In planta multi-omic profiling of pathogenic and commensal bacteria

Plant pathogens can cause serious diseases that impact global agriculture. Molecular mechanisms of the plant immune system have been intensively studied in the past decades, revealing mechanisms for pathogen recognition and immune signaling in plant cells. However, we still lack a fundamental knowledge of how plant immunity affects pathogen metabolisms to inhibit their growth in plants. In the case of bacterial pathogens, a major bottleneck is the difficulty in profiling bacterial responses in planta. Here, I established a method to isolate bacterial cells from Arabidopsis thaliana leaves to enrich bacterial information. I profiled the transcriptomes and proteomes of the foliar bacterial pathogen Pseudomonas syringae by using various combinations of host and bacterial genotypes and pretreatments. This unveiled that bacterial transcriptome changes affected by plant immunity explain bacterial growth suppression in the plant apoplast and identified that a bacterial iron acquisition pathway is a major plant immune target. Bacterial transcriptomes and proteomes were well correlated in general, but I also found that plant immunity affects the abundance of specific components of the bacterial type III secretion system, an essential component for bacterial virulence, only at the protein level. Together, these analyses provided insights into the long-standing question of how biological processes of bacterial pathogens are influenced by plant immunity. I also applied the in planta bacterial transcriptomics method to address an important open question in plant microbiota research: how does plant immunity influence the responses of microbiota members to affect the shape and functions of the plant microbiota? I profiled the co-transcriptomes of plants and bacteria in the monoassociation condition and revealed conserved and specific plant and bacterial responses during interaction events. This approach will help us understand how plants winnow different microbiota members and control the microbiota function, and transform the current plant microbiota research from descriptive studies to mechanistic studies. Taken together, this study sets the foundation for the comprehensive understanding of molecular events on both plant and bacterial sides during their interactions

Effects of the Japanese Herbal Medicine “Sho-saiko-to” (TJ-9) on Interleukin-12 Production in Patients with HCV-Positive Liver Cirrhosis

Interleukin-12 (IL-12) is an important cytokine for maintainence of normal systemic defense and bioregulation. The Japanese herbal medicine Sho-saiko-to (TJ-9) has been administered to 1.5 million Japanese patients with chronic liver diseases. TJ-9 is known to significantly suppress cancer development in the liver and has macrobiotic effects. In the present study, we examined the in vitro production of IL-12 by circulating mononuclear cells from liver cirrhosis patients and the effects of TJ-9 on IL-12 production

An Empirical Study of the I2P Anonymity Network and its Censorship Resistance

Tor and I2P are well-known anonymity networks used by many individuals to protect their online privacy and anonymity. Tor's centralized directory services facilitate the understanding of the Tor network, as well as the measurement and visualization of its structure through the Tor Metrics project. In contrast, I2P does not rely on centralized directory servers, and thus obtaining a complete view of the network is challenging. In this work, we conduct an empirical study of the I2P network, in which we measure properties including population, churn rate, router type, and the geographic distribution of I2P peers. We find that there are currently around 32K active I2P peers in the network on a daily basis. Of these peers, 14K are located behind NAT or firewalls. Using the collected network data, we examine the blocking resistance of I2P against a censor that wants to prevent access to I2P using address-based blocking techniques. Despite the decentralized characteristics of I2P, we discover that a censor can block more than 95% of peer IP addresses known by a stable I2P client by operating only 10 routers in the network. This amounts to severe network impairment: a blocking rate of more than 70% is enough to cause significant latency in web browsing activities, while blocking more than 90% of peer IP addresses can make the network unusable. Finally, we discuss the security consequences of the network being blocked, and directions for potential approaches to make I2P more resistant to blocking.Comment: 14 pages, To appear in the 2018 Internet Measurement Conference (IMC'18

Spatio-temporal clustering of probabilistic region trajectories

We propose a novel model for the spatio-temporal clustering of trajectories based on motion, which applies to challenging street-view video sequences of pedestrians captured by a mobile camera. A key contribution of our work is the introduction of novel probabilistic region trajectories, motivated by the non-repeatability of segmentation of frames in a video sequence. Hierarchical image segments are obtained by using a state-of-the-art hierarchical segmentation algorithm, and connected from adjacent frames in a directed acyclic graph. The region trajectories and measures of confidence are extracted from this graph using a dynamic programming-based optimisation. Our second main contribution is a Bayesian framework with a twofold goal: to learn the optimal, in a maximum likelihood sense, Random Forests classifier of motion patterns based on video features, and construct a unique graph from region trajectories of different frames, lengths and hierarchical levels. Finally, we demonstrate the use of Isomap for effective spatio-temporal clustering of the region trajectories of pedestrians. We support our claims with experimental results on new and existing challenging video sequences

Successful management of tracheo-innominate artery fistula with endovascular stent graft repair

AbstractTracheo-innominate artery fistula is a highly lethal complication after tracheostomy. A 37-year-old man who had undergone a tracheostomy 14 years earlier because of dysphagia after brain surgery had a tracheo-innominate artery fistula with exsanguinating hemorrhage from his tracheostomy site. After temporary control of the bleeding, a stent graft was implanted in the innominate artery through the brachial artery. The patient recovered uneventfully and remained well 14 months after the procedure, with no sign of infection. Endovascular stent grafting may be the treatment of choice for patients with tracheo-innominate artery fistula. (J Vasc Surg 2001;33:1280-2.