Study for the Revision of the plaice box - Draft Final Report

This project has attempted to evaluate the effectiveness of the fisheries management measure known as the “Plaice Box” (PB) for the conservation of plaice and other species of marine organisms in the south-eastern North Sea. The study provides an inventory of existing information and collects new material on the effects of the PB on the conservation of plaice and the impact of the PB on various components of the commercial fishing fleets. Based on an analysis of key processes that affect the impact of the PB, modifications will be explored to improve the positive effect on the conservation of plaice and other species of marine organisms, including catches and bycatches of other marketable fish. An economic assessment of the consequences of those modifications, in terms of their cost-effectiveness, and implications for profitability of the activity is presented. Finally, the data requirements for future evaluations of the effects of the PB on conservation is discussed

Climate fluctuations and the spring invasion of the North Sea by Calanus finmarchicus

The population of Calanus finmarchicus in the North Sea is replenished each spring by invasion from an overwintering stock located beyond the shelf edge. A combincation of field observations, statistical analysis of Continuous Plankton Recorder (CPR) data, and particle tracking model simulations, was used to investigate the processes involved in the cross-shelf invasion. The results showed that the main source of overwintering animals entering the North Sea in the spring is at depths of greater than 600m in the Faroe Shetland Channel, where concentrations of up to 620m -3 are found in association with the overflow of Norwegian Sea Deep Water (NSDW) across the Iceland Scotland Ridge. The input of this water mass to the Faroe Shetland Channel, and hence the supply of overwintering C. finmarchicus, has declined since the late 1960s due to changes in convective processes in the Greenland Sea. Beginning in February, animals start to emerge from the overwintering state and migrate to the surface waters, where their transport into the North Sea is mainly determined by the incidence of north-westerly winds that have declined since the 1960s. Together, these two factors explain a high proportion of the 30-year trends in spring abundance in the North Sea as measured by the CPR survey. Both the regional winds and the NSDW overflow are connected to the North Atlantic Oscillation Index (NAO), which is an atmospheric climate index, but with different time scales of response. Thus, interannual fluctuations in the NAO can cause immediate changes in the incidence of north-westerly winds without leading to corresponding changes in C. finmarchicus abundance in the North Sea, because the NSDW overflow responds over longer (decadal) time scales

A two-fluid single-column model of the dry, shear-free, convective boundary layer

This is the final version. Available on open access from Wiley via the DOI in this record.A single-column model of the dry, shear-free, convective boundary layer is presented in which nonlocal transports by coherent structures such as thermals are represented by the partitioning of the fluid into two components, updraft and environment, each with a full set of prognostic dynamical equations. Local eddy diffusive transport and entrainment and detrainment are represented by parameterizations similar to those used in Eddy Diffusivity Mass Flux schemes. The inclusion of vertical diffusion of the vertical velocity is shown to be important for suppressing an instability inherent in the governing equations. A semi-implicit semi-Lagrangian numerical solution method is presented and shown to be stable for large acoustic and diffusive Courant numbers, though it becomes unstable for large advective Courant numbers. The solutions are able to capture key physical features of the dry convective boundary layer. Some of the numerical challenges posed by sharp features in the solution are discussed, and areas where the model could be improved are highlighted.Natural Environment Research Council (NERC

Chemical Components and Effects on Soil Quality in Temperate Grazed Pasture Systems

Key points 1. Legume/grass pastures retain feedbacks on N supply that may help to reduce losses of N to the wider environment. 2. Intensive use of N fertilisers tends to increase SOM turnover and increase losses of N to the environment. 3. Increased use of fertilisers has contributed little to soil organic matter storage in grazed pastoral systems

Automated Detection of Malarial Retinopathy in Digital Fundus Images for Improved Diagnosis in Malawian Children with Clinically Defined Cerebral Malaria

Cerebral malaria (CM), a complication of malaria infection, is the cause of the majority of malaria-associated deaths in African children. The standard clinical case definition for CM misclassifies ~25% of patients, but when malarial retinopathy (MR) is added to the clinical case definition, the specificity improves from 61% to 95%. Ocular fundoscopy requires expensive equipment and technical expertise not often available in malaria endemic settings, so we developed an automated software system to analyze retinal color images for MR lesions: retinal whitening, vessel discoloration, and white-centered hemorrhages. The individual lesion detection algorithms were combined using a partial least square classifier to determine the presence or absence of MR. We used a retrospective retinal image dataset of 86 pediatric patients with clinically defined CM (70 with MR and 16 without) to evaluate the algorithm performance. Our goal was to reduce the false positive rate of CM diagnosis, and so the algorithms were tuned at high specificity. This yielded sensitivity/specificity of 95%/100% for the detection of MR overall, and 65%/94% for retinal whitening, 62%/100% for vessel discoloration, and 73%/96% for hemorrhages. This automated system for detecting MR using retinal color images has the potential to improve the accuracy of CM diagnosis

