Enhancing cross-evidence reasoning graph for document-level relation extraction.

The objective of document-level relation extraction (RE) is to identify the semantic connections that exist between named entities present within a document. However, most entities are distributed among different sentences, there is a need for inter-entity relation prediction across sentences. Existing research has focused on framing sentences throughout documents to predict relationships between entities. However, not all sentences play a substantial role in relation extraction, which inevitably introduces noisy information. Based on this phenomenon, we believe that we can extract evidence sentences in advance and use these evidence sentences to construct graphs to mine semantic information between entities. Thus, we present a document-level RE model that leverages an Enhancing Cross-evidence Reasoning Graph (ECRG) for improved performance. Specifically, we design an evidence extraction rule based on center-sentence to pre-extract higher-quality evidence. Then, this evidence is constructed into evidence graphs to mine the connections between mentions within the same evidence. In addition, we construct entity-level graphs by aggregating mentions from the same entities within the evidence graphs, aiming to capture distant interactions between entities. Experiments result on both DocRED and RE-DocRED datasets demonstrate that our model improves entity RE performance compared to existing work.

The Carthamus tinctorius L. genome sequence provides insights into synthesis of unsaturated fatty acids.

Domesticated safflower (Carthamus tinctorius L.) is a widely cultivated edible oil crop. However, despite its economic importance, the genetic basis underlying key traits such as oil content, resistance to biotic and abiotic stresses, and flowering time remains poorly understood. Here, we present the genome assembly for C. tinctorius variety Jihong01, which was obtained by integrating Oxford Nanopore Technologies (ONT) and BGI-SEQ500 sequencing results. The assembled genome was 1,061.1 Mb, and consisted of 32,379 protein-coding genes, 97.71% of which were functionally annotated. Safflower had a recent whole genome duplication (WGD) event in evolution history and diverged from sunflower approximately 37.3 million years ago. Through comparative genomic analysis at five seed development stages, we unveiled the pivotal roles of fatty acid desaturase 2 (FAD2) and fatty acid desaturase 6 (FAD6) in linoleic acid (LA) biosynthesis. Similarly, the differential gene expression analysis further reinforced the significance of these genes in regulating LA accumulation. Moreover, our investigation of seed fatty acid composition at different seed developmental stages unveiled the crucial roles of FAD2 and FAD6 in LA biosynthesis. These findings offer important insights into enhancing breeding programs for the improvement of quality traits and provide reference resource for further research on the natural properties of safflower.

Promotion of SO2 resistance of Ce-La/TiO2 denitrification catalysts by V doping.

Conventional cerium-based denitrification catalysts show good catalytic activity at moderate and high temperatures, but their denitrification performance may be decreased due to poisoning by SO2 in the flue gas. In this paper, V was introduced into Ce-La/TiO2 catalysts by a ball-milling method, and the effects of the V content on catalyst denitrification performance and SO2 resistance were investigated. Fourier-transform diffuse reflectance in situ infrared spectroscopy was used to examine the denitrification mechanism and evaluate the catalysts for surface acidity, redox characteristics, and SO2 adsorption. After introducing V, Brønsted acids played the dominant role in the catalytic reaction by increasing the number of acidic sites on the catalyst surface, adsorbing NH3 to participate in the reaction, and improving the sulfur resistance by inhibiting SO2 poisoning. The Ce3+ and O ratio on the catalyst surface were also enhanced by V doping, which reduced interactions between SO2 and the primary metal oxide active ingredients. The modified catalyst inhibited the formation of sulfate species on the catalyst surface and prevented the generation of additional nitrate species on the surface, which protected the main active sites. After V doping, the NH3-SCR reaction on the catalyst surface followed the Langmuir-Hinshelwood mechanism.

Preparation of high temperature NH3-SCR catalysts with carbonate as precursors by ball milling method.

High-temperature 10Ce-2La/TiO2 catalysts for selective catalytic reduction of NO with NH3 were prepared by the ball milling, impregnation and co-precipitation methods and their catalytic performance was compared. The effects of different starting materials of the ball milling method on the catalytic activity were investigated. The results showed that the 10Ce-2La/TiO2 catalyst prepared by the ball milling method using carbonates as starting materials exhibited the highest NO conversion, which was more than 80% in the temperature range of 330-550 °C. The as-prepared catalysts were characterized by XRD, TEM, and XPS. Results showed that the ball milling prepared 10Ce-2La/TiO2 had the advantages of uniform active site distribution, high oxygen storage capacity, and high Ce3+ and Oα ratio. The results of NH3-TPD and H2-TPR showed that the ball milling method not only improved the redox ability but also increased the quantities and concentration of the acidic sites. The green production and economically viable concept of this process provides a new solution for the production application of industrial catalysts.

