Durham - a word sense disambiguation system

Ever since the 1950's when Machine Translation first began to be developed, word sense disambiguation (WSD) has been considered a problem to developers. In more recent times, all NLP tasks which are sensitive to lexical semantics potentially benefit from WSD although to what extent is largely unknown. The thesis presents a novel approach to the task of WSD on a large scale. In particular a novel knowledge source is presented named contextual information. This knowledge source adopts a sub-symbolic training mechanism to learn information from the context of a sentence which is able to aid disambiguation. The system also takes advantage of frequency information and these two knowledge sources are combined. The system is trained and tested on SEMCOR. A novel disambiguation algorithm is also developed. The algorithm must tackle the problem of a large possible number of sense combinations in a sentence. The algorithm presented aims to make an appropriate choice between accuracy and efficiency. This is performed by directing the search at a word level. The performance achieved on SEMCOR is reported and an analysis of the various components of the system is performed. The results achieved on this test data are pleasing, but are difficult to compare with most of the other work carried out in the field. For this reason the system took part in the SENSEVAL evaluation which provided an excellent opportunity to extensively compare WSD systems. SENSEVAL is a small scale WSD evaluation using the HECTOR lexicon. Despite this, few adaptations to the system were required. The performance of the system on the SENSEVAL task are reported and have also been presented in [Hawkins, 2000]

UK guideline for the use of HIV Post-Exposure Prophylaxis Following Sexual Exposure, 2015.

We present the updated British Association for Sexual Health and HIV guidelines for HIV post-exposure prophylaxis following sexual exposure (PEPSE). This document includes a review of the current data to support the use of PEPSE, considers how to calculate the risks of infection after a potential exposure, and provides recommendations on when PEPSE should and should not be considered. We also review which medications to use for PEPSE, provide a checklist for initial assessment, and make recommendations for monitoring individuals receiving PEPSE. Special scenarios, cost-effectiveness of PEPSE, and issues relating to service provision are also discussed. Throughout the document, the place of PEPSE within the broader context of other HIV prevention strategies is considered

Opportunities for improving animal welfare in rodent models of epilepsy and seizures

Animal models of epilepsy and seizures, mostly involving mice and rats, are used to understand the pathophysiology of the different forms of epilepsy and their comorbidities, to identify biomarkers, and to discover new antiepileptic drugs and treatments for comorbidities. Such models represent an important area for application of the 3Rs (replacement, reduction and refinement of animal use). This report provides background information and recommendations aimed at minimising pain, suffering and distress in rodent models of epilepsy and seizures in order to improve animal welfare and optimise the quality of studies in this area. The report includes practical guidance on principles of choosing a model, induction procedures, in vivo recordings, perioperative care, welfare assessment, humane endpoints, social housing, environmental enrichment, reporting of studies and data sharing. In addition, some model-specific welfare considerations are discussed, and data gaps and areas for further research are identified. The guidance is based upon a systematic review of the scientific literature, survey of the international epilepsy research community, consultation with veterinarians and animal care and welfare officers, and the expert opinion and practical experience of the members of a Working Group convened by the United Kingdom's National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs)

The inevitable QSAR renaissance

QSAR approaches, including recent advances in 3D-QSAR, are advantageous during the lead optimization phase of drug discovery and complementary with bioinformatics and growing data accessibility. Hints for future QSAR practitioners are also offered

Effects of analgesic intervention on behavioural responses to Low Atmospheric Pressure Stunning

Worldwide, more than 50 billion chickens are killed annually for food production so their welfare at slaughter is an important concern. Low Atmospheric Pressure Stunning (LAPS) is a novel approach to pre-slaughter stunning of poultry in which birds are rendered unconscious by gradually reducing oxygen tension in the atmosphere to achieve a progressive anoxia (hypobaric hypoxia). Advantages of this approach over electrical stunning are that birds are not shackled while conscious and all birds are reliably and irreversibly stunned. However, concerns remain that birds undergoing LAPS could experience discomfort or pain. Here we investigated whether subjecting birds to LAPS with and without administration of an opioid analgesic (butorphanol) affected behavioural responses. A blocking design was used in which pairs of birds receiving either analgesic or sham treatment were allocated to three types (analgesic/analgesic, analgesic/sham, or sham/sham). In line with previous studies, birds showed a consistent sequence of behaviours during LAPS: ataxia, loss of posture, clonic/tonic convulsions, leg paddling and motionless. Overall, administration of butorphanol had no effect on the range and patterning of behavioural responses during LAPS, but there were some differences in behaviour latencies, counts and durations. For example, latencies to ataxia, mandibulation and deep inhalation were delayed by analgesic treatment, however the duration of ataxia and other behaviours related to loss of consciousness were unaffected. Fewer birds receiving analgesia showed jumping and slow wing flapping behaviour compared to controls, which suggests these may be pain related. These behaviours after the onset of ataxia and the results may reflect a smoother induction to unconsciousness in analgised birds. Collectively, the results do not provide convincing evidence that birds undergoing LAPS are experiencing pain. While there were effects of analgesia on some aspects of behaviour, these could be explained by potential sedative, dysphoric and physiological side effects of butorphanol. The behavioural responses to LAPS appear to be primarily related to exposure to anoxia rather than hypobaric conditions, and thus in terms of welfare, this stunning method may be equivalent to controlled atmosphere stunning with inert gases

