A Topological Method for Comparing Document Semantics

Comparing document semantics is one of the toughest tasks in both Natural Language Processing and Information Retrieval. To date, on one hand, the tools for this task are still rare. On the other hand, most relevant methods are devised from the statistic or the vector space model perspectives but nearly none from a topological perspective. In this paper, we hope to make a different sound. A novel algorithm based on topological persistence for comparing semantics similarity between two documents is proposed. Our experiments are conducted on a document dataset with human judges' results. A collection of state-of-the-art methods are selected for comparison. The experimental results show that our algorithm can produce highly human-consistent results, and also beats most state-of-the-art methods though ties with NLTK.Comment: 9 pages, 3 tables, 9th International Conference on Natural Language Processing (NLP 2020

Study on failure characteristics and control technology of roadway surrounding rock under repeated mining in close-distance coal seam

In this study, taking the Sheng’an coal mine as an engineering background, the failure characteristics of the surrounding rock of a roadway under repeated mining in a close-distance coal seam is comprehensively illustrated through field measurements (e.g., drilling imaging), theory analysis and numerical simulation (finite difference method (FDM)). The results show that although the return airway 10905 remains intact, the apparent failure of the roadway’s roof and the coal pillar can be observed. In addition, the expression of floor failure depth caused by upper coal seam mining is obtained through elastic-plastic theory. Meanwhile, the deformation of the surrounding rock of the roadway increases with the increase of repeated mining times, especially for the horizontal displacement of the roadway on the coal pillar side. Moreover, the cracks’ evolution of surrounding rock in the roadway can be observed as asymmetric characteristics. Finally, the stability control technology of “asymmetric anchor net cable + I-steel” is proposed to prevent potential mining disasters, and the feasibility of this support scheme is verified by numerical simulation and field practices. It can meet the requirement of safe mining and provide guidelines to effectively solve the failure of a roadway in close-distance coal seam mining

A high-Q metasurface signal isolator for 1.5T surface coil magnetic resonance imaging on the go

The combination of surface coils and metamaterials remarkably enhance magnetic resonance imaging (MRI) performance for significant local staging flexibility. However, due to the coupling in between, impeded signal-to-noise ratio (SNR) and low-contrast resolution, further hamper the future growth in clinical MRI. In this paper, we propose a high-Q metasurface decoupling isolator fueled by topological LC loops for 1.5T surface coil MRI system, increasing the magnetic field up to fivefold at 63.8 MHz. We have employed a polarization conversion mechanism to effectively eliminate the coupling between the MRI metamaterial and the radio frequency (RF) surface transmitter-receiver coils. Furthermore, a high-Q metasurface isolator was achieved by taking advantage of bound states in the continuum (BIC) for extremely high-field MRI and spectroscopy. An equivalent physical model of the miniaturized metasurface design was put forward through LC circuit analysis. This study opens up a promising route for the easy-to-use and portable surface coil MRI scanners

Identification of Cancer Dysfunctional Subpathways by Integrating DNA Methylation, Copy Number Variation, and Gene-Expression Data

A subpathway is defined as the local region of a biological pathway with specific biological functions. With the generation of large-scale sequencing data, there are more opportunities to study the molecular mechanisms of cancer development. It is necessary to investigate the potential impact of DNA methylation, copy number variation (CNV), and gene-expression changes in the molecular states of oncogenic dysfunctional subpathways. We propose a novel method, Identification of Cancer Dysfunctional Subpathways (ICDS), by integrating multi-omics data and pathway topological information to identify dysfunctional subpathways. We first calculated gene-risk scores by integrating the three following types of data: DNA methylation, CNV, and gene expression. Second, we performed a greedy search algorithm to identify the key dysfunctional subpathways within pathways for which the discriminative scores were locally maximal. Finally, a permutation test was used to calculate the statistical significance level for these key dysfunctional subpathways. We validated the effectiveness of ICDS in identifying dysregulated subpathways using datasets from liver hepatocellular carcinoma (LIHC), head-neck squamous cell carcinoma (HNSC), cervical squamous cell carcinoma, and endocervical adenocarcinoma. We further compared ICDS with methods that performed the same subpathway identification algorithm but only considered DNA methylation, CNV, or gene expression (defined as ICDS_M, ICDS_CNV, or ICDS_G, respectively). With these analyses, we confirmed that ICDS better identified cancer-associated subpathways than the three other methods, which only considered one type of data. Our ICDS method has been implemented as a freely available R-based tool (https://cran.r-project.org/web/packages/ICDS)

VS-4718 Antagonizes Multidrug Resistance in ABCB1- and ABCG2-Overexpressing Cancer Cells by Inhibiting the Efflux Function of ABC Transporters

