper concentrated sediment gravity flows, and debris flows. Thick heterolithic successions of debrites were likely sourced through regular collapse of an unstable shelf. The presence of hybrid event beds, encountered within the deep-marine turbidite fans, supports a slope that was out-of-grade, and may have been actively retreating towards the hinterland. Together, these factors suggest regional-scale uplift of the eastern margins of the Semantan Basin during Triassic times, most likely facilitated through volcanic activity in the adjacent Palaeo-Tethys Sukhothai Arc. Evidence for contemporaneous, arc-related magmatism includes ubiquitous volcaniclastic sedimentary rocks within formation, including pyroclastic density current deposits and perhaps more-strikingly through the hyaloclastites of the Nanyang Member. The hyaloclastites formed through quenching of magmas delivered into the deep-marine setting from a series of sub-sea vents or mounds

Yield envelope assessment as a preliminary screening tool to determine carbon capture and storage viability in depleted southern north-sea hydrocarbon reservoirs

This paper describes a laboratory study of the hydro-mechanical properties of samples from the Sherwood Sandstone Group (SSG), an onshore analogue of the finer grained, lower porosity portions that make up the Bunter Sandstone Formation (BSF). The study provides a yield envelope for this sandstone, and demonstrates that it is a competent sandstone at relevant reservoir depths. A theoretical yield envelope has been calculated based on the anticipated in situ stress induced by depletion and reinjection, showing that only the high porosity (35%), large grain diameter (290 µm) end-member of the BSF is likely to result in deformation of the reservoir rock. Stress analysis of four fields within the Southern North Sea suggest that depletion of 10 MPa will not result in permanent deformation of the reservoirs assuming similar porosity and grainsize characteristics to the SSG tested. Furthermore, re-inflation is unlikely to result in permanent deformation should the injection pressure not exceed the initial pre-production reservoir pore pressure

Paleozoic to Cenozoic sedimentary bedrock geology and lithostratigraphy of Singapore

A new lithostratigraphical framework for Singapore is proposed, based on the analysis of c. 20,000 m of core recovered from 121 c. 205 m deep boreholes and augmented with 218 field localities from across Singapore. The new framework describes a succession dating from the Carboniferous to the Quaternary. New U-Pb detrital zircon dates and fossil analysis were used to constrain the ages of key sedimentary units. The oldest known sedimentary rocks in Singapore are found to be the deformed Carboniferous (Mississippian) Sajahat Formation. These are succeeded by the newly erected, Middle and Upper Triassic, marine to continental Jurong Group and Sentosa Group successions that accumulated in the southern part of the Semantan Basin. The Jurong Group comprises four formations: the Tuas Formation, the Pulau Ayer Chawan Formation, the Pandan Formation and the Boon Lay Formation. The Sentosa Group contains two formations: the Tanjong Rimau Formation and the Fort Siloso Formation. In Singapore, the depositional record during this time is related to late Permian to Triassic arc magmatism in the southern part of the forearc basin to the Sukhothai Arc. The Jurong and Sentosa groups were deformed and weakly metamorphosed during the final stages of the Late Triassic to Early Jurassic orogenic event, deformation that led to the formation of the syn-orogenic conglomerates of the Buona Vista Formation. Following this, two distinct Lower Cretaceous sedimentary successions overstepped the Jurong and Sentosa group strata, including the Kusu Formation and the Bukit Batok Formation, both deposited in the southern part of the Tembeling Basin. A series of Neogene to Quaternary formations overly the Mesozoic and Palaeozoic stratigraphy, including the Fort Canning Formation, Bedok Formation and the Kallang Group

The Glasgow (Scotland) geotechnical GIS: a desk study tool

Desk study is an essential part of all civil engineering project ground investigations. It is usually a collation and review of existing data and information about a site and, in some cases, the surrounding area, and carried out at an early stage of the ground investigation to inform and guide the ground investigation. It should provide suitable data and information to assess the ground conditions and the implications for the proposed engineering design. A similar approach can be taken to inform local, regional or national government with regard to development and the redevelopment of urban areas where ground investigation data and information are available. This paper describes a spatially defined geotechnical information system (GIS) designed to provide geological, geotechnical and geoenvironmental data and information for Glasgow City Council (Scotland). The system contains three main parts: the geology (bedrock, Quaternary and artificial deposits and the thickness and depth of these deposits); the data are presented as various summary graphs illustrating the variation of various parameters as well as a geotechnical and geoenvironmental database; and tools specifically developed to present the data. As undermining is a hazard in part of Glasgow, a dataset showing the distribution of mining is included. Further interpretation of the characteristics of the geological units has produced an engineering geological classification which may be used to provide rapid assessment of the engineering geological conditions

