A sequential dynamic Bayesian network for pore pressure estimation with uncertainty quantification

Pore-pressure estimation is an important part of oil-well drilling, since drilling into unexpected highly pressured fluids can be costly and dangerous. However, standard estimation methods rarely account for the many sources of uncertainty, or for the multivariate nature of the system. We propose the pore pressure sequential dynamic Bayesian network (PP SDBN) as an appropriate solution to both these issues. The PP SDBN models the relationships between quantities in the pore pressure system, such as pressures, porosity, lithology and wireline log data, using conditional probability distributions based on geophysical relationships to capture our uncertainty about these variables and the relationships between them. When wireline log data is given to the PP SDBN, the probability distributions are updated, providing an estimate of pore pressure along with a probabilistic measure of uncertainty that reflects the data acquired and our understanding of the system. This is the advantage of a Bayesian approach. Our model provides a coherent statistical framework for modelling the pore pressure system. The specific geophysical relationships used can be changed to better suit a particular setting, or reflect geoscientists’ knowledge. We demonstrate the PP SDBN on an offshore well from West Africa. We also perform a sensitivity analysis, demonstrating how this can be used to better understand the working of the model and which parameters are the most influential. The dynamic nature of the model makes it suitable for real time estimation during logging while drilling. The PP SDBN models shale pore pressure in shale rich formations with mechanical compaction as the overriding source of overpressure. The PP SDBN improves on existing methods since it produces a probabilistic estimate that reflects the many sources of uncertainty present

Fishes of the Cocos (Keeling) Islands: new records, community composition and biogeographic significance

The Cocos (Keeling) Islands comprise the most isolated oceanic atoll in the tropical Indian Ocean and are situated 1000 km south-west of Indonesia. The remoteness of the islands has shaped the composition of marine communities but also limited scientific research. This study summarises field research on the marine fishes of the Cocos (Keeling) Islands over the last 14 years (2001–2014). Sixty-seven new records (from 28 families) are described and raise the total number of known fishes to 602 species from 84 families. New records span a variety of body sizes (3 cm TL Gobiodon unicolor to 500 cm TL Rhincodon typus), were observed in all major habitats,and found at both the Southern Atoll and at North Keeling Island. Notable new records include first records for the families Alopiidae, Coryphaenidae, Eleotridae, Gempylidae, Istiophoridae, Molidae, Polymixiidae, Rhincodontidae, Sillaginidae and Xiphiidae. Sampling from pelagic and deepwater (60–300 m) reef environments significantly increased the number of species described from these habitats. New records include species that have dispersed more than 2500 km (Centropyge acanthops) and dispersal ability appears to explain the lack of syngnathids and the high representation of acanthurids and holocentrids in the community. Some of the Indian Ocean species that have colonised the Cocos (Keeling) Islands now co-occur with their Pacific Ocean sister species, increasing the potential for hybridisation. Although the fish community of the Cocos (Keeling) Island resembles that of the Indo-West Pacific, the isolation and co-occurrence of Indian and Pacific Ocean species distinguishes it from all other locations

Checklist and new records of Christmas Island fishes: the influence of isolation, biogeography and habitat availability on species abundance and community composition

Christmas Island (Indian Ocean) is an oceanic high island that is situated 300 km southwest of Java, Indonesia. From 2010 to 2014, the fish community of Christmas Island was surveyed using underwater visual surveys for shallow water (0–60 m) fishes, and line fishing (bottom fishing and trolling) for deepwater (60–300 m) and pelagic fishes. Forty-seven new records (from 22 families) were identified, thereby increasing the total number of fishes described from Christmas Island to 681 (from 91 families). Notable new records include the first records for the families Alopiidae, Anomalopidae, Muraenesocidae, Tetrarogidae and Trichonotidae, and the first reports of Pacific Ocean species Plectranthias yamakawai, and Polylepion russelli in the Indian Ocean. The ten most species-rich families accounted for 58% of the community and included: Labridae (13%), Pomacentridae (8%), Epinephelidae (6%), Acanthuridae (5%), Chaetodontidae (5%), Muraenidae (5%), Gobiidae (5%), Blenniidae (4%), Apogonidae (4%) and Scorpaenidae (3%). The majority (89%) of species inhabit shallow coral reefs, with deep reefs (60–300 m) and pelagic waters only accounting for 7% and 2% of fish community. Approximately 76% of thefishes are widespread Indo-Pacific species, 12% are Pacific Ocean species, 5% are circumtropical, 4% are Indian Ocean species and approximately 1% are endemic. Abundance surveys revealed that endemic species, and species at the edge of their geographic range, do not conform to terrestrial-based predictions of low abundance. The structure and composition of the Christmas Island fish community is influenced by three main factors. Firstly, the isolation of the island means that fishes with poor dispersal abilities (e.g., syngnathids) are underrepresented. Secondly, thebiogeographic position of the island results in a unique mixing of Indian and Pacific Ocean species. Thirdly, the lack of lagoonal habitats means that fishes that use these habitats (e.g., ophichthids, lethrinids, epinephelids) are underrepresented or have low abundance

