Near Neighbor Search via Efficient Average Distortion Embeddings

A recent series of papers by Andoni, Naor, Nikolov, Razenshteyn, and Waingarten (STOC 2018, FOCS 2018) has given approximate near neighbour search (NNS) data structures for a wide class of distance metrics, including all norms. In particular, these data structures achieve approximation on the order of p for ?_p^d norms with space complexity nearly linear in the dataset size n and polynomial in the dimension d, and query time sub-linear in n and polynomial in d. The main shortcoming is the exponential in d pre-processing time required for their construction. In this paper, we describe a more direct framework for constructing NNS data structures for general norms. More specifically, we show via an algorithmic reduction that an efficient NNS data structure for a metric ? is implied by an efficient average distortion embedding of ? into ?? or the Euclidean space. In particular, the resulting data structures require only polynomial pre-processing time, as long as the embedding can be computed in polynomial time. As a concrete instantiation of this framework, we give an NNS data structure for ?_p with efficient pre-processing that matches the approximation factor, space and query complexity of the aforementioned data structure of Andoni et al. On the way, we resolve a question of Naor (Analysis and Geometry in Metric Spaces, 2014) and provide an explicit, efficiently computable embedding of ?_p, for p ? 1, into ?? with average distortion on the order of p. Furthermore, we also give data structures for Schatten-p spaces with improved space and query complexity, albeit still requiring exponential pre-processing when p ? 2. We expect our approach to pave the way for constructing efficient NNS data structures for all norms

Incidence, survival comparison, and novel prognostic evaluation approaches for stage iii-iv pulmonary large cell neuroendocrine carcinoma and small cell lung cancer

Abstract Background Pulmonary large cell neuroendocrine carcinoma (LCNEC) and small cell lung cancer (SCLC) are two types of high-grade neuroendocrine carcinomas of the lung with poor prognosis. LCNEC has not been thoroughly studied due to its rarity, data are also lacking regarding the survival comparison and prognosis analysis of patients with locally advanced or metastatic LCNEC and SCLC. Methods Data of patients with LCNEC, SCLC, and other NSCLC who were diagnosed from 1975 to 2019 were extracted from the Surveillance, Epidemiology and End Results (SEER) database to estimate incidence. Those in stage III-IV and being diagnosed from 2010 to 2015 were utilized further to investigate their clinical characteristics and prognosis. Propensity score matching (PSM) analyses at a ratio of 1:2 was used to compare their survival outcomes. Nomograms of LCNEC and SCLC were established with internal validation, and the nomogram of SCLC was externally validated by 349 patients diagnosed in Cancer hospital, Chinese Academy of Medical Sciences & Peking Union Medical College from January 1, 2012 to December 31, 2018. Results The incidence of LCNEC has been increasing in recent decades, meanwhile that of SCLC and other types of NSCLC were decreasing. A total of 91,635 lung cancer patients, including 785 with LCNEC, 15,776 with SCLC, and 75,074 with other NSCLC were enrolled for further analysis. The survival of stage III-IV LCNEC resembles that of SCLC, and significantly worse than other types of NSCLC before and after PSM analysis. In pretreatment prognostic analysis, age, T stage, N stage, M stage, bone metastasis, liver metastasis, and brain metastasis were found to be associated with the survival of both LCNEC and SCLC, besides sex, bilaterality, and lung metastasis were additional prognostic factors for SCLC. Two nomograms and convenient online tools respectively for LCNEC and SCLC were established accordingly with favorable predicting accuracy of < 1-year, < 2-year, < 3-year survival probabilities. In external validation of the SCLC nomogram with a Chinese cohort, the AUCs of 1-year, 2-year and 3-year ROC were 0.652, 0.669, and 0.750, respectively. All the results of 1-, 2-, 3- year variable-dependent ROC curves verified the superior prognostic value of our nomograms for LCNEC and SCLC over the traditional T/N/M staging system. Conclusions Based on large sample-based cohort, we compared the epidemiological trends and survival outcomes between locally advanced or metastatic LCNEC, SCLC, and other NSCLC. Furthermore, two prognostic evaluation approaches respectively for LCNEC and SCLC might present as practical tools for clinicians to predict the survival outcome of these patients and facilitate risk stratification

Decreased expression of microRNA let-7i and its association with chemotherapeutic response in human gastric cancer

