What is the influence of genre during the perception of structured text for retrieval and search?

This thesis presents an investigation into the high value of structured text (or form) in the context of genre within Information Retrieval. In particular, how are these structured texts perceived and why are they not more heavily used within Information Retrieval & Search communities? The main motivation is to show the features in which people can exploit genre within Information Search & Retrieval, in particular, categorisation and search tasks. To do this, it was vital to record and analyse how and why this was done during typical tasks. The literature review highlighted two previous studies (Toms & Campbell 1999a; Watt 2009) which have reported pilot studies consisting of genre categorisation and information searching. Both studies and other findings within the literature review inspired the work contained within this thesis. Genre is notoriously hard to define, but a very useful framework of Purpose and Form, developed by Yates & Orlikowski (1992), was utilised to design two user studies for the research reported within the thesis. The two studies consisted of, first, a categorisation task (e-mails), and second, a set of six simulated situations in Wikipedia, both of which collected quantitative data from eye tracking experiments as well as qualitative user data. The results of both studies showed the extent to which the participants utilised the form features of the stimuli presented, in particular, how these were used, which ocular behaviours (skimming or scanning) and actual features were used, and which were the most important. The main contributions to research made by this thesis were, first of all, that the task-based user evaluations employing simulated search scenarios revealed how and why users make decisions while interacting with the textual features of structure and layout within a discourse community, and, secondly, an extensive evaluation of the quantitative data revealed the features that were used by the participants in the user studies and the effects of the interpretation of genre in the search and categorisation process as well as the perceptual processes used in the various communities. This will be of benefit for the re-development of information systems. As far as is known, this is the first detailed and systematic investigation into the types of features, value of form, perception of features, and layout of genre using eye tracking in online communities, such as Wikipedia

The evolution of genre in Wikipedia.

This paper presents an overview of the ways in which genres, or structural forms, develop in a community of practice, in this case, Wikipedia. Firstly, we collected data by performing a small search task in the Wikipedia search engine (powered by Lucene) to locate articles related to global car manufacturers, for example, British Leyland, Ferrari and General Motors. We also searched for typical biographical articles about notable people, such as Spike Milligan, Alex Ferguson, Nelson Mandela and Karl Marx. An examination of the data thus obtained revealed that these articles have particular forms and that some genres connect to each other and evolve, merge and overlap. We then looked at the ways in which the purpose and form of a biographical article have evolved over six years within this community. We concluded the work with a discussion on the usefulness of Wikipedia as a vehicle for such genre investigations. This small analysis has allowed us to start generating a number of detailed research questions as to how forms may act as descriptors of genre and to discuss plans for experimental work aimed at answering these questions

Field validation of habitat suitability models for vulnerable marine ecosystems in the South Pacific Ocean:Implications for the use of broad-scale models in fisheries management

AbstractManagement of human activities which impact the seafloor in the deep ocean is becoming increasingly important as bottom trawling and exploration for minerals, oil, and gas continue to extend into regions where fragile ecosystems containing habitat-forming deep-sea corals and sponges may be found. Spatial management of these vulnerable marine ecosystems requires accurate knowledge of their distribution. Predictive habitat suitability modelling, using species presence data and a suite of environmental predictor variables, has emerged as a useful tool for inferring distributions outside of known areas. However, validation of model predictions is typically performed with non-independent data. In this study, we describe the results of habitat suitability models constructed for four deep-sea reef-forming coral species across a large region of the South Pacific Ocean using MaxEnt and Boosted Regression Tree modelling approaches. In order to validate model predictions we conducted a photographic survey on a set of seamounts in an un-sampled area east of New Zealand. The likelihood of habitat suitable for reef-forming corals on these seamounts was predicted to be variable, but very high in some regions, particularly where levels of aragonite saturation, dissolved oxygen, and particulate organic carbon were optimal. However, the observed frequency of coral occurrence in analyses of survey photographic data was much lower than expected, and patterns of observed versus predicted coral distribution were not highly correlated. The poor performance of these broad-scale models is attributed to lack of recorded species absences to inform the models, low precision of global bathymetry models, and lack of data on the geomorphology and substrate of the seamounts at scales appropriate to the modelled taxa. This demonstrates the need to use caution when interpreting and applying broad-scale, presence-only model results for fisheries management and conservation planning in data poor areas of the deep sea. Future improvements in the predictive performance of broad-scale models will rely on the continued advancement in modelling of environmental predictor variables, refinements in modelling approaches to deal with missing or biased inputs, and incorporation of true absence data

