Impact of sea ice transport on Beaufort Gyre liquid freshwater content.

The Arctic Ocean's Beaufort Gyre (BG) is a wind-driven reservoir of relatively fresh seawater, situated beneath time-mean anticyclonic atmospheric circulation, and is covered by mobile pack ice for most of the year. Liquid freshwater accumulation in and expulsion from this gyre is of critical interest due to its potential to affect the Atlantic meridional overturning circulation and due to the importance of freshwater in modulating vertical fluxes of heat, nutrients and carbon in the ocean, and exchanges of heat and moisture with the atmosphere. Here, we investigate the hypothesis that wind-driven sea ice transport into/from the BG region influences the freshwater content of the gyre and its variability.

Future strengthening of the Nordic Seas overturning circulation.

The overturning circulation in the Nordic Seas involves the transformation of warm Atlantic waters into cold, dense overflows. These overflow waters return to the North Atlantic and form the headwaters to the deep limb of the Atlantic meridional overturning circulation (AMOC). The Nordic Seas are thus a key component of the AMOC.

Sources of marine debris for Seychelles and other remote islands in the western Indian Ocean.

Vast quantities of debris are beaching at remote islands in the western Indian Ocean. We carry out marine dispersal simulations incorporating currents, waves, winds, beaching, and sinking, for both terrestrial and marine sources of debris, to predict where this debris comes from. Our results show that most terrestrial debris beaching at these remote western Indian Ocean islands drifts from Indonesia, India, and Sri Lanka.

Skillful prediction of northern climate provided by the ocean.

This corrects the article DOI: 10.1038/ncomms15875.

Skillful prediction of northern climate provided by the ocean.

It is commonly understood that a potential for skillful climate prediction resides in the ocean. It nevertheless remains unresolved to what extent variable ocean heat is imprinted on the atmosphere to realize its predictive potential over land. Here we assess from observations whether anomalous heat in the Gulf Stream's northern extension provides predictability of northwestern European and Arctic climate.

Acquisition and evaluation of verb subcategorization resources for biomedicine.

Background: Biomedical natural language processing (NLP) applications that have access to detailed resources about the linguistic characteristics of biomedical language demonstrate improved performance on tasks such as relation extraction and syntactic or semantic parsing. Such applications are important for transforming the growing unstructured information buried in the biomedical literature into structured, actionable information. In this paper, we address the creation of linguistic resources that capture how individual biomedical verbs behave.

A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools.

Background: We introduce the linguistic annotation of a corpus of 97 full-text biomedical publications, known as the Colorado Richly Annotated Full Text (CRAFT) corpus. We further assess the performance of existing tools for performing sentence splitting, tokenization, syntactic parsing, and named entity recognition on this corpus.

Results: Many biomedical natural language processing systems demonstrated large differences between their previously published results and their performance on the CRAFT corpus when tested with the publicly available models or rule sets.

HIGH-PRECISION BIOLOGICAL EVENT EXTRACTION: EFFECTS OF SYSTEM AND OF DATA.

We approached the problems of event detection, argument identification, and negation and speculation detection in the BioNLP'09 information extraction challenge through concept recognition and analysis. Our methodology involved using the OpenDMAP semantic parser with manually written rules. The original OpenDMAP system was updated for this challenge with a broad ontology defined for the events of interest, new linguistic patterns for those events, and specialized coordination handling.

The structural and content aspects of abstracts versus bodies of full text journal articles are different.

Background: An increase in work on the full text of journal articles and the growth of PubMedCentral have the opportunity to create a major paradigm shift in how biomedical text mining is done. However, until now there has been no comprehensive characterization of how the bodies of full text journal articles differ from the abstracts that until now have been the subject of most biomedical text mining research.

Results: We examined the structural and linguistic aspects of abstracts and bodies of full text articles, the performance of text mining tools on both, and the distribution of a variety of semantic classes of named entities between them.

Exploring species-based strategies for gene normalization.

We introduce a system developed for the BioCreative II.5 community evaluation of information extraction of proteins and protein interactions. The paper focuses primarily on the gene normalization task of recognizing protein mentions in text and mapping them to the appropriate database identifiers based on contextual clues.

Cocaine-exposed infant behavior during Still-Face: risk factor analyses.

Prenatal cocaine exposure and the role of gender were evaluated using risk factor analyses to determine whether 6-month-old cocaine-exposed male infants demonstrated greater disruptions in infant-caregiver socioemotional interactions during a Still-Face test. Overall, non-cocaine-exposed infants spent more time looking at toys, compared with cocaine-exposed infants; nonexposed female infants spent more time scanning the environment, compared with nonexposed male infants. When caregiver behavior during the Still-Face was evaluated, differences emerged in amount of time the caregiver spent vocalizing to the infant.

Concept recognition for extracting protein interaction relations from biomedical text.

Background: Reliable information extraction applications have been a long sought goal of the biomedical text mining community, a goal that if reached would provide valuable tools to benchside biologists in their increasingly difficult task of assimilating the knowledge contained in the biomedical literature. We present an integrated approach to concept recognition in biomedical text. Concept recognition provides key information that has been largely missing from previous biomedical information extraction efforts, namely direct links to well defined knowledge resources that explicitly cement the concept's semantics.

OpenDMAP: an open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression.

Background: Information extraction (IE) efforts are widely acknowledged to be important in harnessing the rapid advance of biomedical knowledge, particularly in areas where important factual information is published in a diverse literature. Here we report on the design, implementation and several evaluations of OpenDMAP, an ontology-driven, integrated concept analysis system. It significantly advances the state of the art in information extraction by leveraging knowledge in ontological resources, integrating diverse text processing applications, and using an expanded pattern language that allows the mixing of syntactic and semantic elements and variable ordering.

A fault model for ontology mapping, alignment, and linking systems.

There has been much work devoted to the mapping, alignment, and linking of ontologies (MALO), but little has been published about how to evaluate systems that do this. A fault model for conducting fine-grained evaluations of MALO systems is proposed, and its application to the system described in Johnson et al. [15] is illustrated.

Corpus refactoring: a feasibility study.

Background: Most biomedical corpora have not been used outside of the lab that created them, despite the fact that the availability of the gold-standard evaluation data that they provide is one of the rate-limiting factors for the progress of biomedical text mining. Data suggest that one major factor affecting the use of a corpus outside of its home laboratory is the format in which it is distributed. This paper tests the hypothesis that corpus refactoring - changing the format of a corpus without altering its semantics - is a feasible goal, namely that it can be accomplished with a semi-automatable process and in a time-effcient way.

Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies.

We used exact term matching, stemming, and inclusion of synonyms, implemented via the Lucene information retrieval library, to discover relationships between the Gene Ontology and three other OBO ontologies: ChEBI, Cell Type, and BRENDA Tissue. Proposed relationships were evaluated by domain experts. We discovered 91,385 relationships between the ontologies.

Neurological and developmental outcomes of prenatally cocaine-exposed offspring from 12 to 36 months.

Second generation studies of prenatal cocaine exposure failed to find gross deficits after controlling for confounders. Concern remained that exposure could cause subtle deficits. This prospective, cohort study evaluated effects of cocaine on development at 12, 18, 24, and 36 months.