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

Functional characterization of the three Drosophila retinal degeneration C (RDGC) protein phosphatase isoforms.

Drosophila retinal degeneration C (RDGC) is the founding member of the PPEF family of protein phosphatases. RDGC mediates dephosphorylation of the visual pigment rhodopsin and the TRP ion channel. From the rdgC locus, three protein isoforms, termed RDGC-S, -M, and -L, with different N-termini are generated. Due to fatty acylation, RDGC-M and -L are attached to the plasma membrane while RDGC-S is soluble. To assign physiological roles to these RDGC isoforms, we constructed flies that express various combinations of RDGC protein isoforms. Expression of the RDGC-L isoform alone did not fully prevent rhodopsin hyperphosphorylation and resulted in impaired photoreceptor physiology and in decelerated TRP dephosphorylation at Ser936. However, expression of RDGC-L alone as well as RDGC-S/M was sufficient to prevent degeneration of photoreceptor cells which is a hallmark of the rdgC null mutant. Membrane-attached RDGC-M displayed higher activity of TRP dephosphorylation than the soluble isoform RDGC-S. Taken together, in vivo activities of RDGC splice variants are controlled by their N-termini

Phosphorylation of the <i>Drosophila</i> Transient Receptor Potential Ion Channel Is Regulated by the Phototransduction Cascade and Involves Several Protein Kinases and Phosphatases

<div><p>Protein phosphorylation plays a cardinal role in regulating cellular processes in eukaryotes. Phosphorylation of proteins is controlled by protein kinases and phosphatases. We previously reported the light-dependent phosphorylation of the <i>Drosophila</i> transient receptor potential (TRP) ion channel at multiple sites. TRP generates the receptor potential upon stimulation of the photoreceptor cell by light. An eye-enriched protein kinase C (eye-PKC) has been implicated in the phosphorylation of TRP by <i>in</i><i>vitro</i> studies. Other kinases and phosphatases of TRP are elusive. Using phosphospecific antibodies and mass spectrometry, we here show that phosphorylation of most TRP sites depends on the phototransduction cascade and the activity of the TRP ion channel. A candidate screen to identify kinases and phosphatases provided <i>in vivo</i> evidence for an involvement of eye-PKC as well as other kinases and phosphatases in TRP phosphorylation.</p></div

MS-based comparison of TRP phosphorylation.

<p>Wild type, <i>norpA^P24</i>, and <i>trp^P365</i>/+ flies were illuminated or kept in the dark prior to immunoprecipitation using an α-TRP antibody. Three independent experiments and two technical replicates for each genotype and light condition were analyzed by mass spectrometry. (A) Results obtained from tryptic peptides and (B) from chymotryptic peptides. Error bars indicate SEM. *, P<0.05; **, P<0.01; ***, P<0.001; n.s., not significant; n.d., not detected (i.e. did not meet the criteria for quantification).</p

Time courses of Thr849 (A) and Thr864 (B) phosphorylation and dephosphorylation.

<p>Prior to protein extraction from fly heads, flies were kept in the dark or were illuminated for 12–18 h before they were subjected to the opposite light conditions for the indicated periods of time. Black bars indicate darkness and white bars indicate white light as the last light condition. Western blots were probed with α-pT849, α-pT864, and α-TRP antibodies as indicated. Signals obtained with the phosphospecific antibodies were normalized to signals obtained with α-TRP antibody. Phosphorylation levels after 4 h of light adaptation were set to 100%. Molecular mass markers (in kilodalton) are indicated to the left.</p

Phosphate occupancy of Thr849 and Thr864.

<p>Flies were kept in the dark for 12–18 h and were then illuminated for 1 h before proteins were extracted from heads. TRP phosphorylated at Thr849 and Thr864 was precipitated using α-pT849 (A) and α-pT864 (B) antibodies. Inputs and immunoprecipitates were loaded onto SDS gels and transferred to PVDF membranes. Membranes were probed with α-pT849 (A) and α-pT864 (B) and α-TRP antibodies as indicated. (C), Phosphate occupancies at Thr849 and Thr864 were calculated from three independent experiments by quantifying the Western blot signals of inputs and immunoprecipitations (see Materials and Methods) and using the formula OC = (α-pTRP_input/α-TRP_input) × (α-TRP_IP/α-pTRP_IP)×100% (see text for explanation). Error bars indicate SEM.</p

Selected results of a candidate screen of kinase and phosphatase mutants that affect TRP phosphorylation at Thr849 and Thr864.

<p>Flies were illuminated for 12–18 h and then kept in the dark for 1 h (black bars) or <i>vice versa</i> (white bars) before they were subjected to Western blot analysis using α-pT849 and α-pT864 antibodies. All Western blots were reprobed with monoclonal α-TRP antibody to reveal the amount of TRP present in the samples. The lower panels show representative Western blots using α-pT849, α-pT864, and α-TRP antibodies. Molecular mass markers (in kilodalton) are indicated to the left. The diagram at the top shows a quantification of signals obtained with the phosphospecific antibodies from 3 independent experiments for each mutant that were normalized to the signals obtained with the generic α-TRP antibody. Relative Phosphorylation in percent was obtained by comparing the values of the mutants with the values of light-adapted wild type flies (set to 100%) on the same Western blot. Error bars show SEM (n = 3). All results of the screen are depicted in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073787#pone.0073787.s005" target="_blank">Table S2</a>. Vertical black lines indicate that the signals were taken from different membranes.</p

Light-Dependent Phosphorylation of the <i>Drosophila</i> Inactivation No Afterpotential D (INAD) Scaffolding Protein at Thr170 and Ser174 by Eye-Specific Protein Kinase C

<div><p><i>Drosophila</i> inactivation no afterpotential D (INAD) is a PDZ domain-containing scaffolding protein that tethers components of the phototransduction cascade to form a supramolecular signaling complex. Here, we report the identification of eight INAD phosphorylation sites using a mass spectrometry approach. PDZ1, PDZ2, and PDZ4 each harbor one phosphorylation site, three phosphorylation sites are located in the linker region between PDZ1 and 2, one site is located between PDZ2 and PDZ3, and one site is located in the N-terminal region. Using a phosphospecific antibody, we found that INAD phosphorylated at Thr170/Ser174 was located within the rhabdomeres of the photoreceptor cells, suggesting that INAD becomes phosphorylated in this cellular compartment. INAD phosphorylation at Thr170/Ser174 depends on light, the phototransduction cascade, and on eye-Protein kinase C that is attached to INAD via one of its PDZ domains.</p></div