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

Paternity assignment in the polyploid Acipenser dabryanus based on a novel microsatellite marker system.

Acipenser dabryanus is listed as a Critical Endangered species in the IUCN Red List and the first class protected animals in China. Fortunately, A. dabryanus specimens are being successfully bred in captivity for conservation. However, for effective ex situ conservation, we should be aware of the genetic diversity and the degree of relatedness of the individuals selected for breeding. In this study, we aimed at the development of novel and reliable microsatellites used for the genetic study of A. dabryanus. A total of 14,321 simple sequence repeats (SSRs) were detected by transcriptome sequencing and screening. We selected 20 novel and polymorphic microsatellites (non-dinucleotide) with good repeatability from the 100 tested loci for a subsequent genetic and paternity study. A set of captive broodstock (F1 stock, n = 43) and their offspring (F2 stock, n = 96) were used to examine the efficiency of the 20 SSRs for assigning parentage to offspring, with an allocation success of 91.7%. We also found that only a few families predominantly contributed to the progeny produced by the 43 breeders. In addition, mitochondrial DNA data showed that the captive broodstock (F1 individuals) had an excellent probability of the same lineage, implying that a high level of inbreeding may have occurred in these individuals. Our research provides useful information on genetic diversity and reproductive pattern of A. dabryanus, and the 20 SSRs developed in this study can be applied to the future breeding program to avoid inbreeding for this stock or other related species of Acipenseriformes

Transcriptome sequencing of the spleen of the Yangtze sturgeon (Acipenser dabryanus) under Edwardsiella tarda and poly(I:C) treatments

Acipenser dabryanus is an ancient living fossil and a flagship species of the Yangtze River. However, A. dabryanus was listed as a critically endangered species due to the dramatic decrease in its population, and disease outbreaks occurring during captive breeding have hindered the protection of this species. Here, we investigated the effect of the pathogenic bacterium Edwardsiella tarda and poly(I:C) on A. dabryanus at the histopathological and transcriptomic levels. After 48 h of infection with E. tarda, A. dabryanus exhibited marked pathological changes in the intestine and liver. We then conducted full-length transcriptome sequencing of the spleen by SMRT sequencing technology. Using the full-length transcriptome data as a reference, transcriptomic results obtained through Illumina sequencing technology revealed that a total of 894 and 963 unigenes were differentially expressed between the PBS and bacterial infection groups and between the PBS and poly(I:C) challenge groups, respectively. E3 ubiquitin ligases family members, T-cell receptor and clusters of differentiation were significantly upregulated by bacteria or poly(I:C) treatment, while the complement was significantly downregulated, suggesting that they might participate in multiple immune pathways in the response to pathogen invasion. Pathogen infection also induced changes in some key rate-limiting enzymes involved in energy metabolism. Our study can provide important information on the molecular mechanisms underlying the immune response of fish to pathogenic microbial infections and help explore the antibacterial and antiviral immunity of A. dabryanus

Integrated biochemical, transcriptomic and metabolomic analyses provide insight into heat stress response in Yangtze sturgeon (Acipenser dabryanus)

Temperature fluctuations caused by climate change and global warming pose a great threat to various species. Most fish are particularly vulnerable to elevated temperatures. Understanding the mechanism of high-temperature tolerance in fish can be beneficial for proposing effective strategies to help fish cope with global warming. In this study, we systematically studied the effects of high temperature on Acipenser dabryanus, an ancient living fossil and flagship species of the Yangtze River, at the histological, biochemical, transcriptomic and metabolomic levels. Intestinal and liver tissues from the control groups (18 °C) and acute heat stress groups (30 °C) of A. dabryanus were sampled for histological observation and liver tissues were assessed for transcriptomic and metabolomic profiling. Histopathological analysis showed that the intestine and liver tissues were damaged after heat stress. The plasma cortisol content and the levels of oxidative stress markers (catalase/glutathione reductase) and two aminotransferases (aspartate aminotransferase/alanine aminotransferase) increased significantly in response to acute heat stress. Transcriptomic and metabolomic methods showed 6707 upregulated and 4189 downregulated genes and 64 upregulated and 78 downregulated metabolites in the heat stress group. Heat shock protein (HSP) genes showed striking changes in expression under heat stress, with 21 genes belonging to the HSP30, HSP40, HSP60, HSP70 and HSP90 families significantly upregulated by short-term heat stress. The majority of genes associated with ubiquitin and various immune-related pathways were also markedly upregulated in the heat stress group. In addition, the combined analysis of metabolites and gene profiles suggested an enhancement of amino acid metabolism and glycometabolism and the suppression of fatty acid metabolism during heat stress, which could be a potential energy conservation strategy for A. dabryanus. To the best of our knowledge, the present study represents the first attempt to reveal the mechanisms of heat stress responses in A. dabryanus, which can provide insights into improved cultivation of fish in response to global warming

