Scalable Inference for Markov Processes with Intractable Likelihoods

Bayesian inference for Markov processes has become increasingly relevant in recent years. Problems of this type often have intractable likelihoods and prior knowledge about model rate parameters is often poor. Markov Chain Monte Carlo (MCMC) techniques can lead to exact inference in such models but in practice can suffer performance issues including long burn-in periods and poor mixing. On the other hand approximate Bayesian computation techniques can allow rapid exploration of a large parameter space but yield only approximate posterior distributions. Here we consider the combined use of approximate Bayesian computation (ABC) and MCMC techniques for improved computational efficiency while retaining exact inference on parallel hardware

Magmatic fluids implicated in the formation of propylitic alteration: oxygen, hydrogen, and strontium isotope constraints from the Northparkes porphyry Cu-Au district, New South Wales, Australia

In porphyry ore deposit models, the propylitic alteration facies is widely interpreted to be caused by convective circulation of meteoric waters. However, recent field-based and geochemical data suggest that magmatic-derived fluids are likely to contribute to development of the propylitic assemblage. In order to test this hypothesis, we determined the oxygen and hydrogen isotope compositions of propylitic mineral separates (epidote, chlorite, and quartz), selected potassic mineral separates (quartz and magnetite), and quartz-hosted fluid inclusions from around the E48 and E26 deposits in the Northparkes porphyry Cu-Au district, New South Wales, Australia. In addition, the strontium isotope composition of epidote was determined to test for the potential contribution of seawater in the Northparkes system given the postulated island-arc setting and submarine character of some country rocks. Oxygen isotope geothermometry calculations indicate potassic alteration occurred between ~600° and 700°C in magmatic/mineralized centers, persisting to ~450°C upon lateral transition into propylitic alteration. Across the propylitic facies, temperature progressively decreased outward to <250°C. These temperature estimates and additional data from chlorite geothermometry were utilized to calculate the oxygen and hydrogen isotope composition of the fluid in equilibrium with the sampled minerals. Results show that propylitic fluids spanned a range of compositions with δ18O between 0.5 and 3.7‰ and δD between –49 and –17‰. Comparison of these results with the modeled compositions of meteoric and/or magmatic fluids during their evolution and isotopic exchange with local country rocks shows that a magmatic fluid component must exist across the propylitic halo during its formation. Strontium isotope data from propylitic epidote provide initial (based on formation at ~450 Ma) 87Sr/86Sr values in the range of 0.704099 to 0.704354, ruling out the presence of seawater as a second fluid in the system. Although we cannot exclude magmatic-meteoric mixing, especially toward the fringes of the system, our results support a model in which magmatic-derived fluid is the primary driver of propylitic alteration as it undergoes cooling and chemical equilibration during outward infiltration into country rocks. This is consistent with chemical mass transfer calculations for Northparkes and published chemical-thermodynamic models that only require a magmatic fluid for the production of propylitic assemblages. In view of this and supporting data from other deposits, we suggest that magmatic fluids are essential drivers of propylitic alteration in porphyry systems

The chlorite proximitor: A new tool for detecting porphyry ore deposits

publisher: Elsevier articletitle: The chlorite proximitor: A new tool for detecting porphyry ore deposits journaltitle: Journal of Geochemical Exploration articlelink: http://dx.doi.org/10.1016/j.gexplo.2015.01.005 content_type: article copyright: Crown copyright © 2015 Published by Elsevier B.V.Copyright © 2016 Elsevier B.V. or its licensors or contributors. ScienceDirect ® is a registered trademark of Elsevier B.V. [Creative Commons License 4.0]. The attached file is the published version of the article

The rapid development of a novel kidney-specific digital intervention for self-management of physical activity and emotional well-being during the COVID-19 pandemic and beyond: Kidney Beam

King's College Hospital; Kidney Research UK; Beam; National Institute for Health Research (NIHR) under (NIHR301893), (NIHR301593), and (ICA-CL-2017-03-020)

Achieving consensus on psychosocial and physical rehabilitation management for people living with kidney disease

