The Pain Ambulatory Monitoring Survey: Development and validation of an instrument for momentary within-day assessments of pain and cognitive-behavioral factors

Objectives & Methods The Pain Ambulatory Monitoring Survey (PAMS), a questionnaire measuring outcomes and mechanisms relevant to cognitive-behavioural models of chronic pain, was developed and validated over two studies. PAMS was designed for use over repeated momentary assessments via electronic diaries (PDAs). The first study aimed to support the factor structure and internal validity of multi-item scales in a mixed chronic pain sample completing a once-off questionnaire-based version of the PAMS scales. The second study aimed to validate average scores from one week of PAMS diary monitoring against a battery of standard questionnaires, in a mixed chronic pain sample. Results The first study revealed clear factor structure for all multi-item PAMS scales and adequate to excellent internal consistency. In the final study, the PAMS scales demonstrated adequate to excellent convergence with standardised questionnaires. Discussion The current set of studies describes a monitoring instrument that assesses pain and certain key functional consequences and cognitive-behavioural mechanisms in a brief yet valid way, making it suitable for use in intensive diary-based studies. The current study sets the stage for further theoretical work exploring the within-person relationships between pain, functioning, and cognitive-behavioural factors

CO2 storage monitoring: leakage detection and measurement in subsurface volumes from 3D seismic data at Sleipner

Demonstrating secure containment is a key plank of CO2 storage monitoring. Here we use the time-lapse 3D seismic surveys at the Sleipner CO2 storage site to assess their ability to provide robust and uniform three-dimensional spatial surveillance of the Storage Complex and provide a quantitative leakage detection tool. We develop a spatial-spectral methodology to determine the actual detection limits of the datasets which takes into account both the reflectivity of a thin CO2 layer and also its lateral extent. Using a tuning relationship to convert reflectivity to layer thickness, preliminary analysis indicates that, at the top of the Utsira reservoir, CO2 accumulations with pore volumes greater than about 3000 m3 should be robustly detectable for layer thicknesses greater than one metre, which will generally be the case. Making the conservative assumption of full CO2 saturation, this pore volume corresponds to a CO2 mass detection threshold of around 2100 tonnes. Within the overburden, at shallower depths, CO2 becomes progressively more reflective, less dense, and correspondingly more detectable, as it passes from the dense phase into a gaseous state. Our preliminary analysis indicates that the detection threshold falls to around 950 tonnes of CO2 at 590 m depth, and to around 315 tonnes at 490 m depth, where repeatability noise levels are particularly low. Detection capability can be equated to the maximum allowable leakage rate consistent with a storage site meeting its greenhouse gas emissions mitigation objective. A number of studies have suggested that leakage rates around 0.01% per year or less would ensure effective mitigation performance. So for a hypothetical large-scale storage project, the detection capability of the Sleipner seismics would far exceed that required to demonstrate the effective mitigation leakage limit. More generally it is likely that well-designed 3D seismic monitoring systems will have robust 3D detection capability significantly superior to what is required to prove greenhouse gas mitigation efficacy

Utilising transmission electron microscopy to better understand viral replication cycles: the characterisation of cytoplasmic replication in Tula virus, rotavirus and herpesvirus

Viruses are intracellular parasites that can subvert host cellular systems to enable the production of progeny viruses, which are then able to infect more cells. Transmission electron microscopy is one the main ways in which viral replication within cells can be directly visualised in a way that reveals ultrastructural details. Throughout this project I have utilised transmission electron microscopy to elucidate aspects of viral replication cycles within the cytoplasm of infected cells. In chapter three I investigated the effects of Tula virus infection on cellular architecture in collaboration with Katherine Davies. Tula virus belongs to the hantavirus genus along with several other hantaviruses which are responsible for zoonotic illness in humans. From our investigation it was found that Tula virus forms large filamentous structures within the cytoplasm of infected cells that increase in size as infection progresses. These filamentous structures have been observed in New World hantavirus infected cells before, but this is the first time that the filaments have been identified in an Old World hantavirus. Furthermore, it was found that Tula virus infection results in the enlargement of the cell endoplasmic reticulum, potentially through inducing endoplasmic reticulum stress. In chapter four I explored the role of liquid-liquid phase separation in rotavirus viroplasm formation. Rotaviruses are the most common cause of diarrhoeal disease in children, and they form viral factories within infected cells known as viroplasms. I found that when rotavirus infected cells were treated with an inhibitor of liquid-liquid phase separation, viroplasms reduced in size. This indicated that liquid-liquid phase separation is an important aspect of rotavirus viroplasm development. Finally, in chapter five I examined the role of the host guanine nucleotide exchange factor DOCK5 on herpesvirus cellular egress. Herpesviruses are known for causing life-long infections in humans in over half the global population. I found that the gammaherpesvirus Kaposi’s sarcoma associated herpesvirus causes endoplasmic reticulum remodelling in infected cells, potentially in a manner similar to herpes simplex virus 1. I also found that evidence that DOCK5 is located within the nucleus of fibroblast and lymphocytes, despite the literature describing it as a cytoplasmic protein. The experiments above demonstrate how transmission electron microscopy can be utilised to better understand viral replication cycles