Duration of Rheumatoid Arthritis and the Risk of Developing Interstitial Lung Disease

Age of ILD onset is similar in patients with RA-UIP and RA-NSIP but duration of RA before ILD onset differs

First-year performance of 1-0 containerized Douglas-fir seedlings on droughty sites in southwestern Oregon

The effects of artificial shading and aspect on the performance of 1-0 container-grown Douglas-fir seedlings were evaluated 1 year after outplanting on four different aspects in southwest Oregon. The test areas, all characterized by steep slopes and shallow, skeletal soils with a surface mantle of loose rock and logging slash, have histories of repeated reforestation failure. Seedling survival was greatest on north and south slopes. Shadecards improved survival by 16 percent on the south slope and significantly increased height growth on the west slope. Artificial shading on east and west aspects produced seedlings with significantly smaller diameters than those without shading. Shadecards are recommended for south and west aspects with skeletal soils. Surface movement of debris and rock may be a significant factor in seedling survival during the first year. Protecting seedlings from animal damage and downslope movement of materials with Vexar tubes is recommended for sites where both problems exist

Clinical impairment in premanifest and early Huntington's disease is associated with regionally specific atrophy.

TRACK-HD is a multicentre longitudinal observational study investigating the use of clinical assessments and 3-Tesla magnetic resonance imaging as potential biomarkers for future therapeutic trials in Huntington's disease (HD). The cross-sectional data from this large well-characterized dataset provide the opportunity to improve our knowledge of how the underlying neuropathology of HD may contribute to the clinical manifestations of the disease across the spectrum of premanifest (PreHD) and early HD. Two hundred and thirty nine gene-positive subjects (120 PreHD and 119 early HD) from the TRACK-HD study were included. Using voxel-based morphometry (VBM), grey and white matter volumes were correlated with performance in four domains: quantitative motor (tongue force, metronome tapping, and gait); oculomotor [anti-saccade error rate (ASE)]; cognition (negative emotion recognition, spot the change and the University of Pennsylvania smell identification test) and neuropsychiatric measures (apathy, affect and irritability). After adjusting for estimated disease severity, regionally specific associations between structural loss and task performance were found (familywise error corrected, P < 0.05); impairment in tongue force, metronome tapping and ASE were all associated with striatal loss. Additionally, tongue force deficits and ASE were associated with volume reduction in the occipital lobe. Impaired recognition of negative emotions was associated with volumetric reductions in the precuneus and cuneus. Our study reveals specific associations between atrophy and decline in a range of clinical modalities, demonstrating the utility of VBM correlation analysis for investigating these relationships in HD

