A statistical normalization method and differential expression analysis for RNA-seq data between different species

Background: High-throughput techniques bring novel tools but also statistical challenges to genomic research. Identifying genes with differential expression between different species is an effective way to discover evolutionarily conserved transcriptional responses. To remove systematic variation between different species for a fair comparison, the normalization procedure serves as a crucial pre-processing step that adjusts for the varying sample sequencing depths and other confounding technical effects. Results: In this paper, we propose a scale based normalization (SCBN) method by taking into account the available knowledge of conserved orthologous genes and hypothesis testing framework. Considering the different gene lengths and unmapped genes between different species, we formulate the problem from the perspective of hypothesis testing and search for the optimal scaling factor that minimizes the deviation between the empirical and nominal type I errors. Conclusions: Simulation studies show that the proposed method performs significantly better than the existing competitor in a wide range of settings. An RNA-seq dataset of different species is also analyzed and it coincides with the conclusion that the proposed method outperforms the existing method. For practical applications, we have also developed an R package named "SCBN" and the software is available at http://www.bioconductor.org/packages/devel/bioc/html/SCBN.html

PrivCheck: Privacy-Preserving Check-in Data Publishing for Personalized Location Based Services

International audienceWith the widespread adoption of smartphones, we have observed an increasing popularity of Location-Based Services (LBSs) in the past decade. To improve user experience, LBSs often provide personalized recommendations to users by mining their activity (i.e., check-in) data from location-based social networks. However, releasing user check-in data makes users vulnerable to inference attacks, as private data (e.g., gender) can often be inferred from the users'check-in data. In this paper, we propose PrivCheck, a customizable and continuous privacy-preserving check-in data publishing framework providing users with continuous privacy protection against inference attacks. The key idea of PrivCheck is to obfuscate user check-in data such that the privacy leakage of user-specified private data is minimized under a given data distortion budget, which ensures the utility of the obfuscated data to empower personalized LBSs. Since users often give LBS providers access to both their historical check-in data and future check-in streams, we develop two data obfuscation methods for historical and online check-in publishing, respectively. An empirical evaluation on two real-world datasets shows that our framework can efficiently provide effective and continuous protection of user-specified private data, while still preserving the utility of the obfuscated data for personalized LBS

Low Levels of p53 Protein and Chromatin Silencing of p53 Target Genes Repress Apoptosis in Drosophila Endocycling Cells

Apoptotic cell death is an important response to genotoxic stress that prevents oncogenesis. It is known that tissues can differ in their apoptotic response, but molecular mechanisms are little understood. Here, we show that Drosophila polyploid endocycling cells (G/S cycle) repress the apoptotic response to DNA damage through at least two mechanisms. First, the expression of all the Drosophila p53 protein isoforms is strongly repressed at a post-transcriptional step. Second, p53-regulated pro-apoptotic genes are epigenetically silenced in endocycling cells, preventing activation of a paused RNA Pol II by p53-dependent or p53-independent pathways. Over-expression of the p53A isoform did not activate this paused RNA Pol II complex in endocycling cells, but over-expression of the p53B isoform with a longer transactivation domain did, suggesting that dampened p53B protein levels are crucial for apoptotic repression. We also find that the p53A protein isoform is ubiquitinated and degraded by the proteasome in endocycling cells. In mitotic cycling cells, p53A was the only isoform expressed to detectable levels, and its mRNA and protein levels increased after irradiation, but there was no evidence for an increase in protein stability. However, our data suggest that p53A protein stability is regulated in unirradiated cells, which likely ensures that apoptosis does not occur in the absence of stress. Without irradiation, both p53A protein and a paused RNA pol II were pre-bound to the promoters of pro-apoptotic genes, preparing mitotic cycling cells for a rapid apoptotic response to genotoxic stress. Together, our results define molecular mechanisms by which different cells in development modulate their apoptotic response, with broader significance for the survival of normal and cancer polyploid cells in mammals

Classification of Online Customer Reviews for Digital Product Innovation: A Motivation Perspective

With rapid technological advances, digital products are becoming increasingly prevalent. Although past studies have examined the contribution of online reviews extensively in the context of physical products, there is limited understanding of the contribution of online reviews in digital product innovation. To this end, this study reviews previous work related to online reviews of physical and digital products in an attempt to reclassify online reviews of digital products from the perspective of consumer motivation. Taking game-related app reviews as an example, we employed a topic modeling model to extract insights related to consumer motivation. An in depth appreciation of consumers’ motivation from analyzing online reviews can yield invaluable insights in driving digital product innovation

