Empirical analysis of current status data for additive hazards model with auxiliary covariates

summary:In practice, it often occurs that some covariates of interest are not measured because of various reasons, but there may exist some auxiliary information available. In this case, an issue of interest is how to make use of the available auxiliary information for statistical analysis. This paper discusses statistical inference problems in the context of current status data arising from an additive hazards model with auxiliary covariates. An empirical log-likelihood ratio statistic for the regression parameter vector is defined and its limiting distribution is shown to be a standard chi-squared distribution. A profile empirical log-likelihood ratio statistic for a sub-vector of the parameters and its asymptotic distribution are also studied. To assess the finite sample performance of the proposed methods, simulation studies are implemented and simulation results show that the methods work well

MiR-143-5p inhibits proliferation, invasion, and epithelial to mesenchymal transition of colorectal cancer cells by downregulation of HMGA2

Purpose: To investigate the regulatory effect and molecular mechanism of miR-143-5p in colorectal cancer (CRC) progression. Methods: Expression of miR-143-5p in CRC cell lines SW620 and HCT116 was determined by quantitative real-time polymerase chain reaction (qRT-PCR). Stable miR-143-5p overexpression was mediated by lentivirus. The effects of miR-143-5p on proliferation, migration, invasion, and epithelial- mesenchymal transition (EMT) of SW620 and HCT116 cells were assessed by colony formation assay, CCK-8, Transwell assay, wound healing assay, and western blot. Target prediction was performed for miR-143-5p, and a dual luciferase assay was used to verify the targeting relationship. Results: Compared to CRC cells transfected with negative controls, cell proliferation, migration and invasion, and EMT were inhibited in miR-143-5p-overexpressing cells. Expression of HMGA2 (high- mobility Group AT-Hook 2), a target gene of miR-143-5p, was repressed by miR-143-5p. Rescue experiments confirmed that upregulation of HMGA2 due to mIR-143-5p overexpression reversed inhibition of CRC cell proliferation, invasion and EMT. Conclusion: MiR-143-5p inhibits the malignant progression of CRC by regulating HMGA2 expression and is expected to provide new therapeutic approaches for clinical treatment of CRC

MorphTE: Injecting Morphology in Tensorized Embeddings

In the era of deep learning, word embeddings are essential when dealing with text tasks. However, storing and accessing these embeddings requires a large amount of space. This is not conducive to the deployment of these models on resource-limited devices. Combining the powerful compression capability of tensor products, we propose a word embedding compression method with morphological augmentation, Morphologically-enhanced Tensorized Embeddings (MorphTE). A word consists of one or more morphemes, the smallest units that bear meaning or have a grammatical function. MorphTE represents a word embedding as an entangled form of its morpheme vectors via the tensor product, which injects prior semantic and grammatical knowledge into the learning of embeddings. Furthermore, the dimensionality of the morpheme vector and the number of morphemes are much smaller than those of words, which greatly reduces the parameters of the word embeddings. We conduct experiments on tasks such as machine translation and question answering. Experimental results on four translation datasets of different languages show that MorphTE can compress word embedding parameters by about 20 times without performance loss and significantly outperforms related embedding compression methods.Comment: 20 pages, 6 figures, 18 tables. Published at NeurIPS 202

Sequencing bias: comparison of different protocols of MicroRNA library construction

<p>Abstract</p> <p>Background</p> <p>MicroRNAs(miRNAs) are 18-25 nt small RNAs playing critical roles in many biological processes. The majority of known miRNAs were discovered by conventional cloning and a Sanger sequencing approach. The next-generation sequencing (NGS) technologies enable in-depth characterization of the global repertoire of miRNAs, and different protocols for miRNA library construction have been developed. However, the possible bias between the relative expression levels and sequences introduced by different protocols of library preparation have rarely been explored.</p> <p>Results</p> <p>We assessed three different miRNA library preparation protocols, SOLiD, Illumina versions 1 and 1.5, using cloning or SBS sequencing of total RNA samples extracted from skeletal muscles from Hu sheep and Dorper sheep, and then validated 9 miRNAs by qRT-PCR. Our results show that SBS sequencing data highly correlate with Illumina cloning data. The SOLiD data, when compared to Illumina's, indicate more dispersed distribution of length, higher frequency variation for nucleotides near the 3'- and 5'-ends, higher frequency occurrence for reads containing end secondary structure (ESS), and higher frequency for reads that do not map to known miRNAs. qRT-PCR results showed the best correlation with SOLiD cloning data. Fold difference of Hu sheep and Dorper sheep between qRT-PCR result and SBS sequencing data correlated well (r = 0.937), and fold difference of miR-1 and miR-206 among SOLiD cloning data, qRT-PCR and SBS sequencing data was similar.</p> <p>Conclusions</p> <p>The sequencing depth can influence the quantitative measurement of miRNA abundance, but the discrepancy caused by it was not statistically significant as high correlation was observed between Illumina cloning and SBS sequencing data. Bias of length distribution, sequence variation, and ESS was observed between data obtained with the different protocols. SOLiD cloning data differ from Illumina cloning data mainly because of distinct methods of adapter ligation. The good correlation between qRT-PCR result and SOLiD data might be due to the similarities of the hybridization-based methods. The fold difference analysis indicated that methods based on hybridization may be superior for quantitative measurement of miRNA abundance. Because of the genome sequence of the sheep is not available, our data may not explain how the entire miRNA bias in the natural miRNAs in sheep or other mammal miRNA expression, unbiased artificially synthesized miRNA will help on evaluating the methodology of miRNA library preparation.</p

