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

Herbivorous insect causes deficiency of pigment-protein complexes in an oval-pointed cecidomyiid gall of Machilus thunbergii leaf

This research compared the chlorophyll biosynthetic and degradation pathways, pigment-protein complexes, and thylakoid morphology of a mature oval-pointed cecidomyiid gall and the infected leaf of host plant Machilus thunbergii Sieb & Zucc (Lauraceae). The mature gall always possesses far less photosynthetic pigment than the infected leaf. The content of anthocyanin and tannin of the gall are much higher than in the infected leaf. Both the mole percent of porphyrin and the ratio of pheophytin/chlorophyllide are much different between the gall and infected leaf, suggesting their chlorophyll biosynthetic and degradation pathways are much different. While the infected leaf may take the degradation pathway of chlorophyll-->pheophytin-->pheophorbide as the major route, the cicedomyiid gall may take chlorophyll-->chlorophyllide-->pheophorbide as the major route. The infected leaf still possesses the CPI and CPII pigment-protein complexes fractionated by Thornber system, or the A1, AB1, AB2, AB3 pigment-protein complexes fractionated by the MARS system while the mature gall contains only CPII or AB3. Electron microscopy demonstrated that the mature gall has normal grana and thylakoid morphology. It is still unknown whether the unique deficiency of pigment-protein complexes is ubiquitous and how the cecidomyiid insects cause the deficiency of some pigment-protein complexes

Time deficiency of photosynthetic pigment-protein complexes CP1, A1, AB1, and AB2 in two cecidomyiid galls derived from Machilus thunbergii leaves

Two kinds of cecidomyiid galls induced by Daphnephila on Machilus thunbergii Sieb. & Zucc. leaves at various developmental stages, i.e., young, growing, and mature, were analyzed for their biochemical composition of photosynthetic pigment-protein complexes located in thylakoid membranes using the Thornber and MARS electrophoretic fractionation systems. Both kinds of galls were totally deficient in the pigment-protein complexes CP1, and A1, AB1, and AB2 through the whole period of gall formation. Immunoblotting of antibody against light-harvesting complex 2b (LHC2b) apoprotein confirmed this deficiency in gall's lifetime, which never recovered under any condition. Electron microscopy demonstrated that already at the early developmental stage the gall chloroplasts had thylakoid morphology like that in a normal leaf

Changes in the morphology and cation content of a Bambusa edulis xylem mutant, vse, derived from somaclonal variation

A xylem mutant (vse) was isolated from a Bambusa edulis (Odashima) Keng plantlet following vegetative micropropagation and subculture for 7 consecutive years and induced to proliferate in medium supplemented with 0.1 mg(.)L(-1) (0.5 mu m) thidiazuron (TDZ) and to develop roots in medium supplemented with 5 mg(.)L(-1) (26.9 mu m) alpha-naphthaleneacetic acid (NAA). Subsequent investigations comparing the growth habits of mutant plantlets with those of the wild type indicated that the growth of the former was retarded in a greenhouse. Several morphological abnormalities were observed in the vse mutant: it had thinner stems with fewer trichromes on the surface; the xylem vessels were smaller in diameter and contained crystal-like structures in the pith; the leaves were shorter and narrower with a sharp leaf blade angle; the roots were thinner and contained fewer xylem cells. The cation concentrations of both the mutant and wild type were similar in the in vitro analysis, except for those of iron and potassium, which were lower in mutant leaves in vivo. In 2-month-old mutant plants, iron chlorosis was observed on young leaves and a potassium deficiency was observed on older leaves. After 1 year of growth in the greenhouse, all of the wild-type plants had survived, but only 27% (16/60) of the mutant vse plants were alive

LZF1, a HY5-regulated transcriptional factor, functions in Arabidopsis de-etiolation

We surveyed differential gene expression patterns during early photomorphogenesis in both wild-type and mutant Arabidopsis defective in HY5, an influential positive regulator of the responses of gene expression to a light stimulus, to identify light-responsive genes whose expression was HY5 dependent. These gene-expression data identified light-regulated zinc finger protein 1 (LZF1), a gene encoding a previously uncharacterized C2C2-CO B-box transcriptional regulator. HY5 has positive trans-activating activity toward LZF1 and binding affinity to LZF1 promoter in vivo. HY5 is needed but not sufficient for the induction of LZF1 expression. Anthocyanin content is significantly diminished in lzf1 under far red, which is the most efficient light for the induction of LZF1. The expression of PAP1/MYB75 is elevated in plants overexpressing LZF1, which leads to the hyperaccumulation of anthocyanin in transgenic Arabidopsis. The transition from etioplast to chloroplast and the accumulation of chlorophyll were notably compromised in the lzf1 mutant. We provide molecular evidence that LZF1 influences chloroplast biogenesis and function via regulating genes encoding chloroplast proteins. In the absence of HY5, mutation of LZF1 leads to further reduced light sensitivity for light-regulated inhibition of hypocotyl elongation and anthocyanin and chlorophyll accumulation. Our data indicate that LZF1 is a positive regulator functioning in Arabidopsis de-etiolation

Differential protein expression of two photosystem II subunits, PsbO and PsbP, in an albino mutant of Bambusa edulis with chloroplast DNA aberration

The chloroplast genome of an albino mutant isolated from tissue culture of the bamboo Bambusa edulis Munro was examined to identify aberrations. A number of the chloroplast genes encoding ATP synthases, photosystem II subunits, NADH dehydrogenase, and ribosomal proteins had been deleted, at least partially, in the albino mutant. Comparison of the two-dimensional electrophoresis profiles of albino and green bamboos revealed three spots of reduced intensity, indicating repression of these proteins in the albino mutants. Mass spectroscopic analysis subsequently revealed that two of these proteins are 33-kDa subunits of the photosystem II oxygen-evolving protein complex (PsbO) and one is a 23-kDa subunit of photosystem II oxygen-evolving protein complex (PsbP). The genes encoding these two proteins were cloned from B. edulis, and were denoted BePsbO (accession no. EF669513) and BePsbP (accession no. EF669512). Reverse transcription polymerase chain reaction and two-dimensional gel analyses of BePsbO and BePsbP in green and albino bamboos grown in the light or dark revealed that the albino mutant, similar to its green counterpart, sensed the light signal, resulting in the induction of BePsbO and BePsbP transcription, but it did not accumulate the protein products. We conclude that the repression of protein-expressing BePsbO and BePsbP is because of a defect in post-transcriptional regulation in the albino mutant