From Crossref journal articles via Jisc Publications RouterHistory: epub 2023-05-19, issued 2023-05-19Article version: AMPublication status: PublishedPelagia Koufaki - ORCID: 0000-0002-1406-3729 https://orcid.org/0000-0002-1406-3729Background People living with chronic kidney disease (CKD) need to be able to live well with their condition. The provision of psychosocial interventions (psychological, psychiatric, and social care) and physical rehabilitation management is variable across England, as well as the rest of the United Kingdom. There is a need for clear recommendations for standards of psychosocial and physical rehabilitation care for people living with CKD, and guidance for the commissioning and measurement of these services. The NHS England Renal Services Transformation Programme (RSTP) supported a programme of work and modified Delphi process to address the management of psychosocial and physical rehabilitation care as part of a larger body of work to formulate a comprehensive commissioning toolkit for renal care services across England. We sought to achieve expert consensus regarding the psychosocial and physical rehabilitation management of people living with CKD in England and the rest of the UK. Method A Delphi consensus method was used to gather and refine expert opinions of senior members of the kidney multi-disciplinary team (MDT) and other key stakeholders in the UK. An agreement was sought on 16 statements reflecting aspects of psychosocial and physical rehabilitation management for people living with CKD. Results Twenty-six expert practitioners and other key stakeholders, including lived experience representatives, participated in the process. The consensus (>80% affirmative votes) amongst the respondents for all 16 statements was high. Nine recommendation statements were discussed and refined further to be included in the final iteration of the ‘Systems’ section of the NHS England RSTP commissioning toolkit. These priority recommendations reflect pragmatic solutions that can be implemented in renal care and include recommendations for a holistic well-being assessment for all people living with CKD who are approaching dialysis, or who are at listing for kidney transplantation, which includes the use of validated measurement tools to assess the need for further intervention in psychosocial and physical rehabilitation management. It is recommended that the scores from these measurement tools be included in the NHS England Renal Data Dashboard. There was also a recommendation for referral as appropriate to NHS Talking therapies, psychology, counselling or psychotherapy, social work or liaison psychiatry for those with identified psychosocial needs. The use of digital resources was recommended to be used in addition to face-to-face care to provide physical rehabilitation, and all healthcare professionals should be educated to recognise psychosocial and physical rehabilitation needs and refer/sign-post people with CKD to appropriate services. Conclusion There was high consensus amongst senior members of the kidney MDT and other key stakeholders, including those with lived experience, in the UK on all aspects of the psychosocial and physical rehabilitation management of people living with CKD. The results of this process will be used by NHS England to inform the ‘Systems’ section of the commissioning toolkit and data dashboard and to inform the National Standards of Care for people living with CKD.inpressinpres

Response to comment on 'Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity'

Lambert et al. question our retrospective and holistic epidemiological assessment of the role of chytridiomycosis in amphibian declines. Their alternative assessment is narrow and provides an incomplete evaluation of evidence. Adopting this approach limits understanding of infectious disease impacts and hampers conservation efforts. We reaffirm that our study provides unambiguous evidence that chytridiomycosis has affected at least 501 amphibian species

Brain Biomarkers and Pre-Injury Cognition are Associated with Long-Term Cognitive Outcome in Children with Traumatic Brain Injury

BACKGROUND: Children with traumatic brain injury (TBI) are frequently at risk of long-term impairments of attention and executive functioning but these problems are difficult to predict. Although deficits have been reported to vary with injury severity, age at injury and sex, prognostication of outcome remains imperfect at a patient-specific level. The objective of this proof of principle study was to evaluate a variety of patient variables, along with six brain-specific and inflammatory serum protein biomarkers, as predictors of long-term cognitive outcome following paediatric TBI. METHOD: Outcome was assessed in 23 patients via parent-rated questionnaires related to attention deficit hyperactivity disorder (ADHD) and executive functioning, using the Conners 3rd Edition Rating Scales (Conners-3) and Behaviour Rating Inventory of Executive Function (BRIEF) at a mean time since injury of 3.1 years. Partial least squares (PLS) analyses were performed to identify factors measured at the time of injury that were most closely associated with outcome on (1) the Conners-3 and (2) the Behavioural Regulation Index (BRI) and (3) Metacognition Index (MI) of the BRIEF. RESULTS: Higher levels of neuron specific enolase (NSE) and lower levels of soluble neuron cell adhesion molecule (sNCAM) were associated with higher scores on the inattention, hyperactivity/impulsivity and executive functioning scales of the Conners-3, as well as working memory and initiate scales of the MI from the BRIEF. Higher levels of NSE only were associated with higher scores on the inhibit scale of the BRI. CONCLUSIONS: NSE and sNCAM show promise as reliable, early predictors of long-term attention-related and executive functioning problems following paediatric TBI