Quantifying Uncertainties in Sequential Chemical Extraction of Soil Phosphorus Using XANES Spectroscopy.

Sequential chemical extraction has been widely used to study soil phosphorus (P) dynamics and inform nutrient management, but its efficacy for assigning P into biologically meaningful pools remains unknown. Here, we evaluated the accuracy of the modified Hedley extraction scheme using P K-edge X-ray absorption near-edge structure (XANES) spectroscopy for nine carbonate-free soil samples with diverse chemical and mineralogical properties resulting from different degrees of soil development. For most samples, the extraction markedly overestimated the pool size of calcium-bound P (Ca-P, extracted by 1 M HCl) due to (1) P redistribution during the alkaline extractions (0.5 M NaHCO3 and then 0.1 M NaOH), creating new Ca-P via formation of Ca phosphates between NaOH-desorbed phosphate and exchangeable Ca2+ and/or (2) dissolution of poorly crystalline Fe and Al oxides by 1 M HCl, releasing P occluded by these oxides into solution. The first mechanism may occur in soils rich in well-crystallized minerals and exchangeable Ca2+ regardless of the presence or absence of CaCO3, whereas the second mechanism likely operates in soils rich in poorly crystalline Fe and Al minerals. The overestimation of Ca-P simultaneously caused underestimation of the pools extracted by the alkaline solutions. Our findings identify key edaphic parameters that remarkably influenced the extractions, which will strengthen our understanding of soil P dynamics using this widely accepted procedure

Translating the Cognitive Model of PTSD to the Treatment of Very Young Children: A Single Case Study of an 8-Year-Old Motor Vehicle Accident Survivor.

Posttraumatic stress disorder (PTSD) is a clinical condition that occurs after a discrete traumatic event, such as an accident or assault. Research into PTSD has primarily been adult-focused; however, there is a growing body of evidence evaluating the theory and treatment of PTSD in young children. Consequently, cognitive behavior therapy (CBT) interventions for PTSD in youth have been developed that focus on 3 core components of the cognitive model-a disorganized memory of the trauma, maladaptive appraisals of the trauma and its effects (meanings), and dysfunctional coping mechanisms (management). Here, we describe the extension of this treatment approach (termed CBT-3M) to very young children (3-8 years) through the case of Dylan, an 8-year-old motor vehicle accident survivor. This serves as an illustration of the underlying theory and its successful application. Further work is intended to provide evidence of the efficacy of this treatment via an ongoing treatment trial

Neutron Thermal Cross Sections, Westcott Factors, Resonance Integrals, Maxwellian Averaged Cross Sections and Astrophysical Reaction Rates Calculated from Major Evaluated Data Libraries

We present calculations of neutron thermal cross sections, Westcott factors, resonance integrals, Maxwellian-averaged cross sections and astrophysical reaction rates for 843 ENDF materials using data from the major evaluated nuclear libraries and European activation file. Extensive analysis of newly-evaluated neutron reaction cross sections, neutron covariances, and improvements in data processing techniques motivated us to calculate nuclear industry and neutron physics quantities, produce s-process Maxwellian-averaged cross sections and astrophysical reaction rates, systematically calculate uncertainties, and provide additional insights on currently available neutron-induced reaction data. Nuclear reaction calculations are discussed and new results are presented.Comment: 145 pages, 15 figures, 19 table

