On a novel numerical quadrature based on cycle index of symmetric group for the Hadamard finite-part integrals

To evaluate the Hadamard finite-part integrals accurately, a novel interpolatory-type quadrature is proposed in this article. In our approach, numerical divided difference is utilized to represent the high order derivatives of the integrated function, which make it possible to reduced the numerical quadrature into a concise formula based on the cycle index for symmetric group. In addition, convergence analysis is presented and the error estimation is given. Numerical results are presented on cases with different weight functions, which substantiate the performance of the proposed method

DiskANN++: Efficient Page-based Search over Isomorphic Mapped Graph Index using Query-sensitivity Entry Vertex

Given a vector dataset $\mathcal{X}$ and a query vector $\vec{x}_q$, graph-based Approximate Nearest Neighbor Search (ANNS) aims to build a graph index $G$ and approximately return vectors with minimum distances to $\vec{x}_q$ by searching over $G$. The main drawback of graph-based ANNS is that a graph index would be too large to fit into the memory especially for a large-scale $\mathcal{X}$. To solve this, a Product Quantization (PQ)-based hybrid method called DiskANN is proposed to store a low-dimensional PQ index in memory and retain a graph index in SSD, thus reducing memory overhead while ensuring a high search accuracy. However, it suffers from two I/O issues that significantly affect the overall efficiency: (1) long routing path from an entry vertex to the query's neighborhood that results in large number of I/O requests and (2) redundant I/O requests during the routing process. We propose an optimized DiskANN++ to overcome above issues. Specifically, for the first issue, we present a query-sensitive entry vertex selection strategy to replace DiskANN's static graph-central entry vertex by a dynamically determined entry vertex that is close to the query. For the second I/O issue, we present an isomorphic mapping on DiskANN's graph index to optimize the SSD layout and propose an asynchronously optimized Pagesearch based on the optimized SSD layout as an alternative to DiskANN's beamsearch. Comprehensive experimental studies on eight real-world datasets demonstrate our DiskANN++'s superiority on efficiency. We achieve a notable 1.5 X to 2.2 X improvement on QPS compared to DiskANN, given the same accuracy constraint.Comment: 15 pages including reference

Outer membrane vesicles of Porphyromonas gingivalis : Novel communication tool and strategy

Extracellular vesicles (EVs) have been recognized as a universal method of cellular communications and are reportedly produced in bacteria, archaea, and eukaryotes. Bacterial EVs are often called “Outer Membrane Vesicles” (OMVs) as they were the result of a controlled blebbing of the outer membrane of gram-negative bacteria such as Porphyromonas gingivalis (P. gingivalis). Bacterial EVs are natural messengers, implicated in intra- and inter-species cell-to-cell communication among microorganism populations present in microbiota. Bacteria can incorporate their pathogens into OMVs; the content of OMVs differs, depending on the type of bacteria. The production of distinct types of OMVs can be mediated by different factors and routes. A recent study highlighted OMVs ability to carry crucial molecules implicated in immune modulation, and, nowadays, they are considered as a way to communicate and transfer messages from the bacteria to the host and vice versa. This review article focuses on the current understanding of OMVs produced from major oral bacteria, P. gingivalis: generation, characteristics, and contents as well as the involvement in signal transduction of host cells and systemic diseases. Our recent study regarding the action of P. gingivalis OMVs in the living body is also summarized

Outer membrane vesicles of Porphyromonas gingivalis: Novel communication tool and strategy

Extracellular vesicles (EVs) have been recognized as a universal method of cellular communications and are reportedly produced in bacteria, archaea, and eukaryotes. Bacterial EVs are often called "Outer Membrane Vesicles" (OMVs) as they were the result of a controlled blebbing of the outer membrane of gram-negative bacteria such as Porphyromonas gingivalis (P. gingivalis). Bacterial EVs are natural messengers, implicated in intra-and inter-species cell-to-cell communication among microorganism populations present in microbiota. Bacteria can incorporate their pathogens into OMVs; the content of OMVs differs, depending on the type of bacteria. The production of distinct types of OMVs can be mediated by different factors and routes. A recent study highlighted OMVs ability to carry crucial molecules implicated in immune modulation, and, nowadays, they are considered as a way to communicate and transfer messages from the bacteria to the host and vice versa. This review article focuses on the current understanding of OMVs produced from major oral bacteria, P. gingivalis: generation, characteristics, and contents as well as the involvement in signal transduction of host cells and systemic diseases. Our recent study regarding the action of P. gingivalis OMVs in the living body is also summarized