A phase 1b study of Selumetinib in combination with Cisplatin and Gemcitabine in advanced or metastatic biliary tract cancer: the ABC-04 study

BACKGROUND: Combined treatment with cisplatin and gemcitabine (CisGem) is the standard of care for patients with advanced biliary tract cancer (ABC). Selumetinib (AZD6244, ARRY-142886) potently and selectively inhibits MEK1/2, an intracellular kinase and has shown activity in ABC. The objective of the ABC-04 trial was to establish the recommended dose of selumetinib in combination with CisGem in patients with ABC. METHODS: Eligible patients were ≥ 18 years, had histologically or cytologically-confirmed unresectable recurrent or metastatic biliary tract, gallbladder or ampullary carcinoma, WHO performance status 0-2, and adequate major organ function. Patients may have had prior surgery, radiotherapy or adjuvant chemotherapy, but no prior CisGem and no prior chemotherapy for locally advanced or metastatic disease. Patients received cisplatin 25 mg/m(2) plus gemcitabine 1000 mg/m(2) intravenously on days 1 and 8 of a 21-day cycle. Selumetinib capsules were taken daily. Patients received up to 8 cycles of CisGem and could receive selumetinib until disease progression. A dose de-escalation scheme was used to determine the recommended dose of selumetinib. The first dose level was 75 mg bd. Patients were recruited in cohorts of 3 and assessed for dose limiting toxicity (DLT) during the first cycle of treatment. RESULTS: Thirteen patients were recruited, of whom 12 were evaluable for DLT (1 did not start treatment). All evaluable patients received the starting dose of selumetinib 75 mg bd and one patient experienced a DLT (cardiac chest pain). The median number of days selumetinib was taken (adjusted for the number of days of dose interruptions) was 171.5 (IQR: 75.5 to 344). Two patients remained on treatment at 14 and 19 months post registration. There were 3 temporary and 1 permanent interruptions of selumetinib in cycle 1. Eight patients were evaluable for objective response (RECIST v1.1): 3 had a partial response and 5 stable disease. The median PFS was 6.4 months (IQR 5.2 to 13.7). Toxicities related to selumetinib were mostly related to oedema and rash, grade 1-2 and manageable. Pharmacokinetic analysis showed that the AUC(0-t), AUC(0-∞) and Cmax of selumetinib increased by 12, 11 and 30 % respectively when it was administered with CisGem, while Cmax for the N-desmethyl metabolite of selumetinib decreased by 40 %. There was no evidence that the time of Cmax for selumetinib or N-desmethyl metabolite of selumetinib were different when selumetinib was administered alone or with CisGem. CONCLUSION: The recommended dose of selumetinib when combined with CisGem was 75 mg bd. Translational studies are underway to identify biomarkers that may predict outcome (ClinicalTrials.gov identifier: NCT01242605 July 6(th) 2010)

Retinal Pathology of Pediatric Cerebral Malaria in Malawi

Introduction The causes of coma and death in cerebral malaria remain unknown. Malarial retinopathy has been identified as an important clinical sign in the diagnosis and prognosis of cerebral malaria. As part of a larger autopsy study to determine causes of death in children with coma presenting to hospital in Blantyre, Malawi, who were fully evaluated clinically prior to death, we examined the histopathology of eyes of patients who died and underwent autopsy. Methodology/Principal Findings Children with coma were admitted to the pediatric research ward, classified according to clinical definitions as having cerebral malaria or another cause of coma, evaluated and treated. The eyes were examined by direct and indirect ophthalmoscopy. If a child died and permission was given, a standardized autopsy was carried out. The patient was then assigned an actual cause of death according to the autopsy findings. The eyes were examined pathologically for hemorrhages, cystoid macular edema, parasite sequestration and thrombi. They were stained immunohistochemically for fibrin and CD61 to identify the components of thrombi, β-amyloid precursor protein to detect axonal damage, for fibrinogen to identify vascular leakage and for glial fibrillary acidic protein to detect gliosis. Sixty-four eyes from 64 patients were examined: 35 with cerebral malaria and 29 with comas of other causes. Cerebral malaria was distinguished by sequestration of parasitized erythrocytes, the presence and severity of retinal hemorrhages, the presence of cystoid macular edema, the occurrence and number of fibrin-platelet thrombi, the presence and amount of axonal damage and vascular leakage. Conclusions/Significance We found significant differences in retinal histopathology between patients who died of cerebral malaria and those with other diagnoses. These histopathological findings offer insights into the etiology of malarial retinopathy and provide a pathological basis for recently described retinal capillary non-perfusion in children with malarial retinopathy. Because of the similarities between the retina and the brain it also suggests mechanisms that may contribute to coma and death in cerebral malaria