<p>Abstract</p> <p>Background</p> <p>MicroRNA let-7i has been proven to be down-regulated in many human malignancies and correlated with tumor progression and anticancer drug resistance. Our study aims to characterize the contribution of miRNA let-7i to the initiation and malignant progression of locally advanced gastric cancer (LAGC), and evaluate its possible value in neoadjuvant chemotherapeutic efficacy prediction.</p> <p>Methods</p> <p>Eighty-six previously untreated LAGC patients who underwent preoperative chemotherapy and radical resection were included in our study. Let-7i expression was examined for pairs of cancer tissues and corresponding normal adjacent tissues (NATs), using quantitative RT-PCR. The relationship of let-7i level to clinicopathological characteristics, pathologic tumor regression grades after chemotherapy, and overall survival (OS) was also investigated.</p> <p>Results</p> <p>Let-7i was significantly down-regulated in most tumor tissues (78/86: 91%) compared with paired NATs (<it>P</it> < 0.001), and low levels of let-7i were significantly correlated with local invasion, lymphatic metastasis, and poor pathologic tumor response. Multivariate Cox regression analysis revealed that low let-7i expression was an unfavorable prognostic factor of OS (hazard ratio (HR) = 2.316, <it>P</it> =0.024) independently of other clinicopathological factors, including tumor node metastasis (TNM) stage (HR = 3.226, <it>P</it> = 0.013), depth of infiltration (HR = 4.167, <it>P</it> < 0.001), and lymph node status (HR = 2.245, <it>P</it> = 0.037).</p> <p>Conclusions</p> <p>These findings indicate that let-7i may be a good candidate for use a therapeutic target and a potential tissue marker for the prediction of chemotherapeutic sensitivity and prognosis in LAGC patients.</p

Transcriptome and Metabolome Analysis Provides Insights into the Heterosis of Yield and Quality Traits in Two Hybrid Rice Varieties (Oryza sativa L.)

Heterosis is a common biological phenomenon that is useful for breeding superior lines. Using heterosis to increase the yield and quality of crops is one of the main achievements of modern agricultural science. In this study, we analysed the transcriptome and metabolome of two three-line hybrid rice varieties, Taiyou 871 (TY871), and Taiyou 398 (TY398) and the parental grain endosperm using RNA-seq (three biological repeats per variety) and untargeted metabolomic (six biological repeats per variety) methods. TY871 and TY398 showed specific heterosis in yield and quality. Transcriptome analysis of the hybrids revealed 638 to 4059 differentially expressed genes in the grain when compared to the parents. Metabolome analysis of the hybrids revealed 657 to 3714 differential grain metabolites when compared to the parents. The honeydew1 and grey60 module core genes Os04g0350700 and Os05g0154700 are involved in the regulation of awn development, grain size, and grain number, as well as the regulation of grain length and plant height, respectively. Rice grain length may be an important indicator for improving the quality of three-line hybrid rice. In addition, the rice quality-related metabolite NEG_M341T662 was highly connected to the module core genes Os06g0254300 and Os03g0168100. The functions of Os06g0254300 and Os03g0168100 are EF-hand calcium binding protein and late embroideries absolute protein repeat containing protein, respectively. These genes may play a role in the formation of rice quality. We constructed a gene and metabolite coexpression network, which provides a scientific basis for the utilization of heterosis in producing high-yield and high-quality hybrid rice

Geographical distribution of Aspergillus flavus in peanut harvest period in China

In order to grasp the distribution of Aspergillus flavus in the soil of peanut production areas in China, A. flavus biomarkers were tested on 555 soil samples from 37 sampling points in 17 provinces, peanut fields in four agroecological zones (Southern area, Yangtze River Basin, Northern area, Northeast area). The results showed that (1) the cultivation amount of A. flavus per gram of soil in the Yangtze River Basin is 1.30 times that of the southern area, 1.56 times that of the northern area, and 6.20 times that of the northeast area, with obvious regional characteristics. (2) In the Yangtze River basin, the change of longitude in the east-west direction has no direct impact on the cultivation amount of A. flavus per gram of soil. (3) In the east coast, the A. flavus cultivated per gram of soil increased first and then decreased with the increase of latitude from south to north. (4) A. flavus can be isolated in the soil samples above 1000 ​m. Field pollution is an important source of aflatoxin contamination in peanut. The study on the distribution of A. flavus in soil in China could provide theoretical support for the early warning and prevention and control measures of aflatoxin contamination in peanut