Prune-and-Score: Learning for Greedy Coreference Resolution

We propose a novel search-based approach for greedy coreference resolution, where the mentions are processed in order and added to previous coreference clusters. Our method is distinguished by the use of two functions to make each corefer-ence decision: a pruning function that prunes bad coreference decisions from fur-ther consideration, and a scoring function that then selects the best among the re-maining decisions. Our framework re-duces learning of these functions to rank learning, which helps leverage powerful off-the-shelf rank-learners. We show that our Prune-and-Score approach is superior to using a single scoring function to make both decisions and outperforms sever-al state-of-the-art approaches on multiple benchmark corpora including OntoNotes.

Dictionary of Invertebrate Zoology

An exhaustive dictionary of over 13,000 terms relating to invertebrate zoology, including etymologies, word derivations and taxonomic classification. Entries cover parasitology, nematology, marine invertebrates, insects, and anatomy, biology, and reproductive processes for the following phyla: Acanthocephala Annelida Arthropoda Brachiopoda Bryozoa Chaetognatha Cnidaria Ctenophora Echinodermata Echiura Entoprocta Gastrotricha Gnathostomulida Kinorhyncha Loricifera Mesozoa Mollusca Nemata Nematomorpha Nemertea Onychophora Pentastoma Phoronida Placozoa Platyhelminthes Pogonophora Porifera Priapula Rotifera Sipuncula Tardigrada.https://digitalcommons.unl.edu/zeabook/1061/thumbnail.jp

2024 Student Symposium Program and Book of Abstracts

The mission of the UMaine Student Symposium is to give graduate and undergraduate students from UMaine and UMaine Machias the opportunity to showcase their work, research, and creative activities to the greater community, fostering conversations and collaborations that will benefit the future of Maine and beyond

Cellular Oxidative Stress

This book collects 17 original research papers and 9 reviews that are part of the Special Issue “Cellular Oxidative Stress”, published in the journal Antioxidants. Oxidative stress on a cellular level affects the function of tissues and organs and may eventually lead to disease. Therefore, a precise understanding of how oxidative stress develops and can be counteracted is of utmost importance. The scope of the book is to emphasize the latest findings on the cellular targets of oxidative stress and the potential beneficial effect of antioxidants on human health

Training Manual on "Know Your Marine Biodiversity and Environment (MarBiE 2)" Taxonomy of Marine Organisms

Sustainable fisheries management aims to protect fishery resources to ensure the long-term viability of fish stocks and marine ecosystems. It combines theoretical disciplines, like population dynamics, with practical strategies, like avoiding overfishing and curbing illegal fishing practices. Correct taxonomy and systematics tools permit the classification of practically all fish species. This capacity is of particular value for fisheries management biological and ecological research as well as to issues related to fisheries products for human consumption. However, its usefulness is hindered by the lack of expertise in this area and the decrease in the number of taxonomists. Specimens have to be identified at species level using standard morphometric and meristic procedures applied by taxonomists. With sustainability being the critical issue of the hour, developing a younger breed of qualified taxonomists in the different marine realm is of outmost importance. It is physically difficult to identify and collect data on every organism in an ecosystem; therefore, taxonomic studies focus exclusively on specific taxonomic groups, which highlights their significance. The application of contemporary techniques will enhance our understanding of evolutionary linkages. This can entail educating a new generation of specialists on the systematics of the relevant group or persuading more experienced experts to write assessments of the group. The credibility of species occurrence records from current databases and literature needs to be thoroughly evaluated

Handbook of Marine Model Organisms in Experimental Biology

"The importance of molecular approaches for comparative biology and the rapid development of new molecular tools is unprecedented. The extraordinary molecular progress belies the need for understanding the development and basic biology of whole organisms. Vigorous international efforts to train the next-generation of experimental biologists must combine both levels – next generation molecular approaches and traditional organismal biology. This book provides cutting-edge chapters regarding the growing list of marine model organisms. Access to and practical advice on these model organisms have become aconditio sine qua non for a modern education of advanced undergraduate students, graduate students and postdocs working on marine model systems. Model organisms are not only tools they are also bridges between fields – from behavior, development and physiology to functional genomics. Key Features Offers deep insights into cutting-edge model system science Provides in-depth overviews of all prominent marine model organisms Illustrates challenging experimental approaches to model system research Serves as a reference book also for next-generation functional genomics applications Fills an urgent need for students Related Titles Jarret, R. L. & K. McCluskey, eds. The Biological Resources of Model Organisms (ISBN 978-1-1382-9461-5) Kim, S.-K. Healthcare Using Marine Organisms (ISBN 978-1-1382-9538-4) Mudher, A. & T. Newman, eds. Drosophila: A Toolbox for the Study of Neurodegenerative Disease (ISBN 978-0-4154-1185-1) Green, S. L. The Laboratory Xenopus sp. (ISBN 978-1-4200-9109-0)