Nitrolinoleate inhibits superoxide generation, degranulation, and integrin expression by human neutrophils: novel antiinflammatory properties of nitric oxide-derived reactive species in vascular cells

Nitration of unsaturated fatty acids such as linoleate by NO-derived reactive species forms novel derivatives (including nitrolinoleate [LNO2]) that can stimulate smooth muscle relaxation and block platelet activation by either NO/cGMP or cAMP-dependent mechanisms. Here, LNO2 was observed to inhibit human neutrophil function. LNO2, but not linoleic acid or the nitrated amino acid 3-nitrotyrosine, dose-dependently (0.2 to 1 µmol/L) inhibited superoxide (O2·-) generation, Ca2+ influx, elastase release, and CD11b expression in response to either phorbol 12-myristate 13-acetate or N-formyl-Met-Leu-Phe. LNO2 did not elevate cGMP, and inhibition of guanylate cyclase by 1H-[1,2,4]oxadiazole[4,3-a]quinoxalin-1-one did not restore neutrophil responses, ruling out a role for NO. In contrast, LNO2 caused elevations in intracellular cAMP in the presence and absence of phosphodiesterase inhibition, suggesting activation of adenylate cyclase. Compared with phorbol 12-myristate 13-acetate–activated neutrophils, N-formyl-Met-Leu-Phe–activated neutrophils were more susceptible to the inhibitory effects of LNO2, indicating that LNO2 may inhibit signaling both upstream and downstream of protein kinase C. These data suggest novel signaling actions for LNO2 in mediating its potent inhibitory actions. Thus, nitration of lipids by NO-derived reactive species yields products with antiinflammatory properties, revealing a novel mechanism by which NO-derived nitrated biomolecules can influence the progression of vascular disease

Linear discriminant analysis reveals differences in root architecture in wheat seedlings by nitrogen uptake efficiency

Root architecture impacts water and nutrient uptake efficiency. Identifying exactly which root architectural properties influence these agronomic traits can prove challenging. In this paper approximately 300 wheat plants were divided into four groups using two binary classifications, high vs. low nitrogen uptake efficiency (NUpE), and high vs. low nitrate in medium. The root system architecture for each wheat plant was captured using 16 quantitative variables. The multivariate analysis tool, linear discriminant analysis, was used to construct composite variables, each a linear combination of the original variables, such that the score of the wheat plants on the new variables showed the maximum between-group variability. The results show that the distribution of root system architecture traits differ between low and high NUpE wheat plants and, less strongly, between low NUpE wheat plants grown on low vs. high nitrate media

Phenotyping pipeline reveals major seedling root growth QTL in hexaploid wheat

Seedling root traits of wheat (Triticum aestivum L.) have been shown to be important for efficient establishment and linked to mature plant traits such as height and yield. A root phenotyping pipeline, consisting of a germination paper-based screen combined with image segmentation and analysis software, was developed and used to characterize seedling traits in 94 doubled haploid progeny derived from a cross between the winter wheat cultivars Rialto and Savannah. Field experiments were conducted to measure mature plant height, grain yield, and nitrogen (N) uptake in three sites over 2 years. In total, 29 quantitative trait loci (QTLs) for seedling root traits were identified. Two QTLs for grain yield and N uptake co-localize with root QTLs on chromosomes 2B and 7D, respectively. Of the 29 root QTLs identified, 11 were found to co-localize on 6D, with four of these achieving highly significant logarithm of odds scores (>20). These results suggest the presence of a major-effect gene regulating seedling root vigour/growth on chromosome 6D