Assessment of bioavailable organic phosphorus in tropical forest soils by organic acid extraction and phosphatase hydrolysis

Soil organic phosphorus contributes to the nutrition of tropical trees, but is not accounted for in standard soil phosphorus tests. Plants and microbes can release organic anions to solubilize organic phosphorus from soil surfaces, and synthesize phosphatases to release inorganic phosphate from the solubilized compounds. We developed a procedure to estimate bioavailable organic phosphorus in tropical forest soils by simulating the secretion processes of organic acids and phosphatases. Five lowland tropical forest soils with contrasting properties (pH 4.4–6.1, total P 86–429 mg P kg− 1) were extracted with 2 mM citric acid (i.e., 10 μmol g− 1, approximating rhizosphere concentrations) adjusted to soil pH in a 4:1 solution to soil ratio for 1 h. Three phosphatase enzymes were then added to the soil extract to determine the forms of hydrolysable organic phosphorus. Total phosphorus extracted by the procedure ranged between 3.22 and 8.06 mg P kg− 1 (mean 5.55 ± 0.42 mg P kg− 1), of which on average three quarters was unreactive phosphorus (i.e., organic phosphorus plus inorganic polyphosphate). Of the enzyme-hydrolysable unreactive phosphorus, 28% was simple phosphomonoesters hydrolyzed by phosphomonoesterase from bovine intestinal mucosa, a further 18% was phosphodiesters hydrolyzed by a combination of nuclease from Penicillium citrinum and phosphomonoesterase, and the remaining 51% was hydrolyzed by a broad-spectrum phytase from wheat. We conclude that soil organic phosphorus can be solubilized and hydrolyzed by a combination of organic acids and phosphatase enzymes in lowland tropical forest soils, indicating that this pathway could make a significant contribution to biological phosphorus acquisition in tropical forests. Furthermore, we have developed a method that can be used to assess the bioavailability of this soil organic phosphorus

Airborne radar imaging of subaqueous channel evolution in Wax Lake Delta, Louisiana, USA

Shallow coastal regions are among the fastest evolving landscapes but are notoriously difficult to measure with high spatiotemporal resolution. Using Uninhabited Aerial Vehicle Synthetic Aperture Radar (UAVSAR) data, we demonstrate that high signal‐to‐noise L band synthetic aperture radar (SAR) can reveal subaqueous channel networks at the distal ends of river deltas. Using 27 UAVSAR images collected between 2009 and 2015 from the Wax Lake Delta in coastal Louisiana, USA, we show that under normal tidal conditions, planform geometry of the distributary channel network is frequently resolved in the UAVSAR images, including ~700 m of seaward network extension over 5 years for one channel. UAVSAR also reveals regions of subaerial and subaqueous vegetation, streaklines of biogenic surfactants, and what appear to be small distributary channels aliased by the survey grid, all illustrating the value of fine resolution, low noise, L band SAR for mapping the nearshore subaqueous delta channel network

A comparison of plot-based satellite and Earth system model estimates of tropical forest net primary production

Net primary production (NPP) by plants represents the largest annual flux of carbon dioxide (CO2) from the atmosphere to the terrestrial biosphere, playing a critical role in the global carbon (C) cycle and the Earth’s climate. Rates of NPP in tropical forests are thought to be among the highest on Earth, but debates about the magnitude, patterns, and controls of NPP in the tropics highlight uncertainty in our understanding of how tropical forests may respond to environmental change. Here, we compared tropical NPP estimates generated using three common approaches: (1) field-based methods scaled from plot-level measurements of plant biomass, (2) radiation-based methods that model NPP from satellite-derived radiation absorption by plants, (3) and biogeochemical model-based methods. For undisturbed tropical forests as a whole, the three methods produced similar NPP estimates (i.e. about 10 Pg C yr1). However, the three different approaches produced vastly different patterns of NPP both in space and through time, suggesting that our understanding of tropical NPP is poor and that our ability to predict the response of NPP in the tropics to environmental change is limited. To address this shortcoming, we suggest the development of an expanded, high-density, permanent network of sites where NPP is continuously evaluated using multiple approaches. Well-designed NPP megatransects that include a high-density plot network would significantly increase the accuracy and certainty in the observed rates and patterns of tropical NPP and improve the reliability of Earth system models used to predict NPP–carbon cycle–climate interactions into the futur