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

(A) Representative immunoblot reactions of PCM patients' sera (1∶1,000) with rPlp43 and Endo H-deglycosylated (EH-) gp43.

<p>The overall results are shown in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003111#pntd-0003111-t001" target="_blank">Table 1</a> for sera groups 1, 2, 3, and individual sera 99M, 100M, and101M. On the right, CBB-stained SDS-PAGE gel showing the amount of antigen used in the reactions. Results with Endo H-deglycosylated gp43r3 were similar to (EH-)gp43 and are not shown. (<b>B</b>) <b>PCR amplification of </b><i>HSP70</i><b> using primers for the </b><i>P. lutzii</i><b> gene as shown in an agarose gel.</b> Partial <i>HSP70</i> PCR (529 bp) amplification shows that clinical isolates Pb51M and Pb52M are <i>P. lutzii</i>. DNA extracted from Pb01 (<i>P. lutzii</i>) and Pb18 (<i>P. brasiliensis</i>) were used as species control. Crt-, in the absence of DNA.</p

Overall results of the I.D. and immunoblot reactivity of recombinant <i>P. lutzii</i> (rPlp43), native or recombinant gp43 (gp43, gp43r3) and their Endo H-deglycosylated forms (EH-gp43, EH-gp43r3) with PCM patients' sera from Brazilian Southeastern (S) and Midwestern (M) regions (Table S1).

<p>*Sera groups: 1, 1S–50S and 82M–95M; 2, 51M–81M; 3, 96M–98M.</p>#<p>ID titers with purified gp43 or Pb339 culture supernantant are specified in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003111#pntd.0003111.s002" target="_blank">Table S2</a>.</p><p>Overall results of the I.D. and immunoblot reactivity of recombinant <i>P. lutzii</i> (rPlp43), native or recombinant gp43 (gp43, gp43r3) and their Endo H-deglycosylated forms (EH-gp43, EH-gp43r3) with PCM patients' sera from Brazilian Southeastern (S) and Midwestern (M) regions (<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003111#pntd.0003111.s001" target="_blank">Table S1</a>).</p

Amino acid sequence alignment and molecular models show differences between Plp43 (from Pb01) and gp43 (from Pb18).

<p>Differences in amino acid residues can be seen. Known sequence features are indicated: SP (signal peptide), MAb3e epitope (D/purple), T-cell P10 epitope (grey shade with boxed antigenic core; A/navy), N-glycosylation site (N-gly, C/green), and NEP glucanase active site (Glu, B). The sequences corresponding to primers gp01S and gp01AS used to amplify Pl<i>P43</i> ORF are shown. In the molecular models below, arrows (1–4) point to remarkable differences between Plp43 and gp43; caps letters indicate the motifs above specified. Yellow, beta-sheets; magenta, alpha-helix.</p

Recombinant rPlp43 is not glycosylated and seems to be enzymatically active.

<p>(<b>A</b>) Heterologous expression of rPlp43 in <i>P. pastoris</i> culture supernatants from methanol-induced recombinant yeasts containing the Pl<i>P43</i> insert or not (EV, empty vector). (<b>B</b>) SDS-PAGE profile of rPlp43 and control gp43 before (−) and after (+) treatment with Endo H. (<b>C</b>) Glucanase activity against PNPG in culture supernatants from <i>P. pastoris</i> expressing rPlp43 when compared with that, at equivalent total protein amount, of yeasts containing empty vector (EV), wild type <i>P. pastoris</i> and <i>S. cerevisiae</i>. Purified gp43 was used as protein negative control at equivalent protein amount to rPlp43, as estimated in SDS-PAGE gels. BSA was also included as negative control at higher amounts. PBS+rPlp43 (without substrate) and PNPG+enzyme buffer (without substrate) were used as negative controls. Migration of standard molecular masses is indicated.</p

Immunoblot reactivity of anti-gp43 monoclonal antibodies with gp43 and rPlp43.

<p>Reactivity of rPlp43 was tested with five different anti-gp43 MAbs (indicated) in immunoblot, using gp43 as positive control. On the right, CBB-stained SDS-PAGE gel showing the amount of antigen used in the assay. The results were the same for HisPlp43 expressed as inclusion bodies in bacteria.</p

Phylogenetic analysis reveals a high level of speciation in the Paracoccidioides genus

Paracoccidioidomycosis (PCM) is a systemic disease endemic to most of Latin America, with greatest impact in rural areas. The taxonomic status of one of the best studied Paracoccidioides isolates (Pb01) as A brasiliensis remains unresolved due to its genomic differences from the other three previously described phylogenetic species (S1, PS2 and PS3; Carrero et al., 2008. Fungal Genet. Biol. 45, 605). Using the genealogic concordance method of phylogenetic species recognition (GCPSR) via maximum parsimony and Bayesian analysis, we identified a clade of 17 genotypically similar isolates, including Pb01, which are distinct from the S1/PS2/P3 clade. Consistent with GCPSR, this "Pb01-like" group can be considered a new phylogenetic species, since it is strongly supported by all independent and concatenated genealogies. "Pb01-like" species exhibit great sequence and morphological divergence from the S1/PS2/PS3 species clade, and we estimate that these groups last shared a common ancestor approximately 32 million years ago. In addition, recombination analysis revealed independent events inside both main groups suggesting reproductive isolation. Consequently, we recommend the formal description of the "Pb01-like" cluster as the new species Paracoccidioides lutzii, a tribute to Adolpho Lutz, discoverer of P. brasiliensis in 1908. (C) 2009 Elsevier B.V. All rights reserved.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Cryptococcus spp isolated from dust microhabitat in Brazilian libraries

Abstract Background The Cryptococcus spp is currently composed of encapsulated yeasts of cosmopolitan distribution, including the etiological agents of cryptococcosis. The fungus are found mainly in substrates of animal and plant origin. Human infection occurs through inhalation of spores present in the environment. Methods Eighty-four swab collections were performed on dust found on books in three libraries in the city of Cuiabá, state of Mato Grosso, Brazil. The material was seeded in Sabouraud agar and then observed for characteristics compatible with colonies with a creamy to mucous aspect; the material was then isolated in birdseed (Niger) agar and cultivated at a temperature of 37°C for 5 to 7 days. Identification of isolated colonies was performed by microscopic observation in fresh preparations dyed with India ink, additional tests performed on CGB (L-canavanine glycine bromothymol blue), urea broth, and carbohydrate assimilation tests (auxanogram). Results Of the 84 samples collected from book dust, 18 (21.4%) were positive for Cryptococcus spp totalizing 41 UFC’s. The most frequently isolated species was C. gattii 15 (36.6%); followed by C. terreus, 12 (29.3%); C. luteolus 4 (9.8%); C. neoformans, and C. uniguttulatus 3 (7.3%), and C. albidus and C. humiculus with 2 (4.6%) of the isolates. Conclusion The high biodiversity of the yeasts of the Cryptococcus genus, isolated from different environmental sources in urban areas of Brazil suggests the possibility of individuals whose immune systems have been compromised or even healthy individuals coming into sources of fungal propagules on a daily bases throughout their lives. This study demonstrates the acquisition possible of cryptococcosis infection from dust in libraries.</p