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

Effect of Austenite Deformation on the Microstructure Evolution and Grain Refinement Under Accelerated Cooling Conditions

Although there has been much research regarding the effect of austenite deformation on accelerated cooled microstructures in microalloyed steels, there is still a lack of accurate data on boundary densities and effective grain sizes. Previous results observed from optical micrographs are not accurate enough, because, for displacive transformation products, a substantial part of the boundaries have disorientation angles below 15 deg. Therefore, in this research, a niobium microalloyed steel was used and electron backscattering diffraction mappings were performed on all of the transformed microstructures to obtain accurate results on boundary densities and grain refinement. It was found that with strain rising from 0 to 0.5, a transition from bainitic ferrite to acicular ferrite occurs and the effective grain size reduces from 5.7 to 3.1 μm. When further increasing strain from 0.5 to 0.7, dynamic recrystallization was triggered and postdynamic softening occurred during the accelerated cooling, leading to an inhomogeneous and coarse transformed microstructure. In the entire strain range, the density changes of boundaries with different disorientation angles are distinct, due to different boundary formation mechanisms. Finally, the controversial influence of austenite deformation on effective grain size of low-temperature transformation products was argued to be related to the differences in transformation conditions and final microstructures

Electronic Structure of EuMo6Se8 Studied by X-Ray Absorption Spectroscopy

[[abstract]]The rare-earth based molybdenum chalcogenides, REMo6Se8 (RE = rare-earth metals) have been extensively studied because of their unique crystal structure based on Mo6Se8 clusters and their outstanding properties involving coexistence of superconductivity and magnetism. Among all these compounds, Ce and Eu based chalcogenides are magnetic and non-superconductors and possess many novel properties. Understanding their electronic structure is likely to provide valuable information about these materials. We employ X-ray absorption near-edge structure (XANES) spectroscopy at Mo and Se K-edges of EuMo6Se8 to identify the local environment respectively around Mo and Se ions and XANES spectra at L3-edge of Eu ion to identify their valence state. Results from this study demonstrate that Se ions in EuMo6Se8 are in two inequivalent sites and the valency of Eu is divalent.[[incitationindex]]SCI[[booktype]]紙本[[countrycodes]]US

Uncovering Small RNA-Mediated Responses to Phosphate Deficiency in Arabidopsis by Deep Sequencing

Recent studies have demonstrated the important role of plant microRNAs (miRNAs) under nutrient deficiencies. In this study, deep sequencing of Arabidopsis (Arabidopsis thaliana) small RNAs was conducted to reveal miRNAs and other small RNAs that were differentially expressed in response to phosphate (Pi) deficiency. About 3.5 million sequence reads corresponding to 0.6 to 1.2 million unique sequence tags from each Pi-sufficient or Pi-deficient root or shoot sample were mapped to the Arabidopsis genome. We showed that upon Pi deprivation, the expression of miR156, miR399, miR778, miR827, and miR2111 was induced, whereas the expression of miR169, miR395, and miR398 was repressed. We found cross talk coordinated by these miRNAs under different nutrient deficiencies. In addition to miRNAs, we identified one Pi starvation-induced DICER-LIKE1-dependent small RNA derived from the long terminal repeat of a retrotransposon and a group of 19-nucleotide small RNAs corresponding to the 5' end of tRNA and expressed at a high level in Pi-starved roots. Importantly, we observed an increased abundance of TAS4-derived trans-acting small interfering RNAs (ta-siRNAs) in Pi-deficient shoots and uncovered an autoregulatory mechanism of PAP1/MYB75 via miR828 and TAS4-siR81(-) that regulates the biosynthesis of anthocyanin. This finding sheds light on the regulatory network between miRNA/ta-siRNA and its target gene. Of note, a substantial amount of miR399* accumulated under Pi deficiency. Like miR399, miR399* can move across the graft junction, implying a potential biological role for miR399*. This study represents a comprehensive expression profiling of Pi-responsive small RNAs and advances our understanding of the regulation of Pi homeostasis mediated by small RNAs

Electronic structure of aligned carbon nanotubes studied by scanning photoelectron microscopy

We have investigated the local electronic structures from tip and sidewall regions of aligned multi-walled carbon nanotubes (MWCNTs) by employing scanning photoelectron microscopy (SPEM) and micro-photoemission spectroscopy. Spatially resolved spectra of C 1s, Si 2p and valence band have been measured. In particular, we compared the results from MWCNTs grown on Fe thin film catalyst with those using Ti catalyst, where the quality of alignment is much lower. For Fe catalyst, the SPEM data show that the tips have a larger density of states (DOS) and a higher C 1s binding energy than those of the sidewalls. In the case of Ti catalyst, Si 2p signal is detected within the CNT bundles. Different Si species can be identified. It is suggested that during the plasma-enhanced growth process, Si is transported into the CNT layer

Electronic structures of hexagonal manganites HoMnO3 studied by X-ray absorption near-edge structure

AIP Conf. Proceed., 2007, CP879, 1659-166

Induction of hepatotoxicity by sanguinarine is associated with oxidation of protein thiols and disturbance of mitochondrial respiration

Sanguinarine (SANG) has been suggested to be one of the principle constituents responsible for the toxicity of Argemone mexicana seed oil. In this study, we focused on the possible mechanism of SANG-induced hepatotoxicity. The serum asparatate aminotransferase (AST), alanine aminotransferase (ALT), and lactate dehydrogenase (LDH) activities, hepatic vacuolization, lipid accumulation and lipid peroxidation of the liver were increased, and triglyceride (TG) was decreased in SANG-treated mice (10 mg kg(-1) i.p.), indicating damage to the liver. SANG induced cell death and DNA fragmentation, in a concentration- (0-30 mu M) and time-dependent (0-24 h) manner, and the cytotoxicity of SANG (15 mu M) was accompanied by an increase in reactive oxygen species and a lessening in protein thiol content; these outcomes were reversed by glutathione, N-acetyl-L-cysteine and 1,4-dithiothretol, and slightly improved by other antioxidants in hepatocytes. SANG can affect the function of mitochondria, leading to the depletion of the mitochondrial membrane potential and adenosine 5'-triphosphate content of hepatocytes. SANG caused an upcoupling effect of the respiratory chain at lower concentrations, but inhibited the respiratory chain at higher concentrations in mitochondira isolated from rat liver. In conclusion, the data suggest that SANG is a liver toxin that induces cytotoxicity in liver cells, possibly through oxidation of protein thiols, resulting in oxidative stress on the cells and disturbance of mitochondrial function. Copyright (C) 2008 John Wiley & Sons, Ltd

Electronic structures and bonding properties of chlorine-treated nitrogenated carbon nanotubes: X-ray absorption and scanning photoelectron microscopy studies

[[abstract]]The electronic and bonding properties of nitrogenated carbon nanotubes (N-CNTs) exposed to chlorine plasma were investigated using C and N K-edge x-ray absorption near-edge structure (XANES) and scanning photoelectron microscopy (SPEM). The C and N K-edge XANES spectra of chlorine-treated N-CNTs consistently reveal the formation of pyridinelike N-CNTs by the observation of 1s→π*(e2u) antibonding and 1s→π*(b2g) bonding states. The valence-band photoemission spectra obtained from SPEM images indicate that chlorination of the nanotubes enhances the C–N bonding. First-principles calculations of the partial densities of states in conjunction with C K-edge XANES data identify the presence of C–Cl bonding in chlorine treated N-CNTs.[[notice]]補正完畢[[booktype]]紙本[[booktype]]電子