The Concise Guide to PHARMACOLOGY 2023/24:Catalytic receptors

The Concise Guide to PHARMACOLOGY 2023/24 is the sixth in this series of biennial publications. The Concise Guide provides concise overviews, mostly in tabular format, of the key properties of approximately 1800 drug targets, and nearly 6000 interactions with about 3900 ligands. There is an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (https://www.guidetopharmacology.org/), which provides more detailed views of target and ligand properties. Although the Concise Guide constitutes almost 500 pages, the material presented is substantially reduced compared to information and links presented on the website. It provides a permanent, citable, point-in-time record that will survive database updates. The full contents of this section can be found at http://onlinelibrary.wiley.com/doi/10.1111/bph.16180. Catalytic receptors are one of the six major pharmacological targets into which the Guide is divided, with the others being: G protein-coupled receptors, ion channels, nuclear hormone receptors, enzymes and transporters. These are presented with nomenclature guidance and summary information on the best available pharmacological tools, alongside key references and suggestions for further reading. The landscape format of the Concise Guide is designed to facilitate comparison of related targets from material contemporary to mid-2023, and supersedes data presented in the 2021/22, 2019/20, 2017/18, 2015/16 and 2013/14 Concise Guides and previous Guides to Receptors and Channels. It is produced in close conjunction with the Nomenclature and Standards Committee of the International Union of Basic and Clinical Pharmacology (NC-IUPHAR), therefore, providing official IUPHAR classification and nomenclature for human drug targets, where appropriate.</p

Can we monitor heart attack in the troponin era: evidence from a population-based cohort study

<p>Abstract</p> <p>Background</p> <p>Troponins (highly sensitive biomarkers of myocardial damage) increase counts of myocardial infarction (MI) in clinical practice, but their impact on trends in admission rates for MI in National statistics is uncertain.</p> <p>Methods</p> <p>Cases coded as MI or other cardiac diagnoses in the Hospital Morbidity Data Collection (MI-HMDC) in Western Australia in 1998 and 2003 were classified using revised criteria for MI developed by an International panel convened by the American Heart Association (AHA criteria) using information on symptoms, ECGs and cardiac biomarkers abstracted from samples of medical notes. Age-sex standardized rates of MI-HMDC were compared with rates of MI based on AHA criteria including troponins (MI-AHA) or traditional biomarkers only (MI-AHAck).</p> <p>Results</p> <p>Between 1998 and 2003, rates of MI-HMDC decreased by 3.5% whereas rates of MI-AHA increased by 17%, a difference largely due to increased false-negative cases in the HMDC associated with marked increased use of troponin tests in cardiac admissions generally, and progressively lower test thresholds. In contrast, rates of MI-AHA_ckdeclined by 18%.</p> <p>Conclusions</p> <p>Increasing misclassification of MI-AHA by the HMDC may be due to reluctance by clinicians to diagnose MI based on relatively small increases in troponin levels. These influences are likely to continue. Monitoring MI using AHA criteria will require calibration of commercially available troponin tests and agreement on lower diagnostic thresholds for epidemiological studies. Declining rates of MI-AHA_ckare consistent with long-standing trends in MI in Western Australia, suggesting that neither MI-HMDC nor MI-AHA reflect the true underlying population trends in MI.</p

Maternal Genome-Wide DNA Methylation Patterns and Congenital Heart Defects

The majority of congenital heart defects (CHDs) are thought to result from the interaction between multiple genetic, epigenetic, environmental, and lifestyle factors. Epigenetic mechanisms are attractive targets in the study of complex diseases because they may be altered by environmental factors and dietary interventions. We conducted a population based, case-control study of genome-wide maternal DNA methylation to determine if alterations in gene-specific methylation were associated with CHDs. Using the Illumina Infinium Human Methylation27 BeadChip, we assessed maternal gene-specific methylation in over 27,000 CpG sites from DNA isolated from peripheral blood lymphocytes. Our study sample included 180 mothers with non-syndromic CHD-affected pregnancies (cases) and 187 mothers with unaffected pregnancies (controls). Using a multi-factorial statistical model, we observed differential methylation between cases and controls at multiple CpG sites, although no CpG site reached the most stringent level of genome-wide statistical significance. The majority of differentially methylated CpG sites were hypermethylated in cases and located within CpG islands. Gene Set Enrichment Analysis (GSEA) revealed that the genes of interest were enriched in multiple biological processes involved in fetal development. Associations with canonical pathways previously shown to be involved in fetal organogenesis were also observed. We present preliminary evidence that alterations in maternal DNA methylation may be associated with CHDs. Our results suggest that further studies involving maternal epigenetic patterns and CHDs are warranted. Multiple candidate processes and pathways for future study have been identified