Benefits of laboratory personalized antiplatelet therapy in patients undergoing percutaneous coronary intervention: A meta-analysis of randomized controlled trials

   Background: The preventive effects of laboratory personalized antiplatelet therapy (PAPT) strategy in­cluding genetic detection and platelet function testing (PFT) on major adverse cardiac events (MACEs) and bleeding events in coronary artery disease (CAD) patients undergoing stenting has been extensively studied. Despite that, no clear conclusion can be drawn. In this study, a meta-analysis was performed to explore a more precise estimation of the benefits of laboratory PAPT. Methods: Randomized controlled trials were identified by the use of search databases such as PubMed, Embase, and Cochrane Controlled Trials Register up to May 2017, and the estimates were pooled. Results: Fourteen studies including 9497 patients met the inclusion criteria. The laboratory PAPT reduced MACEs risk (risk ratio [RR] 0.58, 95% confidence interval [CI] 0.42–0.80, p = 0.001), stent thrombosis (RR 0.60, 95% CI 0.41–0.87, p = 0.008) and myocardial infarctions (RR 0.43, 95% CI 0.21–0.88, p = 0.02) compared to the non-PAPT group. No statistically significant difference was observed between the two groups regarding cardiovascular death (RR 0.77, 95% CI 0.51–1.16, p = 0.21), bleeding events (RR 0.96, 95% CI 0.81–1.13, p = 0.59) and ischemic stroke (RR 0.81; 95% CI 0.39–1.66, p = 0.57). The preventive effect on MACEs was more significant in patients with high on-treatment platelet reactivity (RR 0.46; 95% CI 0.27–0.80, p = 0.006). Conclusions: Coronary artery disease patients after stenting could obtain benefits from laboratory PAPT. (Cardiol J 2018; 25, 1: 128–141

Abundant Exact Solition-Like Solutions to the Generalized Bretherton Equation with Arbitrary Constants

The Riccati equation is employed to construct exact travelling wave solutions to the generalized Bretherton equation. Taking full advantage of the Riccati equation which has more new solutions, abundant new multiple solition-like solutions are obtained for the generalized Bretherton equation

Effect of Extrusion Parameters on Soybean Protein Conformation

The study investigated the effect of different extrusion parameters: temperature, material moisture of raw material, and screw speed on the conformation of soybean protein. After being extruded, soy protein isolate (SPI) was measured for protein solubility, zeta potential, particle size, protein subunits and protein secondary structure. Additionally, the formation mechanism of fibrous soybean protein was uncovered. The results showed that with an increase in extrusion temperature, the natural structure of SPI was destroyed, the internal groups were exposed, and the content of disulfide bonds increased, promoting the formation of protein aggregates. Too high or too low temperature was not conducive to the formation and stability of protein aggregates. At too low or too high raw material moisture content, a relatively complete extrudate was difficult to form at the extrusion mouth, while at raw material moisture contents of 20%–22%, the extrudate was in the best state due to the protective effect of water, and a uniform SPI aggregate was formed. Low screw speed (below 130 r/min) could lead to insufficient mechanical energy input, so that the protein was not completely denatured and depolymerized. While at high screw speed (above 140 r/min), the effect of high shear force promotes the destruction of the original natural structure of proteins, resulting in the formation of large protein aggregates. In summary, under appropriate extrusion conditions, the optimal extrudate quality can be obtained, while extreme extrusion conditions make extrusion molding difficult or result in nonuniform texture. This study can provide a theoretical basis for optimizing the quality of fibrous soybean protein