An Injection System for the CHIME/FRB Experiment

Dedicated surveys searching for Fast Radio Bursts (FRBs) are subject to selection effects which bias the observed population of events. Software injection systems are one method of correcting for these biases by injecting a mock population of synthetic FRBs directly into the realtime search pipeline. The injected population may then be used to map intrinsic burst properties onto an expected signal-to-noise ratio (SNR), so long as telescope characteristics such as the beam model and calibration factors are properly accounted for. This paper presents an injection system developed for the Canadian Hydrogen Intensity Mapping Experiment Fast Radio Burst project (CHIME/FRB). The system was tested to ensure high detection efficiency, and the pulse calibration method was verified. Using an injection population of ~85,000 synthetic FRBs, we found that the correlation between fluence and SNR for injected FRBs was consistent with that of CHIME/FRB detections in the first CHIME/FRB catalog. We also noted that the sensitivity of the telescope varied strongly as a function of the broadened burst width, but not as a function of the dispersion measure. We conclude that some of the machine-learning based Radio Frequency Interference (RFI) mitigation methods used by CHIME/FRB can be re-trained using injection data to increase sensitivity to wide events, and that planned upgrades to the presented injection system will allow for determining a more accurate CHIME/FRB selection function in the near future.Comment: 13 pages, 8 figures. Submitted to A

3DKL v1.0: creating the first 3D geological model of Kuala Lumpur

The objective of UN Sustainable Development Goal 11 is to make cities and human settlements inclusive, safe, resilient and sustainable. Geoscience can play a significant role in achieving targets within this goal by developing a better understanding of geological properties and processes within urban environments, and by ensuring that this understanding is integrated into urban development. A key step in this process will be enhancing awareness of urban geology among non-geoscience decision-makers, so that inherent subsurface risks and benefits are understood and accounted for during all phases of development. Three-dimensional geological models are an effective tool for geologists to communicate with stakeholders in government and industry during that process. They can also provide a framework to enable geological data and information to be integrated into Building and City Information Models, and thus facilitate more effective infrastructure and utility asset management. This paper describes the modelling workflow adopted by a consortium of geoscientists from government, industry and academia to deliver the first 3D geological model of Kuala Lumpur – 3DKL v1.0. The modelling workflow involved: digitising borehole logs from site investigation reports and storing them in a dedicated geospatially-enabled SQLite borehole database; viewing and interpreting that borehole data using QGIS software; generating multiple orthogonally oriented cross-section profiles across the modelled area using Groundhog Desktop software; and integrating the information derived from the interpreted boreholes, surface data and cross-section profiles to generate a 3D geological model in Leapfrog Geo software. 3DKL v1.0 has demonstrated proof-of-concept: we have developed a workflow, based largely on freely-available software, for transforming borehole information, previously captured in paper records, into a conceptual 3D model. The modelling process has also identified areas where geological knowledge and data need to be enhanced if 3DKL is to fulfil its potential to support more sustainable and resilient urban development in Kuala Lumpur

Sub-second periodicity in a fast radio burst

Fast radio bursts (FRBs) are millisecond-duration flashes of radio waves that are visible at distances of billions of light-years. The nature of their progenitors and their emission mechanism remain open astrophysical questions. Here we report the detection of the multi-component FRB 20191221A and the identification of a periodic separation of 216.8(1) ms between its components with a significance of 6.5 sigmas. The long (~3 s) duration and nine or more components forming the pulse profile make this source an outlier in the FRB population. Such short periodicity provides strong evidence for a neutron-star origin of the event. Moreover, our detection favours emission arising from the neutron-star magnetosphere, as opposed to emission regions located further away from the star, as predicted by some models.Comment: Updated to conform to the accepted versio

Molecular mechanisms and cellular functions of cGAS-STING signalling

The cGAS–STING signalling axis, comprising the synthase for the second messenger cyclic GMP–AMP (cGAS) and the cyclic GMP–AMP receptor stimulator of interferon genes (STING), detects pathogenic DNA to trigger an innate immune reaction involving a strong type I interferon response against microbial infections. Notably however, besides sensing microbial DNA, the DNA sensor cGAS can also be activated by endogenous DNA, including extranuclear chromatin resulting from genotoxic stress and DNA released from mitochondria, placing cGAS–STING as an important axis in autoimmunity, sterile inflammatory responses and cellular senescence. Initial models assumed that co-localization of cGAS and DNA in the cytosol defines the specificity of the pathway for non-self, but recent work revealed that cGAS is also present in the nucleus and at the plasma membrane, and such subcellular compartmentalization was linked to signalling specificity of cGAS. Further confounding the simple view of cGAS–STING signalling as a response mechanism to infectious agents, both cGAS and STING were shown to have additional functions, independent of interferon response. These involve non-catalytic roles of cGAS in regulating DNA repair and signalling via STING to NF-κB and MAPK as well as STING-mediated induction of autophagy and lysosome- dependent cell death. We have also learnt that cGAS dimers can multimerize and undergo liquid–liquid phase separation to form biomolecular condensates that could importantly regulate cGAS activation. Here, we review the molecular mechanisms and cellular functions underlying cGAS–STING activation and signalling, particularly highlighting the newly emerging diversity of this signalling pathway and discussing how the specificity towards normal, damage-induced and infection-associated DNA could be achieved

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead