Selecting a semantic similarity measure for concepts in two different CAD model data ontologies

Semantic similarity measure technology based approach is one of the most popular approaches aiming at implementing semantic mapping between two different CAD model data ontologies. The most important problem in this approach is how to measure the semantic similarities of concepts between two different ontologies. A number of measure methods focusing on this problem have been presented in recent years. Each method can work well between its specific ontologies. But it is unclear how accurate the measured semantic similarities in these methods are. Moreover, there is yet no evidence that any of the methods presented how to select a measure with high similarity calculation accuracy. To compensate for such deficiencies, this paper proposes a method for selecting a semantic similarity measure with high similarity calculation accuracy for concepts in two different CAD model data ontologies. In this method, the similarity calculation accuracy of each candidate measure is quantified using Pearson correlation coefficient or residual sum of squares. The measure with high similarity calculation accuracy is selected through a comparison of the Pearson correlation coefficients or the residual sums of squares of all candidate measures. The paper also reports an implementation of the proposed method, provides an example to show how the method works, and evaluates the method by theoretical and experimental comparisons. The evaluation result suggests that the measure selected by the proposed method has good human correlation and high similarity calculation accuracy

Protective effect of five-flavor sophora flavescens enteric-coated capsules on inflammatory bowel disease and its molecular mechanism

Abstract This study aims to investigate the effect of five-flavor sophora flavescens enteric-coated capsules (FSEC) on TNF-α-induced inflammatory bowel disease and its molecular mechanism. Wistar Rats were divided divided into 6 groups: Normal control group (group A): normal diet, drinking water; Model group (group B): 100 μg/L TNF-α; FSEC high-dose group (group C): 100μg/L TNF-α + FSEC (432 mg/kg); FSEC medium-dose group (group D): 100 μg/L TNF-α + FSEC (216 mg/kg); FSEC low-dose group (group E): 100 μg/L TNF-α + FSEC (108 mg/kg); Positive control group (group F): 100 μg/L TNF-α + 500 mg/kg sulfasalazine (SAZ). Animals in each group were intragastrically administered twice daily for 7 days. Animals were sacrificed 24 hours after the last treatment and colon tissues were collected for subsequent experiments. The results of HE staining showed that the colonic tissue of TNF-α-fed animals appeared damage, while the colonic tissue of animals treated with FSEC was improved to various degrees, and the histological characteristics of colon were basically recovered in the high-dose group, suggesting that FSEC could be used to treat TNF-α-induced colonic tissue damage. According to the results of ELISA and immunohistochemistry, the recovery of colonic tissue structure in rats treated with different doses of FSEC might be related to the decrease of TNF-α, IL-6, IL-17, TLR-4 and NF-κB proteins expression. According to the results of Western blotting, TNF-α-pretreated IEC-6 cells cultured with medicated serum decreased the expression of TRIF and IFN-γ proteins. These results suggest that FSEC has a protective effect on ulcerative colitis (UC), and the mechanism may be through inhibiting the activation of TLR-4/NF-κB signaling pathway and preventing the release of related inflammatory factors

Bos taurus genome assembly

We present here the assembly of the bovine genome. The assembly method combines the BAC plus WGS local assembly used for the rat and sea urchin with the whole genome shotgun (WGS) only assembly used for many other animal genomes including the rhesus macaque. The assembly process consisted of multiple phases: First, BACs were assembled with BAC generated sequence, then subsequently in combination with the individual overlapping WGS reads. Different assembly parameters were tested to separately optimize the performance for each BAC assembly of the BAC and WGS reads. In parallel, a second assembly was produced using only the WGS sequences and a global whole genome assembly method. The two assemblies were combined to create a more complete genome representation that retained the high quality BAC-based local assembly information, but with gaps between BACs filled in with the WGS-only assembly. Finally, the entire assembly was placed on chromosomes using the available map information. Over 90% of the assembly is now placed on chromosomes. The estimated genome size is 2.87 Gb which represents a high degree of completeness, with 95% of the available EST sequences found in assembled contigs. The quality of the assembly was evaluated by comparison to 73 finished BACs, where the draft assembly covers between 92.5 and 100% (average 98.5%) of the finished BACs. The assembly contigs and scaffolds align linearly to the finished BACs, suggesting that misassemblies are rare. Genotyping and genetic mapping of 17,482 SNPs revealed that more than 99.2% were correctly positioned within the Btau_4.0 assembly, confirming the accuracy of the assembly. The biological analysis of this bovine genome assembly is being published, and the sequence data is available to support future bovine research