The Victorian Naturalist

v.116 (1999

Os efeitos das alterações climáticas na fisiologia e fotobiologia das lesmas do mar fotossintéticas

Doutoramento em BiologiaThe vulnerability of marine photosynthetic symbioses to climate-driven changes has deserved particular attention in recent years. However, while there is an increasing number of studies on emblematic species such as symbiotic corals, little is known about less charismatic groups such as solar-powered sea slugs. These organisms display one of the most puzzling features observed in the animal kingdom: the mollusc-plastid association, which results from their ability to retain photosynthetically active chloroplasts (kleptoplasts) “stolen” from their algal food sources. Given their peculiar biology, sea slugs have stood out as tool organisms for academic research on photobiology, biomedical studies and bioprospecting of new marine drugs, becoming also desired critters in the marine aquarium trade. In order to provide an overview of state-of-the-art on our knowledge on these fascinating organisms, and lay down the foundations for climate change research, the biological and ecological features of the mollusc-plastid association were reviewed and optimal culture conditions for their different life stages were identified. The impact of ocean acidification and warming was evaluated on early stages and adults of temperate (Elysia viridis) and tropical (Elysia clarki) sea slugs. In this context, new methodological approaches were developed to non-invasively assess the photophysiology of kleptoplasts under future ocean conditions. Our results have shown that acidification and warming may impact several biological features of solar-powered sea slugs, including survival, reproductive success, growth, incidence of deformities, kleptoplasts photosynthetic efficiency, metabolism, heat shock and antioxidant responses. However, sea slug tolerance to future ocean conditions was shown to be species-specific. The temperate sea slug E. viridis, in spite of their low survival, presented efficient heat shock and antioxidant defence mechanisms and high rates of photosynthesis and respiration when exposed to acidification and warming, suggesting the existence of a more tolerant mollusc-kleptoplast complex and capacity to cope with future scenarios. In contrast, the tropical sea slug E. clarki showed to be quite vulnerable to future ocean conditions. The reduced capacity or lack of mechanisms to deal with environmental stress may, in part, explain the metabolic depression of the holobiont and the reduced photosynthetic efficiency of kleptoplasts, leading to bleaching and a lower survival. This work is the first reporting the occurrence of bleaching under climate change in other photosynthetic symbiosis than the cnidarian-dinoflagellate association. These results have broad implications and may help us to anticipate potential negative impacts on the recruitment of solar-powered sea slugs in the oceans of tomorrow. However, it is worth noting that solar-powered sea slugs may have time and evolutionary opportunities to adapt to future ocean conditions.A vulnerabilidade das simbioses fotossintéticas marinhas face às alterações climáticas tem recebido particular atenção nos últimos anos. Porém, enquanto existe um número crescente de estudos para as espécies emblemáticas, como os corais, pouco se sabe acerca dos grupos menos carismáticos como as lesmas do mar “movidas a energia solar”. Estes organismos possuem uma das particularidades mais intrigantes do reino animal: uma associação molusco-plasto, que resulta da sua capacidade de reter cloroplastos fotossinteticamente ativos (cleptoplastos) “roubados” às algas de que se alimentam. Dada a sua biologia peculiar, as lesmas do mar destacaram-se nos últimos anos como organismo “ferramenta” na investigação da fotobiologia, modelo nos estudos biomédicos e de bioprospeção de novos compostos marinhos, tornando-se ainda pretendidas para o comercio da aquariofilia marinha. Por forma a apresentar uma visão global acerca do conhecimento destes organismos fascinantes e estabelecer critérios para a investigação sobre as alterações climáticas, as características biológicas e ecológicas da associação molusco-plasto foram revistas e ainda identificadas as condições ótimas de cultivo para diferentes fases do seu ciclo de vida. O impacto da acidificação e o aquecimento dos oceanos foi avaliado nos estágios iniciais do desenvolvimento e nos adultos da lesma do mar temperada (Elysia viridis) e na tropical (Elysia clarki). Neste contexto, novas abordagens metodológicas foram desenvolvidas por forma a aceder de forma não invasiva à foto-fisiologia dos cleptoplastos de acordo com as futuras condições do oceano. Os resultados mostraram que a acidificação e o aquecimento do oceano podem influenciar as características biológicas das lesmas do mar “movidas a energia solar”, incluindo a sobrevivência, sucesso reprodutivo, crescimento, incidência de deformações, eficiência fotossintética dos cleptoplastos, metabolismo, e as respostas contra o choque térmico e de ação antioxidante. Contudo, a tolerância das lesmas do mar às condições futuras do oceano revelou ser especifica de cada espécie. A lesma do mar temperada E. viridis, apesar da baixa sobrevivência, apresentou mecanismos eficientes contra o choque térmico, defesa antioxidante e elevadas taxas de fotossíntese e respiração quando exposta à acidificação e ao aquecimento, sugerindo um complexo molusco-cleptoplasto mais tolerante e capacidade em lidar contra os cenários futuros. Por outro lado, a lesma do mar tropical E. clarki mostrou ser vulnerável às condições futuras do oceano. A reduzida capacidade e ausência de mecanismos para lidar com o stress ambiental pode, em parte, explicar a depressão metabólica do holobionte e a reduzida eficiência fotossintética dos cleptoplastos, que levaram ao branqueamento das lesmas do mar e a reduzida sobrevivência. Este trabalho é o primeiro a reportar a ocorrência de branqueamento em circunstâncias de alterações climáticas noutras simbioses marinhas que não as associações cnidário-dinoflagelado. Estes resultados têm amplas implicações e podem ajudar a antecipar os possíveis impactos negativos no recrutamento das lesmas do mar “movidas a energia solar” nos oceanos de amanhã. Contudo, é importante notar que as lesmas do mar “movidas a energia solar” poderão ter tempo e oportunidades evolutivas de adaptação às condições do futuro oceano

