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

The Paleogene Intertropical Convergence Zone (abstract of paper presented at AGU Fall Meeting, San Francisco, 6-10 Dec 2002)

Latitudinal transects of eolian deposition can help define patterns of equatorial zonal winds during Paleogene warm periods and their movement in response to global climatic transitions of the Cenozoic. We examined geochemical and mineralogical data from a number of piston cores and ODP drill sites in the tropical and subtropical Pacific Ocean. In the modern Pacific, dust deposited beneath the northeast trade winds reflects Asian provenance and is likely transported back west through the trade wind system via input from the mid-latitude westerly winds. The amount of dust supplied from American source regions is an order of magnitude lower and has limited influence on the dust record in the offshore pelagic realm of the Pacific. The inter-tropical convergence zone (ITCZ) forms an effective barrier to inter-hemispheric dust transport and marks the southern boundary of the Asian dust component. Just south of the ITCZ, dust is transported by southern trade winds predominantly from andesitic source regions of Central and South America.During warm periods of the early Paleogene, andesitic sources appear to dominate eolian deposition throughout the central and equatorial Pacific. Two hypotheses are offered to explain this observation. First, increased andesitic input is associated with trade wind transport from a North American provenance because Asian dust flux, which overwhelms this component in the modern Pacific, was significantly reduced at this time. Mineralogical data collected by light-absorption spectroscopy techniques on bulk sediments recovered during ODP Leg 199 supports this scenario showing increased illite/smectite ratios during the late Cenozoic near the time when Asian dust flux increased. Alternatively, the increased andesitic component during the Paleogene may reflect eolian deposition beneath the southern trade winds with the position of the ITCZ at a latitude as far north as perhaps 25°N. Data from clay mineralogy (from XRD), elemental geochemistry and Nd isotopic ratios from piston cores EW9709-01 and LL44-GPC3 support this hypothesis and show a transition to Asian-like dust provenance occurring by the early Miocene

Disseminated toxoplasmosis in a patient with non-Hodgkin lymphoma

Toxoplasmosis is a well-recognized opportunistic disease in HIV-infected individuals that is caused by the reactivation of a previous infection, primarily in the central nervous system, during profound immunodeficiency. Toxoplasmosis has been described more rarely in patients with cancer and chemotherapy. We report a case of a patient with a history of chemotherapy for non-Hodgkin lymphoma who developed pain and progressive paresthesia of the right arm 6 weeks after remission. Relapsing lymphoma was suspected, and steroid and radiation treatment were initiated, but the patient died 5 days later due to multiple organ failure. Autopsy revealed disseminated toxoplasmosis. This case illustrates that toxoplasmosis should be suspected in patients with neoplastic disease, especially lymphomas, who present with unexplained neurologic, pulmonary, or febrile symptoms during or after chemotherapy