Tritophic phenological match-mismatch in space and time

Increasing temperatures associated with climate change may generate phenological mismatches that disrupt previously synchronous trophic interactions. Most work on mismatch has focused on temporal trends, whereas spatial variation in the degree of trophic synchrony has largely been neglected, even though the degree to which mismatch varies in space has implications for meso-scale population dynamics and evolution. Here we quantify latitudinal trends in phenological mismatch, using phenological data on an oak–caterpillar–bird system from across the UK. Increasing latitude delays phenology of all species, but more so for oak, resulting in a shorter interval between leaf emergence and peak caterpillar biomass at northern locations. Asynchrony found between peak caterpillar biomass and peak nestling demand of blue tits, great tits and pied flycatchers increases in earlier (warm) springs. There is no evidence of spatial variation in the timing of peak nestling demand relative to peak caterpillar biomass for any species. Phenological mismatch alone is thus unlikely to explain spatial variation in population trends. Given projections of continued spring warming, we predict that temperate forest birds will become increasingly mismatched with peak caterpillar timing. Latitudinal invariance in the direction of mismatch may act as a double-edged sword that presents no opportunities for spatial buffering from the effects of mismatch on population size, but generates spatially consistent directional selection on timing, which could facilitate rapid evolutionary change

What is the recovery rate and risk of long-term consequences following a diagnosis of COVID-19?:A harmonised, global longitudinal observational study protocol

Introduction: Very little is known about possible clinical sequelae that may persist after resolution of acute COVID-19. A recent longitudinal cohort from Italy including 143 patients followed up after hospitalisation with COVID-19 reported that 87% had at least one ongoing symptom at 60-day follow-up. Early indications suggest that patients with COVID-19 may need even more psychological support than typical intensive care unit patients. The assessment of risk factors for longer term consequences requires a longitudinal study linked to data on pre-existing conditions and care received during the acute phase of illness. The primary aim of this study is to characterise physical and psychosocial sequelae in patients post-COVID-19 hospital discharge. Methods and analysis: This is an international open-access prospective, observational multisite study. This protocol is linked with the International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) and the WHO’s Clinical Characterisation Protocol, which includes patients with suspected or confirmed COVID-19 during hospitalisation. This protocol will follow-up a subset of patients with confirmed COVID-19 using standardised surveys to measure longer term physical and psychosocial sequelae. The data will be linked with the acute phase data. Statistical analyses will be undertaken to characterise groups most likely to be affected by sequelae of COVID-19. The open-access follow-up survey can be used as a data collection tool by other follow-up studies, to facilitate data harmonisation and to identify subsets of patients for further in-depth follow-up. The outcomes of this study will inform strategies to prevent long-term consequences; inform clinical management, interventional studies, rehabilitation and public health management to reduce overall morbidity; and improve long-term outcomes of COVID-19. Ethics and dissemination: The protocol and survey are open access to enable low-resourced sites to join the study to facilitate global standardised, longitudinal data collection. Ethical approval has been given by sites in Colombia, Ghana, Italy, Norway, Russia, the UK and South Africa. New sites are welcome to join this collaborative study at any time. Sites interested in adopting the protocol as it is or in an adapted version are responsible for ensuring that local sponsorship and ethical approvals in place as appropriate. The tools are available on the ISARIC website (www.isaric.org)

Methamphetamine Use, Transmission Risk Behavior and Internet Use Among HIV-Infected Patients in Medical Care, San Francisco, 2008

Methamphetamine use is associated with adverse health outcomes and HIV incidence. Few studies have assessed methamphetamine use, sexual behavior and Internet use among HIV-infected patients. Surveys were administered to a sample of HIV-infected patients seeking medical care in a San Francisco county hospital and university-based clinic. In 2008, 35% of homosexual participants, 26% of heterosexual participants and 11% of female participants reported methamphetamine use in the past year. Of participants, 29% reported using the Internet to find sex partners; Internet-users versus non-Internet-users reported a higher median number of sex partners in 6 months (4 vs. 1), were more likely to report unprotected sex (32 vs. 10%), and higher rates of methamphetamine use in the past 12 months (48 vs. 24%). Given the association among methamphetamine use, increased sex partners and Internet use, the Internet may present a new and effective medium for interventions to reduce methamphetamine-associated sexual risk behavior