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

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds

status: publishe

The Ultraviolet-Visible Luminescence of Ce3+ in Ca2Mg(BO3)2 Phosphors with Potential Applications

New phosphors Ca2Mg(BO3)2: Ce3+ were synthesized by the solid-state reaction method at a high temperature. The phase purity was characterized by powder X-ray diffraction (XRD). The ultraviolet-visible (UV-Vis) optical properties of Ce3+ have been investigated, and the lowest 5d levels, the emission, and the Stokes shifts of Ce3+ in the host lattice were identified. In addition, its concentration quenching process was also studied. The results show that Ce3+ ions enter Ca2+ sites with only one emission in a UV-Vis range and that the optimum doping concentration is x = 0.05. The excitation and emission spectra were evaluated to clearly reveal luminescence features

Self-Organized Patchy Target Searching and Collecting with Heterogeneous Swarm Robots Based on Density Interactions

The issue of searching and collecting targets with patchy distribution in an unknown environment is a challenging task for multiple or swarm robots because the targets are unevenly dispersed in space, which makes the traditional solutions based on the idea of path planning and full spatial coverage very inefficient and time consuming. In this paper, by employing a novel framework of spatial-density-field-based interactions, a collective searching and collecting algorithm for heterogeneous swarm robots is proposed to solve the challenging issue in a self-organized manner. In our robotic system, two types of swarm robots, i.e., the searching robots and the collecting robots, are included. To start with, the searching robots conduct an environment exploration by means of formation movement with Levy flights; when the targets are detected by the searching robots, they spontaneously form a ring-shaped envelope to estimate the spatial distribution of targets. Then, a single robot is selected from the group to enter the patch and locates at the patch’s center to act as a guiding beacon. Subsequently, the collecting robots are recruited by the guiding beacon to gather the patch targets; they first form a ring-shaped envelope around the target patch and then push the scattered targets inward by using a spiral shrinking strategy; in this way, all targets eventually are stacked near the center of the target patch. With the cooperation of the searching robots and the collecting robots, our heterogeneous robotic system can operate autonomously as a coordinated group to complete the task of collecting targets in an unknown environment. Numerical simulations and real swarm robot experiments (up to 20 robots are used) show that the proposed algorithm is feasible and effective, and it can be extended to search and collect different types of targets with patchy distribution

Characteristics and Geological Significance of High-Frequency Cycles in Salinized Lake Basins: The Paleogene Kumugeliemu Group in the Xinhe Area, Northern Tarim Basin

Salinized lake basins have distinctive sedimentary response characteristics, similar to marine shallow-water carbonate platforms. High-frequency cycles can also be used to reveal more sedimentological information, such as relative lake-level fluctuations, lithofacies sequence combinations, and paleogeographic evolution. In this article, a comprehensive study on the stratigraphic shelf delineation and high-frequency cycles of the Paleozoic Kumugeliemu Group in Xinhe area, northern Tarim Basin, was performed using drilling cores, logging curves, and seismic analyses. As a result of the study, the following data were obtained: the three sets of marker beds in the Kumugeliemu Group in the study area could be divided into a bottom sandstone component (E1-2 km1), a lower gypsum mudstone component (E1-2 km2), a salt rock component (E1-2 km3), and an upper gypsum mudstone component (E1-2 km4) by petrology vertical overlay combination and isochronous tracking correlation, which constituted two third-order cycles (ESQ1, ESQ2). They were further divided into seven fourth-order cycles (Esq1–Esq7). Due to the droughty and saline lacustrine depositional system background, the internal rock fabric changed frequently and showed a periodic vertical overlay pattern. Stratified gypsum salt, gypsum mud (sand) rock, and gypsum rock were used as the cycle interface. A single cycle was mainly characterized by an upward shallower depositional sequence of rapid lake transgression followed by a slow lake regression, composed of massive sandstone–lamellar mudstone–lime dolomite–gypsum rock, massive sandstone–lamellar mudstone–gypsum rock (gypsum salt), massive sandstone–massive gypsum mud (sand) rock–gypsum rock, and other cycle structure types. The complete sedimentary cycle was superposed by a single cycle and compared by the inter-well thickness difference, indicating that the study area had a paleogeomorphology pattern of “West-Low–East-High”. The thickness of the cycles decreased gradually from bottom to top vertically, and five sedimentary stages were determined, i.e., freshwater, brackish, brackish water, salt lake, and semi-saltwater, reflecting the evolutionary process of increasing salinity, lake basin filling, and gradual salinization and shrinkage