Germline Genetic Variants and Pediatric Rhabdomyosarcoma Outcomes: A Report From the Children’s Oncology Group

BACKGROUND: Relative to other pediatric cancers, survival for rhabdomyosarcoma (RMS) has not improved in recent decades, suggesting the need to enhance risk stratification. Therefore, we conducted a genome-wide association study for event-free survival (EFS) and overall survival (OS) to identify genetic variants associated with outcomes in individuals with RMS. METHODS: The study included 920 individuals with newly diagnosed RMS who were enrolled in Children\u27s Oncology Group protocols. To assess the association of each single nucleotide polymorphism (SNP) with EFS and OS, we estimated hazard ratios (HRs) and 95% confidence intervals (CIs) using multivariable Cox proportional hazards models, adjusted for clinical covariates. All statistical tests were two sided. We also performed stratified analyses by histological subtype (alveolar and embryonal RMS) and carried out sensitivity analyses of statistically significant SNPs by PAX3/7-FOXO1 fusion status and genetic ancestry group. RESULTS: We identified that rs17321084 was associated with worse EFS (HR = 2.01, 95% CI = 1.59 to 2.53, P = 5.39 × 10-9) and rs10094840 was associated with worse OS (HR = 1.84, 95% CI = 1.48 to 2.27, P = 2.13 × 10-8). Using publicly available data, we found that rs17321084 lies in a binding region for transcription factors GATA2 and GATA3, and rs10094840 is associated with SPAG1 and RNF19A expression. We also identified that CTNNA3 rs2135732 (HR = 3.75, 95% CI = 2.34 to 5.99, P = 3.54 × 10-8) and MED31 rs74504320 (HR = 3.21, 95% CI = 2.12 to 4.86, P = 3.60 × 10-8) were associated with worse OS among individuals with alveolar RMS. CONCLUSIONS: We demonstrated that common germline variants are associated with EFS and OS among individuals with RMS. Additional replication and investigation of these SNP effects may further support their consideration in risk stratification protocols

Investigating the impact of CO2 on low-frequency variability of the AMOC in HadCM3

This study investigates the impact of CO2 on the amplitude, frequency, and mechanisms of Atlantic meridional overturning circulation (AMOC) variability in millennial simulations of the HadCM3 coupled climate model. Multichannel singular spectrum analysis (MSSA) and empirical orthogonal functions (EOFs) are applied to the AMOC at four quasi-equilibrium CO2 forcings. The amount of variance explained by the first and second eigenmodes appears to be small (i.e., 11.19%); however, the results indicate that both AMOC strength and variability weaken at higher CO2 concentrations. This accompanies an apparent shift from a predominant 100–125-yr cycle at 350 ppm to 160 yr at 1400 ppm. Changes in amplitude are shown to feed back onto the atmosphere. Variability may be linked to salinity-driven density changes in the Greenland–Iceland– Norwegian Seas, fueled by advection of anomalies predominantly from the Arctic and Caribbean regions. A positive density anomaly accompanies a decrease in stratification and an increase in convection and Ekman pumping, generating a strong phase of the AMOC (and vice versa). Arctic anomalies may be generated via an internal ocean mode that may be key in driving variability and are shown to weaken at higher CO2, possibly driving the overall reduction in amplitude. Tropical anomalies may play a secondary role in modulating variability and are thought to be more influential at higher CO2, possibly due to an increased residence time in the subtropical gyre and/or increased surface runoff driven by simulated dieback of the Amazon rain forest. These results indicate that CO2 may not only weaken AMOC strength but also alter the mechanisms that drive variability, both of which have implications for climate change on multicentury time scales

