Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices

Wurst is a protein threading program with an emphasis on high quality sequence to structure alignments (http://www.zbh.uni-hamburg.de/wurst). Submitted sequences are aligned to each of about 3000 templates with a conventional dynamic programming algorithm, but using a score function with sophisticated structure and sequence terms. The structure terms are a log-odds probability of sequence to structure fragment compatibility, obtained from a Bayesian classification procedure. A simplex optimization was used to optimize the sequence-based terms for the goal of alignment and model quality and to balance the sequence and structural contributions against each other. Both sequence and structural terms operate with sequence profiles.

Preliminary study of shunt related death in paediatric patients

Hydrocephalus is a condition commonly encountered in paediatric and adult neurosurgery and cerebrospinal fluid (CSF) shunting remains the treatment of choice for many cases. Despite improvements in shunt technology and technique, morbidity and mortality remain. The incidence of early shunt obstruction is high with later failures seen less frequently. This review aims to examine mortality associated with mechanical failure of CSF shunts within Queensland. Neurosurgical and Intensive Care databases were reviewed for cases of mortality associated with shunt failure. Eight cases were identified between the years of 1992 and 2002 with the average age at death 7.7 years. Deaths occurred on average 2 years after last shunt revision. Seven of the eight patients lived outside the metropolitan area. Shunting remains an imperfect means of treating hydrocephalus. Mortality may be encountered at any time post surgery and delays to surgical intervention influence this. Alternative measures such as third ventriculostomy or the placement of a separate access device should be considered. In the event of emergency, a spinal needle could be used to access the ventricle along the course of the ventricular catheter. (C) 2004 Elsevier Ltd. All rights reserved.

Supportive care needs of people with brain tumours and their carers

Goals of work: The diagnosis and treatment of a brain tumour may result in long-term changes in a patient's functional and social abilities and/or in a greatly reduced life span. A qualitative investigation was conducted to examine the supportive care needs of patients with brain tumour and their carers. Materials and methods: Overall, 18 patients and 18 carers participated in focus groups or telephone interviews, following a structured interview guide to elicit supportive care services of importance to these patients and carers. Main results: Six major themes were identified using the framework analysis method, including needs for information and coping with uncertainty, practical support, support to return to pretreatment responsibilities or prepare for long-term care, support to deal with social isolation and organize respite care, support to overcome stigma/discrimination and support to discuss potentially reduced life expectancy. Conclusions: Five recommendations to improve service delivery include: assignment of a dedicated member of the care team or case manager; proactive dissemination of information, education and psychosocial support; access to objective assessment of neuropsychological functioning; facilitating easier access to welfare payments; and services facilitating communication about difficult illness-related topics. Provision of services along these recommendations could improve supportive care of brain tumour patients and their carers.

Molybdenum and sulphur isotope ratios of early Pleistocene sapropels of ODP Hole 160-969D

Organic-rich sediments (sapropels) deposited in the Mediterranean are presumed to have formed during periods of increased productivity, and/or deep water oxygen depletion, possibly including the development of sulfidic conditions (euxinia). Geochemical redox proxies (Re, Mo, Mo isotopes, V, Fe/Al, and multiple S isotopes) in 8 sapropels from the Pleistocene confirm water column euxinic conditions of varying intensity during sapropel deposition. These same proxies indicate an oxic origin for hemipelagic sediments deposited between sapropel-forming episodes. In one intensively sampled sapropel, deposited between 1.450 and 1.458 Ma, changing concentrations of organic carbon, Ba, Re, Mo, V, and Fe/Al track one another closely, reflecting coupling between water column euxinia and biological productivity. Multiple S isotope data from this sapropel suggest that the redox interface where oxidative sulfur cycling occurred was present in the sediments during hemipelagic sedimentation, but moved into the water column during sapropel deposition. Molybdenum isotopes of these 8 sapropels encompass a range of values (d98Mo = +0.2 to +1.7), but are all 98Mo-depleted relative to seawater (d98Mo = +2.3 per mil), suggesting that quantitative removal of Mo did not occur. This finding contrasts with modern Black Sea sediments. In general, Re/Mo ratios in sapropels are greater than in modern seawater, implying that the water column was not sufficiently sulfidic during sapropel-forming episodes to induce complete removal of both these elements. Surprisingly, the heaviest d98Mo values are found within hemipelagic sediments. Very few of the hemipelagic samples preserve the negative d98Mo values commonly associated with modern oxic marine sediments. Many of the hemipelagic samples also contained higher concentrations of Re and Mo than are common in oxic sediments. These features may be attributable to diffusion from the sapropels of a 98Mo-enriched component into the hemipelagic sediments.