Grounding event references in news

Events are frequently discussed in natural language, and their accurate identification is central to language understanding. Yet they are diverse and complex in ontology and reference; computational processing hence proves challenging. News provides a shared basis for communication by reporting events. We perform several studies into news event reference. One annotation study characterises each news report in terms of its update and topic events, but finds that topic is better consider through explicit references to background events. In this context, we propose the event linking task which—analogous to named entity linking or disambiguation—models the grounding of references to notable events. It defines the disambiguation of an event reference as a link to the archival article that first reports it. When two references are linked to the same article, they need not be references to the same event. Event linking hopes to provide an intuitive approximation to coreference, erring on the side of over-generation in contrast with the literature. The task is also distinguished in considering event references from multiple perspectives over time. We diagnostically evaluate the task by first linking references to past, newsworthy events in news and opinion pieces to an archive of the Sydney Morning Herald. The intensive annotation results in only a small corpus of 229 distinct links. However, we observe that a number of hyperlinks targeting online news correspond to event links. We thus acquire two large corpora of hyperlinks at very low cost. From these we learn weights for temporal and term overlap features in a retrieval system. These noisy data lead to significant performance gains over a bag-of-words baseline. While our initial system can accurately predict many event links, most will require deep linguistic processing for their disambiguation

Numerical and Experimental Investigations on Corrosion and Self-Protection Processes in Reinforced Concrete

The chloride induced corrosion of steel in concrete is one of the biggest durability issues affecting structures worldwide. Concrete structures that are installed in marine environment and those exposed frequently to de-icing salts in the winter season, such as bridges and parking structures, are particularly susceptible to corrosion induced damage. In worst cases, the structure is unable to fulfil its entire service life and needs extensive repairs or is decommissioned quite early. Such situations can have a strong impact on society which is dependent on infrastructures for mobility and transportation of essential materials. Moreover, the economic losses are predicted in billions in the coming future and can impact the global economy. In an attempt to increase the service life of concrete structures with respect to chloride durability, Layered Double Hydroxides (LDH) are introduced as chloride ion entrapping additive in concrete. LDH encapsulates chloride ions from the environment which can extend the service life of concrete structures. It can also be tailored to deliver corrosion inhibiting ions which can mitigate the chloride induced damage in concrete. A new concrete mix with LDH was developed in this work for building long lasting infrastructure exposed to chloride ingress in submerged marine zones. Predictive modelling approaches are used to study the corrosion processes and chloride durability of concrete. Multi-ion transport model is used to predict the efficiency of LDH in concrete concerning chloride ingress. Computational results are presented which compare chloride ingress in concrete with and without LDH. Formation factor has been used in this study to determine the microstructure related properties of concrete with and without LDH. Additionally, experimental investigations are presented which report on the stability and chloride binding capacity of LDH in synthetic alkaline solutions, concrete pore solutions, mortars and also in concrete. The compatibility of LDH with cement is also presented. The work highlights that LDH is able to improve the chloride durability of concrete. Furthermore, In-situ investigations are carried out to understand the stability of LDH inside concrete

The Impacts of Biofuel Expansion on the Resilience of Social-Ecological Systems in Ethiopia

Abstract This thesis investigates biofuel expansion as a disturbance to the resilience of social-ecological systems. Examining this issue through a resilience framework illustrates the dynamics of such systems, identifying potential trade-offs and regime shifts. Additionally, this research highlights the differentiated impacts for actors across multiple scales, allowing power relations to be taken into account – the lack of which is a common criticism of resilience studies. The thesis presents a systems analysis of sugarcane-ethanol expansion in Ethiopia at the current and planned levels of production, incorporating both the production and consumption sub-systems. To create an integrated systems analysis multiple methods were utilised between 2010 and 2012 to collect primary data – household surveys and interviews in multiple localities and interviews with key stakeholders, supplemented with documentary evidence. The production sub-system analysis incorporates food system impacts at the household scale and ecological impacts at the regional scale, whilst the consumption sub-system analysis investigates the impacts of ethanol adoption as a household fuel. The findings of these analyses are then synthesised in a resilience assessment at the national scale. The results show that current levels of sugarcane and ethanol production have not surpassed the majority of potential critical thresholds that would induce regime shifts. Therefore, most of the sub-systems under study, and actors within them, are resilient to the perturbation of biofuel expansion to date. However, a detrimental regime shift is underway for pastoralists being relocated for sugarcane expansion. The planned expansion will replicate this regime shift across a much larger population. In addition, the larger scale of operation will more severely influence the ecological sub-system. The analysis of multiple nested scales using a resilience model demonstrates the need to examine all scales to highlight the winners and losers, as only examining one scale conceals the dynamic nature of interactions

Washington University Senior Undergraduate Research Digest (WUURD), Spring 2018

From the Washington University Office of Undergraduate Research Digest (WUURD), Vol. 13, 05-01-2018. Published by the Office of Undergraduate Research. Joy Zalis Kiefer, Director of Undergraduate Research and Associate Dean in the College of Arts & Scien

Computer-based tools for supporting forest management. The experience and the expertise world-wide