Object Detection Difficulty: Suppressing Over-aggregation for Faster and Better Video Object Detection

Current video object detection (VOD) models often encounter issues with over-aggregation due to redundant aggregation strategies, which perform feature aggregation on every frame. This results in suboptimal performance and increased computational complexity. In this work, we propose an image-level Object Detection Difficulty (ODD) metric to quantify the difficulty of detecting objects in a given image. The derived ODD scores can be used in the VOD process to mitigate over-aggregation. Specifically, we train an ODD predictor as an auxiliary head of a still-image object detector to compute the ODD score for each image based on the discrepancies between detection results and ground-truth bounding boxes. The ODD score enhances the VOD system in two ways: 1) it enables the VOD system to select superior global reference frames, thereby improving overall accuracy; and 2) it serves as an indicator in the newly designed ODD Scheduler to eliminate the aggregation of frames that are easy to detect, thus accelerating the VOD process. Comprehensive experiments demonstrate that, when utilized for selecting global reference frames, ODD-VOD consistently enhances the accuracy of Global-frame-based VOD models. When employed for acceleration, ODD-VOD consistently improves the frames per second (FPS) by an average of 73.3% across 8 different VOD models without sacrificing accuracy. When combined, ODD-VOD attains state-of-the-art performance when competing with many VOD methods in both accuracy and speed. Our work represents a significant advancement towards making VOD more practical for real-world applications.Comment: 11 pages, 6 figures, accepted by ACM MM202

Two new genera of Apsilocephalidae from mid-Cretaceous Burmese amber

Apsilocephalidae is an enigmatic dipteran family erected by Nagatomi et al. (1991), including three extant genera and three additional extinct genera from the Eocene Baltic amber, Eocene Florissant, and mid-Cretaceous Burmese amber. We describe herein two new taxa, Myanmarpsilocephala grimaldii gen. et sp. nov. and Irwinimyia spinosa gen. et sp. nov., from mid-Cretaceous Burmese amber. The female genitalia of Myanmarpsilocephala gen. nov. and male genitalia of Irwinimyia gen. nov. are described and illustrated. The distribution of all Apsilocephalidae species and a key to all genera of Apsilocephalidae is provided. The described diversity of Apsilocephalidae in Burmese amber strongly suggests that apsilocephalid flies diversified at least by the mid-Cretaceous.This research was supported by the National Natural Science Foundation of China (41572010, 41622201, 41688103), the Chinese Academy of Sciences (XDPB05), and Youth Innovation Promotion Association of CAS (No. 2011224)

A META-ANALYSIS OF ABNORMAL GLUCOSE METABOLISM IN FIRST-EPISODE DRUG-NAIVE SCHIZOPHRENIA

Background: Patients with schizophrenia exhibit a higher mortality rate compared with the general population. This mortality has been attributed predominantly by the high risk of type 2 diabetes mellitus in the patients. We aimed to assess the inherent risk of glucose metabolism abnormalities in first-episode drug-naïve schizophrenia. Subjects and methods: We searched English database (PubMed, EMBASE, MEDLINE, Cochrane Library databases) and Chinese database (Wan Fang Data, CBM disc, VIP, and CNKI) from their inception until Jul 2018 for case-control studies examining glucose metabolism abnormalities. Measurements, such as fasting plasma glucose levels, fasting plasma insulin levels, insulin resistance and HbA1c levels in first episode antipsychotic-naive patients were used to test for prediabetes. Standardized/weighted mean differences and 95% confidence intervals were calculated and analyzed. Results: 19 studies (13 in English and 6 in Chinese) consisting of 1065 patients and 873 controls were included. Fasting plasma glucose levels (95% CI; 0.02 to 0.29; P=0.03), 2 h plasma glucose levels after an OGTT (95% CI; 0.63 to 1.2; P<0.00001), fasting plasma insulin levels (95% CI; 0.33 to 0.73; P<0.00001), insulin resistance (95% CI; 0.29 to 0.6; P<0.00001) in patients with firstepisode schizophrenia were significant elevated. There was no significant difference in HbA1c level (95% CI; -0.34 to 0.18; P=0.54) in patients with first-episode schizophrenia compared with controls. Conclusions: This meta-analysis showed that glucose metabolism was impaired in patients with first-episode schizophrenia. Higher quality studies with larger samples are warranted to confirm these findings