A Generalized Assessment of the Impact of Regionalization and Provider Learning on Patient Outcomes.

We present a generalized model to assess the impact of regionalization on patient care outcomes in the presence of heterogeneity in provider learning. The model characterizes best regionalization policies as optimal allocations of patients across providers with heterogeneous learning abilities. We explore issues that arise when solving for best regionalization, which depends on statistically estimated provider learning curves. We explain how to maintain the problem's tractability and reformulate it into a binary integer program problem to improve solvability. Using our model, best regionalization solutions can be computed within reasonable time using current-day computers. We apply the model to minimally invasive radical prostatectomy and estimate that, in comparison to current care delivery, within-state regionalization can shorten length of stay by at least 40.8%.

Discovery and analysis of microRNAs in Leymus chinensis under saline-alkali and drought stress using high-throughput sequencing.

Leymus chinensis (Trin.) Tzvel. is a perennial rhizome grass of the Poaceae (also called Gramineae) family, which adapts well to drought, saline and alkaline conditions. However, little is known about the stress tolerance of L. chinensis at the molecular level. microRNAs (miRNAs) are known to play critical roles in nutrient homeostasis, developmental processes, pathogen responses, and abiotic stress in plants. In this study, we used Solexa sequencing technology to generate high-quality small RNA data from three L. chinensis groups: a control group, a saline-alkaline stress group (100 mM NaCl and 200 mM NaHCO3), and a drought stress group (20% polyethylene glycol 2000). From these data we identified 132 known miRNAs and 16 novel miRNAs candidates. For these miRNAs we also identified target genes that encode a broad range of proteins that may be correlated with abiotic stress regulation. This is the first study to demonstrate differentially expressed miRNAs in L. chinensis under saline-alkali and drought stress. These findings may help explain the saline-alkaline and drought stress responses in L. chinensis.

Identifying Human Genome-Wide CNV, LOH and UPD by Targeted Sequencing of Selected Regions.

Copy-number variations (CNV), loss of heterozygosity (LOH), and uniparental disomy (UPD) are large genomic aberrations leading to many common inherited diseases, cancers, and other complex diseases. An integrated tool to identify these aberrations is essential in understanding diseases and in designing clinical interventions. Previous discovery methods based on whole-genome sequencing (WGS) require very high depth of coverage on the whole genome scale, and are cost-wise inefficient. Another approach, whole exome genome sequencing (WEGS), is limited to discovering variations within exons. Thus, we are lacking efficient methods to detect genomic aberrations on the whole genome scale using next-generation sequencing technology. Here we present a method to identify genome-wide CNV, LOH and UPD for the human genome via selectively sequencing a small portion of genome termed Selected Target Regions (SeTRs). In our experiments, the SeTRs are covered by 99.73%~99.95% with sufficient depth. Our developed bioinformatics pipeline calls genome-wide CNVs with high confidence, revealing 8 credible events of LOH and 3 UPD events larger than 5M from 15 individual samples. We demonstrate that genome-wide CNV, LOH and UPD can be detected using a cost-effective SeTRs sequencing approach, and that LOH and UPD can be identified using just a sample grouping technique, without using a matched sample or familial information.

An integrated tool to study MHC region: accurate SNV detection and HLA genes typing in human MHC region using targeted high-throughput sequencing.