Report of Cost Action FP 0804 Forest Management Decision Support Systems (FORSYS)Computer-based tools for supporting forest management. The experience and the expertise world-wide answers a call from both the research and the professional communities for a synthesis of current knowledge about the use of computerized tools in forest management planning. According to the aims of the Forest Management Decision Support Systems (FORSYS) (http://fp0804.emu.ee/) this synthesis is a critical success factor to develop a comprehensive quality reference for forest management decision support systems. The emphasis of the book is on identifying and assessing the support provided by computerized tools to enhance forest management planning in real-world contexts. The book thus identifies the management planning problems that prevail world-wide to discuss the architecture and the components of the tools used to address them. Of importance is the report of architecture approaches, models and methods, knowledge management and participatory planning techniques used to address specific management planning problems. We think that this synthesis may provide effective support to research and outreach activities that focus on the development of forest management decision support systems. It may contribute further to support forest managers when defining the requirements for a tool that best meets their needs. The first chapter of the book provides an introduction to the use of decision support systems in the forest sector and lays out the FORSYS framework for reporting the experience and expertise acquired in each country. Emphasis is on the FORSYS ontology to facilitate the sharing of experiences needed to characterize and evaluate the use of computerized tools when addressing forest management planning problems. The twenty six country reports share a structure designed to underline a problem-centric focus. Specifically, they all start with the identification of the management planning problems that are prevalent in the country and they move on to the characterization and assessment of the computerized tools used to address them. The reports were led by researchers with background and expertise in areas that range from ecological modeling to forest modeling, management planning and information and communication technology development. They benefited from the input provided by forest practitioners and by organizations that are responsible for developing and implementing forest management plans. A conclusions chapter highlights the success of bringing together such a wide range of disciplines and perspectives. This book benefited from voluntary contributions by 94 authors and from the involvement of several forest stakeholders from twenty six countries in Europe, North and South America, Africa and Asia over a three-year period. We, the chair of FORSYS and the editorial committee of the publication, acknowledge and thank for the valuable contributions from all authors, editors, stakeholders and FORSYS actors involved in this project

Expression of the ARTEMISIA ANNUA β-CARYOPHYLLENE synthase in Synechocystis sp. strain PCC6803 results in cyanobacterial sesquiterpene accumulation

The sesquiterpene β-caryophyllene is a ubiquitous component of many plant resins and has been used in the cosmetic industry to provide a woody, spicy aroma. Recent clinical studies have shown its potential effectiveness as an antibiotic, anesthetic, and anti-inflammatory agent. Additionally, there is significant interest in sesquiterpene accumulation in phototrophic microorganisms for the production of biofuels. Currently, the isolation of β-caryophyllene relies on purification methods from oleoresins extracted from large amounts of plant material. The design of a cyanobacterium platform that produces β-caryophyllene may provide a more sustainable and controllable means of production, allowing for an increase in yield without the potential deleterious effects to natural sources. To this end, the β-caryophyllene synthase gene (QHS1) from Artemisia annua (Chinese wormwood) was stably inserted via double homologous recombination into the genome of the cyanobacterium Synechocystis sp. strain PCC6803, under the control of the strong endogenous psbAII promoter. Gene insertion into Synechocystis was confirmed through polymerase chain reaction assays and sequencing reactions. Transcription and expression of QHS1 was confirmed using reverse transcription PCR assays and production of β-caryophyllene was confirmed in the transgenic strain using gas chromatography with flame ionization detection and mass-spectrometry detection

The Gene Ontology Handbook

bioinformatics; biotechnolog

Investigation of proteins and their modifications using high-resolution mass spectrometry

Advances in mass spectrometry (MS) has allowed for the deep analysis of various proteomes, providing identifications of proteins and their modifications. The true power in modern-day proteomics is the application of MS techniques to address various biological questions, propelling disease research and biochemical understanding of organisms. We have utilized high-resolution mass spectrometry to investigate biological questions leading to a greater knowledge of cellular biology. The transcriptional co-activator with PDZ-binding motif (TAZ), is regulated by reversible phosphorylation. However, sequence analysis suggests many potential uncharacterized sites of TAZ phosphorylation, specifically in regions in close proximity to a critical phosphorylation site making site assignment challenging. Using both targeted and untargeted approaches, we identified novel TAZ phosphorylation sites, using a reaction monitoring scheme to resolve positional phosphoisomers, and determined the biological consequence of a novel site, serine 93, on TAZ localization. Spinal muscular atrophy (SMA) is a motor neuron disease affecting 1 in 10,000 individuals. SMA has been shown to involve the release of extracellular vesicles (EVs), which have been used as a source of biomarkers for disease. We examined the use of EVs as a source of SMA biomarkers. We isolated and quantified \u3e650 proteins from SMA-derived vesicles finding potential biomarkers, one of which was confirmed in patients, suggesting these vesicles coupled with our methods are suitable for SMA biomarker discovery. In the model plant species Arabidopsis thaliana gene expression is heavily regulated through post-translational ubiquitination, however a gap between the number of ubiquitinated substrates identified and genes encoding the ubiquitin machinery exists, suggesting many unidentified modifications exist. The main strategy for studying ubiquitomes across species uses diglycine enrichment followed by MS analysis. We developed a DIA-based MS method coupled with novel sample preparation methods to overcome plant-specific challenges and increase the repository of the Arabidopsis ubiquitome, identifying 160 proteins with over 400 ubiquitination sites. The prevalent Charcot-Marie-Tooth disease can be caused by mutations in the lipid phosphatase MTMR2, a protein critical for regulating endosomal dynamics. MTMR2 is regulated by phosphorylation at serine 58. However, the phosphatase and the alterations in protein-protein interactions occurring with this modification have not been thoroughly investigated. To isolate MTMR2 interacting proteins, we utilized in vivo labeling fusing BirA biotin ligase to MTMR2, followed by MS analysis, identifying a putative interactor, TSSC1. We also provide evidence that MTMR2 itself may be subjected to phosphorylation-dependent degradation. This work utilizes high-resolution MS techniques to link protein regulation and function in a variety of biological and cellular contexts. The techniques presented here can be applied to address the gaps of knowledge in various proteomes and are amenable to user-specific modifications. The techniques here provide a framework for determining disease biomarkers for neurological diseases from EVs, investigating proteome-wide changes through protein modifications, and ultimately link high-resolution analytical mass spectrometry techniques and data to address critical biological events in a robust fashion