Gonadal transcriptome sequencing of the critically endangered Acipenser dabryanus to discover candidate sex-related genes

Background Acipenser dabryanus, an endemic Chinese species, has been listed as a first-class protected animal in China. Sturgeons are among the oldest and most primitive group of existing fish in the world and occupy a special place in the evolutionary history of fish. Thus, a study of the reproduction and sex differentiation of sturgeon will be of great value for fish as well as the whole vertebrate group. Methods In this study, we conducted comparative analysis of the testes and ovaries transcriptomes of A. dabryanus to screen for sex-differentiation and sexual development-related genes. Results The transcriptome sequencing of six cDNA libraries generated 265 million clean reads, encompassing 79 Gb of sequences. The N50 and mean length of the identified 91,375 unigenes were 1,718 and 989 bp, respectively. A total of 6,306, 9,961, 13,170, 15,484, and 23,588 unigenes were annotated in the clusters of orthologous groups, gene ontology categories, Kyoto Encyclopedia of Genes and Genomes Pathway, euKaryotic orthologous groups, and NCBI non-redundant protein databases, respectively. A total of 5,396 differentially expressed genes were found between the two sexes, with 1,938 predicted to be up-regulated in ovaries and 3,458 in testes. A total of 73 candidate genes known to be involved in sex differentiation and sexual development were searched in the transcriptome of A. dabryanus of which 52 showed significant similarity. We highlighted six genes that are differentially expressed between the two sexes and may play important roles in sex differentiation and gonad maintenance. In addition, 24,271 simple sequence repeats (SSRs) and 550,519 single-nucleotide polymorphisms (SNPs) were detected. Discussion This work represents the first transcriptome study comparing the ovary and testis in A. dabryanus. The putative differentially expressed genes between the gonads provide an important source of information for further study of the sex-differentiation related genes and the sex-differentiation mechanism in sturgeons. The SSRs or SNPs identified in this study will be helpful in the discovery of sex-related markers in A. dabryanus

A high-strength heterogeneous structural dual-phase steel

The strengthening and ductilization of steels are of great importance to weight reduction of vehicles. In this work, the strength-ductility synergy of dual-phase (DP) steels was obtained by properly tailoring the structural heterogeneity, including the distribution and fraction of constituent phases. It was demonstrated that heterogeneous structural DP steels with high volume fraction of martensite (from 64 to 83%) led to a good combination of strength and ductility. Compared with the cold-rolled sheets, the tensile strength and uniform elongation of heterogeneous DP steel increased by 700MPa (from 1.06 to 1.76GPa) and 2.7% (from 1.3 to 4%), respectively. The contributions from back stress and effective stress were analyzed by cyclic loading-unloading experiments. The underlying deformation mechanism was discussed based on the results of mechanical test and microstructure observation

Proportion of the offspring assigned to each mating pair inferred from the parentage analysis.

<p>The number of offspring in each cohort is shown above the bar.</p

Characteristics of the novel microsatellite marker system of <i>Acipenser dabryanus</i>.

<p>Characteristics of the novel microsatellite marker system of <i>Acipenser dabryanus</i>.</p

Resveratrol Improves the Digestive Ability and the Intestinal Health of Siberian Sturgeon

The lack of detailed information on nutritional requirement results in limited feeding in Siberian sturgeon. In this study, resveratrol, a versatile natural extract, was supplemented in the daily diet, and the digestive ability and microbiome were evaluated in the duodena and valvular intestines of Siberian sturgeon. The results showed that resveratrol increased the activity of pepsin, α-amylase, and lipase, which was positively associated with an increase in the digestive ability, but it did not influence the final body weight. Resveratrol improved the digestive ability probably by distinctly enhancing intestinal villus height. Microbiome analysis revealed that resveratrol changed the abundance and composition of the microbial community in the intestine, principally in the duodenum. Random forests analysis found that resveratrol significantly downregulated the abundance of potential pathogens (Citrobacter freundii, Vibrio rumoiensis, and Brucella melitensis), suggesting that resveratrol may also improve intestinal health. In summary, our study revealed that resveratrol improved digestive ability and intestinal health, which can contribute to the development of functional feed in Siberian sturgeon