Detection of copy number variations and their effects in Chinese bulls

BACKGROUND: Copy number variations (CNVs) are a main source of genomic structural variations underlying animal evolution and production traits. Here, with one pure-blooded Angus bull as reference, we describe a genome-wide analysis of CNVs based on comparative genomic hybridization arrays in 29 Chinese domesticated bulls and examined their effects on gene expression and cattle growth traits. RESULTS: We identified 486 copy number variable regions (CNVRs), covering 2.45% of the bovine genome, in 24 taurine (Bos taurus), together with 161 ones in 2 yaks (Bos grunniens) and 163 ones in 3 buffaloes (Bubalus bubalis). Totally, we discovered 605 integrated CNVRs, with more “loss” events than both “gain” and “both” ones, and clearly clustered them into three cattle groups. Interestingly, we confirmed their uneven distributions across chromosomes, and the differences of mitochondrion DNA copy number (gain: taurine, loss: yak & buffalo). Furthermore, we confirmed approximately 41.8% (253/605) and 70.6% (427/605) CNVRs span cattle genes and quantitative trait loci (QTLs), respectively. Finally, we confirmed 6 CNVRs in 9 chosen ones by using quantitative PCR, and further demonstrated that CNVR22 had significantly negative effects on expression of PLA2G2D gene, and both CNVR22 and CNVR310 were associated with body measurements in Chinese cattle, suggesting their key effects on gene expression and cattle traits. CONCLUSIONS: The results advanced our understanding of CNV as an important genomic structural variation in taurine, yak and buffalo. This study provides a highly valuable resource for Chinese cattle’s evolution and breeding researches. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-480) contains supplementary material, which is available to authorized users

Acceptability and feasibility of smartphone-assisted 24 h recalls in the Chinese population

Abstract Objective To examine the acceptability and feasibility of using smartphone technology to assess beverage intake and evaluate whether the feasibility of smartphone use is greater among key sub-populations. Design An acceptability and feasibility study of recording the video dietary record, the acceptability of the ecological momentary assessment (EMA), wearing smartphones and whether the videos helped participants recall intake after a cross-over validation study. Setting Rural and urban area in Shanghai, China. Subjects Healthy adults ( n 110) aged 20–40 years old. Results Most participants reported that the phone was acceptable in most aspects, including that videos were easy to use (70 %), helped with recalls (77 %), EMA reminders helped them record intake (75 %) and apps were easy to understand (85 %). However, 49 % of the participants reported that they had trouble remembering to take videos of the beverages before consumption or 46 % felt embarrassed taking videos in front of others. Moreover, 72 % reported that the EMA reminders affected their consumption. When assessing overall acceptability of using smartphones, 72 % of the participants were favourable responders. There were no statistically significant differences in overall acceptability for overweight v. normal-weight participants or for rural v. urban residents. However, we did find that the overall acceptability was higher for males (81 %) than females (61 %, P =0·017). Conclusions Our study did not find smartphone technology helped with dietary assessments in a Chinese population. However, simpler approaches, such as using photographs instead of videos, may be more feasible for enhancing 24 h dietary recalls

Cassava genome from a wild ancestor to cultivated varieties

Cassava is a major tropical food crop in the Euphorbiaceae family that has high carbohydrate production potential and adaptability to diverse environments. Here we present the draft genome sequences of a wild ancestor and a domesticated variety of cassava and comparative analyses with a partial inbred line. We identify 1,584 and 1,678 gene models specific to the wild and domesticated varieties, respectively, and discover high heterozygosity and millions of single-nucleotide variations. Our analyses reveal that genes involved in photosynthesis, starch accumulation and abiotic stresses have been positively selected, whereas those involved in cell wall biosynthesis and secondary metabolism, including cyanogenic glucoside formation, have been negatively selected in the cultivated varieties, reflecting the result of natural selection and domestication. Differences in microRNA genes and retrotransposon regulation could partly explain an increased carbon flux towards starch accumulation and reduced cyanogenic glucoside accumulation in domesticated cassava. These results may contribute to genetic improvement of cassava through better understanding of its biology

Follicle-Stimulating Hormone Receptor: Advances and Remaining Challenges

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