Overexpression of ATP-binding cassette (ABC) transporters is one of the most important mechanisms responsible for multi-drug resistance (MDR). VS-4718, a tyrosine kinase inhibitor targeting focal adhesion kinase (FAK) with a potential anticancer effect, is currently evaluated in clinical trials. In this study, we investigated whether VS-4718 could reverse MDR mediated by ABC transporters, including ABCB1, ABCG2, and ABCC1. The results showed that VS-4718 significantly reversed ABCB1- and ABCG2-mediated MDR, but not MDR mediated by ABCC1. Treatment of VS-4718 did not alter the protein level and subcellular localization of ABCB1 or ABCG2. Mechanism studies indicated that the reversal effects of VS-4718 were related to attenuation of the efflux activity of ABCB1 and ABCG2 transporters. ATPase analysis indicated that VS-4718 stimulated the ATPase activity of ABCB1 and ABCG2. Docking study showed that VS-4718 interacted with the substrate-binding sites of both ABCB1 and ABCG2, suggesting that VS-4718 may affect the activity of ABCB1 and ABCG2 competitively. This study provided a novel insight for MDR cancer treatment. It indicated that combination of VS-4718 with antineoplastic drugs could attenuate MDR mediated by ABCB1 or ABCG2 in ABCB1- or ABCG2-overexpressing cancer cells

Sequencing and de novo assembly of 150 genomes from Denmark as a population reference

Hundreds of thousands of human genomes are now being sequenced to characterize genetic variation and use this information to augment association mapping studies of complex disorders and other phenotypic traits. Genetic variation is identified mainly by mapping short reads to the reference genome or by performing local assembly. However, these approaches are biased against discovery of structural variants and variation in the more complex parts of the genome. Hence, large-scale de novo assembly is needed. Here we show that it is possible to construct excellent de novo assemblies from high-coverage sequencing with mate-pair libraries extending up to 20 kilobases. We report de novo assemblies of 150 individuals (50 trios) from the GenomeDenmark project. The quality of these assemblies is similar to those obtained using the more expensive long-read technology. We use the assemblies to identify a rich set of structural variants including many novel insertions and demonstrate how this variant catalogue enables further deciphering of known association mapping signals. We leverage the assemblies to provide 100 completely resolved major histocompatibility complex haplotypes and to resolve major parts of the Y chromosome. Our study provides a regional reference genome that we expect will improve the power of future association mapping studies and hence pave the way for precision medicine initiatives, which now are being launched in many countries including Denmark

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Tirofiban for Stroke without Large or Medium-Sized Vessel Occlusion

The effects of the glycoprotein IIb/IIIa receptor inhibitor tirofiban in patients with acute ischemic stroke but who have no evidence of complete occlusion of large or medium-sized vessels have not been extensively studied. In a multicenter trial in China, we enrolled patients with ischemic stroke without occlusion of large or medium-sized vessels and with a National Institutes of Health Stroke Scale score of 5 or more and at least one moderately to severely weak limb. Eligible patients had any of four clinical presentations: ineligible for thrombolysis or thrombectomy and within 24 hours after the patient was last known to be well; progression of stroke symptoms 24 to 96 hours after onset; early neurologic deterioration after thrombolysis; or thrombolysis with no improvement at 4 to 24 hours. Patients were assigned to receive intravenous tirofiban (plus oral placebo) or oral aspirin (100 mg per day, plus intravenous placebo) for 2 days; all patients then received oral aspirin until day 90. The primary efficacy end point was an excellent outcome, defined as a score of 0 or 1 on the modified Rankin scale (range, 0 [no symptoms] to 6 [death]) at 90 days. Secondary end points included functional independence at 90 days and a quality-of-life score. The primary safety end points were death and symptomatic intracranial hemorrhage. A total of 606 patients were assigned to the tirofiban group and 571 to the aspirin group. Most patients had small infarctions that were presumed to be atherosclerotic. The percentage of patients with a score of 0 or 1 on the modified Rankin scale at 90 days was 29.1% with tirofiban and 22.2% with aspirin (adjusted risk ratio, 1.26; 95% confidence interval, 1.04 to 1.53, P = 0.02). Results for secondary end points were generally not consistent with the results of the primary analysis. Mortality was similar in the two groups. The incidence of symptomatic intracranial hemorrhage was 1.0% in the tirofiban group and 0% in the aspirin group. In this trial involving heterogeneous groups of patients with stroke of recent onset or progression of stroke symptoms and nonoccluded large and medium-sized cerebral vessels, intravenous tirofiban was associated with a greater likelihood of an excellent outcome than low-dose aspirin. Incidences of intracranial hemorrhages were low but slightly higher with tirofiban