New Directions in Search-based Structured Prediction: Multi-Task Learning and Integration of Deep Models

This thesis studies the problem of structured prediction (SP), where the agent needs to predict a structured output for a given structured input (e.g., Part-of-Speech tagging sequence for an input sentence). Many important applications including machine translation in natural language processing (NLP) and image interpretation in computer vision can be naturally formulated as structured prediction problems. These prediction problems have an exponentially number of candidate outputs, which poses significant challenges for inference and learning. Search-based structured prediction views the prediction of structured outputs as a search process in the space of candidate outputs guided by a learned scoring function. Search-based approaches offer several advantages including, incorporation of expressive representations over inputs and outputs with negligible overhead in inference complexity, and providing a way to trade off accuracy for efficient inference. In this thesis, I make three contributions to advance search-based structured prediction methods towards the goal of improving their accuracy and computational-efficiency. First, I developed a search-based learning approach called “Prune-and-Score” to improve the accuracy of greedy policy based structured prediction for search spaces with large action spaces. The key idea is to learn a pruning function that prunes bad decisions and a scoring function that then selects the best among the remaining decisions. I show the efficacy of this approach for coreference resolution, i.e., clustering mentions that refer to the same entity, which is a hard NLP task. Second, I studied multi-task structured prediction (MTSP) problems in the context of entity analysis, which includes the three tasks of named entity recognition, co-reference resolution, and entity linking. I developed three different search-based learning architectures for MTSP problem that make different trade-offs between speed and accuracy of training and inference. I performed empirical evaluation of the proposed architectures for entity analysis with state-of-the-art results. Finally, I developed the HC-Nets framework by integrating the advances in deep learning with search-based SP methods. I formulate structured prediction as a complete output space search problem, and employ two neural network functions to guide the search: a heuristic function H for generating candidate outputs and a cost function C for selecting the best output from the generated candidates. Unlike prior methods such as structured prediction energy networks and deep value networks that perform gradient-based inference in relaxed space, HC-Nets allows to incorporate prior knowledge in the form of constraints. The decomposition of heuristic and cost functions makes the representation more expressive and learning more modular. Our experimental results show that HC-Nets achieves better performance than prior methods on multiple benchmark domains

Biomineralization

This open access book is the proceedings of the 14th International Symposium on Biomineralization (BIOMIN XIV) held in 2017 at Tsukuba. Over the past 45 years, biomineralization research has unveiled details of the characteristics of the nano-structure of various biominerals; the formation mechanism of this nano-structure, including the initial stage of crystallization; and the function of organic matrices in biominerals, and this knowledge has been applied to dental, medical, pharmaceutical, materials, agricultural and environmental sciences and paleontology. As such, biomineralization is an important interdisciplinary research area, and further advances are expected in both fundamental and applied research