The major histocompatibility complex (MHC) is one of the most variable and gene-dense regions of the human genome. Most studies of the MHC, and associated regions, focus on minor variants and HLA typing, many of which have been demonstrated to be associated with human disease susceptibility and metabolic pathways. However, the detection of variants in the MHC region, and diagnostic HLA typing, still lacks a coherent, standardized, cost effective and high coverage protocol of clinical quality and reliability. In this paper, we presented such a method for the accurate detection of minor variants and HLA types in the human MHC region, using high-throughput, high-coverage sequencing of target regions. A probe set was designed to template upon the 8 annotated human MHC haplotypes, and to encompass the 5 megabases (Mb) of the extended MHC region. We deployed our probes upon three, genetically diverse human samples for probe set evaluation, and sequencing data show that ∼97% of the MHC region, and over 99% of the genes in MHC region, are covered with sufficient depth and good evenness. 98% of genotypes called by this capture sequencing prove consistent with established HapMap genotypes. We have concurrently developed a one-step pipeline for calling any HLA type referenced in the IMGT/HLA database from this target capture sequencing data, which shows over 96% typing accuracy when deployed at 4 digital resolution. This cost-effective and highly accurate approach for variant detection and HLA typing in the MHC region may lend further insight into immune-mediated diseases studies, and may find clinical utility in transplantation medicine research. This one-step pipeline is released for general evaluation and use by the scientific community.

Transcriptome exploration in Leymus chinensis under saline-alkaline treatment using 454 pyrosequencing.

BACKGROUND: Leymus chinensis (Trin.) Tzvel. is a high saline-alkaline tolerant forage grass genus of the tribe Gramineae family, which also plays an important role in protection of natural environment. To date, little is known about the saline-alkaline tolerance of L. chinensis on the molecular level. To better understand the molecular mechanism of saline-alkaline tolerance in L. chinensis, 454 pyrosequencing was used for the transcriptome study. RESULTS: We used Roche-454 massive parallel pyrosequencing technology to sequence two different cDNA libraries that were built from the two samples of control and under saline-alkaline treatment (optimal stress concentration-Hoagland solution with 100 mM NaCl and 200 mM NaHCO(3)). A total of 363,734 reads in control group and 526,267 reads in treatment group with an average length of 489 bp and 493 bp were obtained, respectively. The reads were assembled into 104,105 unigenes with MIRA sequence assemable software, among which, 73,665 unigenes were in control group, 88,016 unigenes in treatment group and 57,576 unigenes in both groups. According to the comparative expression analysis between the two groups with the threshold of "log2 Ratio ≥1", there were 36,497 up-regulated unegenes and 18,218 down-regulated unigenes predicted to be the differentially expressed genes. After gene annotation and pathway enrichment analysis, most of them were involved in stress and tolerant function, signal transduction, energy production and conversion, and inorganic ion transport. Furthermore, 16 of these differentially expressed genes were selected for real-time PCR validation, and they were successfully confirmed with the results of 454 pyrosequencing. CONCLUSIONS: This work is the first time to study the transcriptome of L. chinensis under saline-alkaline treatment based on the 454-FLX massively parallel DNA sequencing platform. It also deepened studies on molecular mechanisms of saline-alkaline in L. chinensis, and constituted a database for future studies.

Gene expression profiling of soybean leaves and roots under salt, saline-alkali and drought stress by high-throughput Illumina sequencing.

Salt, saline-alkali and drought stresses are major environmental constraints for the production and yield of soybean worldwide. To identify genes responsible for stress tolerance, the transcriptional profiles of genes in leaves and roots of seedlings (two-leaf stage) of the soybean inbred line HJ-1 were examined after 48 h under various stress conditions; salt (120 mM NaCl), saline-alkali (70 mM NaCl and 50mM NaHCO(3)) and drought (2% PEG 8000). Gene expression at the transcriptional level was investigated using high-throughput Illumina sequencing technology and bioinformatics tools. Under salt, saline-alkali and drought stress, 874, 1897, and 535 genes, respectively, were up-regulated in leaves, and 1822, 1731 and 1690 genes, respectively, were up-regulated in roots, compared with expression in the corresponding organ in control plants. Comparisons among salt, saline-alkali and drought stress yielded similar results in terms of the percentage of genes classified into each GO category. Moreover, 69 genes differentially expressed in both organs with similar expression patterns clustered together in the taxonomic tree across all conditions. Furthermore, comparison of gene expression among salt, saline-alkali and drought treated plants revealed that genes associated with calcium-signaling and nucleic acid pathways were up-regulated in the responses to all three stresses, indicating a degree of cross-talk among these pathways. These results could provide new insights into the stress tolerance mechanisms of soybean.

Species-specific size expansion and molecular evolution of the oleosins in angiosperms.