Crop Updates 2002 - Lupins

This session covers twenty four papers from different authors: LUPIN INDUSTRY ISSUES AND RESEARCH DIRECTIONS ACKNOWLEDGMENTS Amelia McLarty LUPIN CONVENOR DEPARTMENT OF AGRICULTURE VARIETIES 1. Evaluation of lupinus mutabilis in Western Australia, Bob French, Laurie Wahlsten and Martin Harries, Department of Agriculture 2. Adaption of restricted-branching lupins in short-growing season environments, Bob French, Laurie Wahlsten, Department of Agriculture ESTABLISHMENT 3. Moisture delving for better lupin establishment, Dr Paul Blackwell, Department of Agriculture 4. Lupins, tramlines, 600mm rows, rolling and shield spraying … a good result in a dry season! Paul Blackwell and Mike Collins, Department of Agriculture 5. Lupin wider row spacing data and observations, Bill CrabtreeA, Geoff FosberyB, Angie RoeB, Mike CollinsCand Matt BeckettA,AWANTFA, BFarm Focus Consultants and CDepartment of Agriculture NUTRITION 6. Lupin genotypes respond differently to potash, Bob French and Laurie Wahlsten, Department of Agriculture 7. Consequence of radish competition on lupin nutrients in a wheat-lupin rotation, Abul Hashem and Nerys Wilkins, Department of Agriculture 8. Consequence of ryegrass competition on lupin nutrients in a wheat-lupin rotation, Abul Hashem and Nerys Wilkins, Department of Agriculture PESTS AND DISEASES 9. Fungicide sprays for control of lupin anthracnose, Geoff Thomas and Ken Adcock, Department of Agriculture 10. Estimated yield losses in lupin varieties from sowing anthracnose infected seed, Geoff Thomas, Department of Agriculture 11. Effect of variety and environment (northern and southern wheatbelt) on yield losses in lupins due to anthracnose, Geoff Thomas and Ken Adcock, Department of Agriculture, 12. A decision support system for the control of aphids and CMV in lupin crops, Debbie Thackray, Jenny Hawkes and Roger Jones, Centre for Legumes in Mediterranean Agriculture and Department of Agriculture 13. Integrated management strategies for virus diseases of lupin, Roger Jones, Crop Improvement Institute, Department of Agriculture, and Centre for Legumes in Mediterranean Agriculture, University of WA 14. Quantifying yield losses caused by the non-necrotic strain of BYMV in lupin, Roger Jones and Brenda Coutts, Department of Agriculture, and Centre for Legumes in Mediterranean Agriculture 15. Screening for pod resistance to phomopsis in various lupin species, Manisha Shankar1, Mark Sweetingham1&2and Bevan Buirchell2 1Co-operative Research Centre for Legumes in Mediterranean Agriculture, The University of Western Australia, 2 Department of Agriculture 16. Lupin disease diagnostics, Nichole Burges and Dominie Wright, Department of Agriculture QUALITY AND MARKET DEVELOPMENT 17. To GM or not to GM pulses – that is the question, Dr Susan J. Barker, The University of Western Australia 18. Towards a management package for grain protein in lupins, Bob French, Senior Research Officer, Department of Agriculture 19. Yield and seed protein response to foliar application of N among lupin genotypes, Jairo A Palta1&2, Bob French2&3and Neil C Turner1&2 , 1 CSIRO Plant Industry, Floreat Park, 2 CLIMA, University of Western Australia,3Department of Agriculture 20. Foliar nitrogen application to improve protein content in narrow-leafed lupin, Martin Harries, Bob French, Laurie Wahlsten, Department of Agriculture, Matt Evans, CSBP 21. Effect of time of swathing of lupins on grain protein content, Martin Harries, Department of Agriculture 22. Putting a value on protein premiums for the animal feed industries: Aquaculture, Brett Glencross and John Curnow, Department of Fisheries, Wayne Hawkins, Department of Agriculture 23. Progress in selecting for reduced seed hull and pod wall in lupin, Jon C. Clements, CLIMA, University of Western Australia 24. Contact details for principal author

Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.

Multiple sclerosis is a common disease of the central nervous system in which the interplay between inflammatory and neurodegenerative processes typically results in intermittent neurological disturbance followed by progressive accumulation of disability. Epidemiological studies have shown that genetic factors are primarily responsible for the substantially increased frequency of the disease seen in the relatives of affected individuals, and systematic attempts to identify linkage in multiplex families have confirmed that variation within the major histocompatibility complex (MHC) exerts the greatest individual effect on risk. Modestly powered genome-wide association studies (GWAS) have enabled more than 20 additional risk loci to be identified and have shown that multiple variants exerting modest individual effects have a key role in disease susceptibility. Most of the genetic architecture underlying susceptibility to the disease remains to be defined and is anticipated to require the analysis of sample sizes that are beyond the numbers currently available to individual research groups. In a collaborative GWAS involving 9,772 cases of European descent collected by 23 research groups working in 15 different countries, we have replicated almost all of the previously suggested associations and identified at least a further 29 novel susceptibility loci. Within the MHC we have refined the identity of the HLA-DRB1 risk alleles and confirmed that variation in the HLA-A gene underlies the independent protective effect attributable to the class I region. Immunologically relevant genes are significantly overrepresented among those mapping close to the identified loci and particularly implicate T-helper-cell differentiation in the pathogenesis of multiple sclerosis

Spoken language processing: piecing together the puzzle

Attempting to understand the fundamental mechanisms underlying spoken language processing, whether it is viewed as behaviour exhibited by human beings or as a faculty simulated by machines, is one of the greatest scientific challenges of our age. Despite tremendous achievements over the past 50 or so years, there is still a long way to go before we reach a comprehensive explanation of human spoken language behaviour and can create a technology with performance approaching or exceeding that of a human being. It is argued that progress is hampered by the fragmentation of the field across many different disciplines, coupled with a failure to create an integrated view of the fundamental mechanisms that underpin one organism's ability to communicate with another. This paper weaves together accounts from a wide variety of different disciplines concerned with the behaviour of living systems - many of them outside the normal realms of spoken language - and compiles them into a new model: PRESENCE (PREdictive SENsorimotor Control and Emulation). It is hoped that the results of this research will provide a sufficient glimpse into the future to give breath to a new generation of research into spoken language processing by mind or machine. (c) 2007 Elsevier B.V. All rights reserved