Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Cognitive dysfunction in patients treated for pituitary tumours

Assessment of neuropsychological status and mood was carried out on 36 patients who had been treated for pituitary tumour and on 36 healthy controls. Impairments in memory and executive function were exhibited by the patients even when other known causes of cognitive dysfunction had been excluded. There was no difference in mood between the two groups, and the deficits in cognitive dysfunction were not related to mood disturbance or to the effects of radiotherapy. The deficits were, however, related to the presence of surgery, although not to the type of surgery. Reasons for the cognitive dysfunction are unclear but are likely to be multifactorial, possibly including the effects of neurosurgery and/or hormone imbalance resulting from pituitary surgery

The effect of treatment variables on mood and social adjustment in adult patients with pituitary disease

OBJECTIVE Studies of mood in hypopituitary adults have yielded inconsistent results. This investigation was carried out to investigate whether treatment characteristics may be responsible for the inconsistent results. DESIGN AND MEASUREMENTS We compared three groups of patients with a group of matched healthy controls on self‐report measures of mood and social adjustment (Beck depression inventory, State‐trait anxiety inventory, Social adjustment scale (modified)) and a measure of quality of life (Nottingham health profile, NHP). PATIENTS The patient groups were those treated with transfrontal surgery (n=23), transsphenoidal surgery (n=23) or medication only (n=23). In addition, a close informant of each subject was asked to complete a social adjustment measure about the subject’s level of adjustment. RESULTS On the self‐report mood and social adjustment measures and the emotion sub‐scale of the NHP, the transsphenoidal and medication patient groups rated themselves as being more depressed, anxious and having poorer social adjustment than the transfrontal or control groups. The close informants, however, rated all three patient groups as having poorer social adjustment than the controls. Patients treated with surgery and without radiotherapy reported fewer symptoms of depression than those treated with radiotherapy. Realistic self‐appraisal of social adjustment in surgical patients was found only in those treated with transsphenoidal surgery without radiotherapy. CONCLUSIONS Patients treated for pituitary tumour, excepting those treated with transfrontal surgery and to a lesser extent those treated with radiotherapy, suffer from mild mood disturbance and self‐perceived decreased social adjustment. All patient groups are seen by others as having decreased social adjustment, raising the possibility that the transfrontal patients and possibly those who have had radiotherapy, lack insight. This may explain some of the discrepancies in the previous literature and needs to be taken into account when using self‐report measures with these patients

Ranking of interventions to reduce dwelling overheating during heatwaves

Extreme weather events, including heatwaves, are predicted to increase in both frequency and severity over the coming decades. Low house building rates and a growing population mean there is a need to adapt existing dwellings. Research presented here uses dynamic thermal simulation to model the effect of passive heatwave mitigating interventions for UK dwellings. Interventions include a range of additions and modifications to solar shading, insulation and ventilation. Results are presented for typical end and mid terrace houses, with four orientations, two occupancy profiles and using weather data from the 2003 heatwave. Results show the effectiveness of interventions that reduce solar gains through the building fabric, such as external wall insulation and solar reflective coatings. Internal wall insulation is shown to be less effective and can increase the overheating problem in some cases. Control of solar gains through glazing, using shutters and fixed shading, are also effective, particularly for south, east and west-facing rooms. Results are also presented which demonstrate how it is possible to select combinations of interventions that both eliminate overheating and reduce space heating energy use. The cost of interventions is also considered in the final analysis

An in vivo comparison of bacillus Calmette–Guérin (BCG) and cytokine-secreting BCG vaccines

A recombinant bacillus Calmette–Guérin (BCG) vaccine has been developed, which constitutively secretes interleukin (IL)-2. Groups of deer were immunized with either normal BCG (Pasteur 1173 P2 strain) or recombinant BCG (rBCG/IL-2) and their immune responses were monitored over 3 months. Animals gained weight over this period and showed no signs of adverse reactions to either vaccine. Lymphocyte transformation responses did not differ significantly between the two groups. No antibody that was specific for BCG was detected in any animal. Intradermal skin-test responses to BCG antigens showed that the rBCG/IL-2 induced a smaller delayed-type hypersensitivity response than the normal BCG. Cytokine transcription was determined by reverse transcription–polymerase chain reaction (RT–PCR). While IL-2 and interferon-γ (IFN-γ) levels did not differ significantly between the two groups, the level of IL-4 was found to be lower in the group given rBCG/IL-2. This resulted in a strong interferon-γ:IL-4 ratio, suggesting a skewing of the immune response towards a Type 1 response. The rate at which the vaccine was eliminated from the host was the same regardless of whether BCG or rBCG was used. At autopsy (3 months after vaccination) 99·99% of the organisms had been eliminated. The small number of organisms isolated from the draining lymph node of animals given rBCG/IL-2 were grown in antibiotic-containing media. They were shown to still contain the shuttle plasmid and to secrete biologically active IL-2, indicating that the plasmid was stably maintained despite the host's immune response and in the absence of antibiotic selection