Oleosins are hydrophobic plant proteins thought to be important for the formation of oil bodies, which supply energy for seed germination and subsequent seedling growth. To better understand the evolutionary history and diversity of the oleosin gene family in plants, especially angiosperms, we systematically investigated the molecular evolution of this family using eight representative angiosperm species. A total of 73 oleosin members were identified, with six members in each of four monocot species and a greater but variable number in the four eudicots. A phylogenetic analysis revealed that the angiosperm oleosin genes belonged to three monophyletic lineages. Species-specific gene duplications, caused mainly by segmental duplication, led to the great expansion of oleosin genes and occurred frequently in eudicots after the monocot-eudicot divergence. Functional divergence analyses indicate that significant amino acid site-specific selective constraints acted on the different clades of oleosins. Adaptive evolution analyses demonstrate that oleosin genes were subject to strong purifying selection after their species-specific duplications and that rapid evolution occurred with a high degree of evolutionary dynamics in the pollen-specific oleosin genes. In conclusion, this study serves as a foundation for genome-wide analyses of the oleosins. These findings provide insight into the function and evolution of this gene family in angiosperms and pave the way for studies in other plants.

De novo sequencing and comparative analysis of the blueberry transcriptome to discover putative genes related to antioxidants.

Blueberry (Vaccinium spp.) is an important small fruit crop rich in antioxidants. However, tissue-specific transcriptome and genomic data in public databases are not sufficient for an understanding of the molecular mechanisms associated with antioxidants, especially the biosynthesis of anthocyanins. Here, we obtained more than 64 million sequencing reads from blueberry skin and pulp using Illumina sequencing technology. De novo assemblies yielded 34,464 unigenes, among them 1236 transcripts and 862 putative transcription factors involved in the main antioxidant biosynthesis pathway were identified. Comparative transcript profiling allowed the identification of 92 differentially expressed genes with potential relevance in regulating the fruit metabolism and anthocyanin content during ripening. A series of qRT-PCR confirmed the high expression level of the anthocyanin pathway genes in the skin of the blue fruit from the in silico study. This sequence collection provides a significant resource for the blueberry research and breeding work.

Sequence mining and transcript profiling to explore differentially expressed genes associated with lipid biosynthesis during soybean seed development.

BACKGROUND: Soybean (Glycine max L.) is one of the most important oil crops in the world. It is desirable to increase oil yields from soybean, and so this has been a major goal of oilseed engineering. However, it is still uncertain how many genes and which genes are involved in lipid biosynthesis. RESULTS: Here, we evaluated changes in gene expression over the course of seed development using Illumina (formerly Solexa) RNA-sequencing. Tissues at 15 days after flowering (DAF) served as the control, and a total of 11592, 16594, and 16255 differentially expressed unigenes were identified at 35, 55, and 65 DAF, respectively. Gene Ontology analyses detected 113 co-expressed unigenes associated with lipid biosynthesis. Of these, 15 showed significant changes in expression levels (log2fold values ≥ 1) during seed development. Pathway analysis revealed 24 co-expressed transcripts involved in lipid biosynthesis and fatty acid biosynthesis pathways. We selected 12 differentially expressed genes and analyzed their expressions using qRT-PCR. The results were consistent with those obtained from Solexa sequencing. CONCLUSION: These results provide a comprehensive molecular biology background for research on soybean seed development, particularly with respect to the process of oil accumulation. All of the genes identified in our research have significance for breeding soybeans with increased oil contents.

Investigation of the microRNAs in safflower seed, leaf, and petal by high-throughput sequencing.

Safflower (Carthamus tinctorius L.) is one of the most important crop plants that has been utilized for production of oleosins. miRNAs (microRNAs) are a class of small and non-coding RNAs that negatively regulate gene expression at post-transcriptional level thus playing a role in plant growth, development, and stress response. In this study, high-throughput Illumina sequencing technology has been used to comprehensively investigate the small RNA transcriptomes of safflower seed, flower, and leaf. It is found that there are at least 236 known miRNAs expressed in safflower, of which 100 miRNAs with relatively high expression abundance exhibited evolutionary conservation across multiple plants. Comparison of their expression abundance among different tissues shows that a total of 116, 133, and 128 miRNAs are significantly differentially expressed with higher abundance or lower abundance between safflower seed/leaf, seed/petal, and leaf/petal. The majority of the most significant differences in miRNA abundance between tissues are tissue-specific miRNAs. In addition, 13 putative novel miRNAs have been identified in safflower. The small RNA transcriptomes obtained in this study provide a basis for further investigation of the physiological roles of identified miRNAs in safflower.