Using co-occurrence network structure to extract synonymous gene and protein names from MEDLINE abstracts

BACKGROUND: Text-mining can assist biomedical researchers in reducing information overload by extracting useful knowledge from large collections of text. We developed a novel text-mining method based on analyzing the network structure created by symbol co-occurrences as a way to extend the capabilities of knowledge extraction. The method was applied to the task of automatic gene and protein name synonym extraction. RESULTS: Performance was measured on a test set consisting of about 50,000 abstracts from one year of MEDLINE. Synonyms retrieved from curated genomics databases were used as a gold standard. The system obtained a maximum F-score of 22.21% (23.18% precision and 21.36% recall), with high efficiency in the use of seed pairs. CONCLUSION: The method performs comparably with other studied methods, does not rely on sophisticated named-entity recognition, and requires little initial seed knowledge

Language and theory of mind in autism spectrum disorder : the relationship between complement syntax and false belief task performance.

This study aimed to test the hypothesis that children with autism spectrum disorder (ASD) use their knowledge of complement syntax as a means of “hacking out” solutions to false belief tasks, despite lacking a representational theory of mind (ToM). Participants completed a “memory for complements” task, a measure of receptive vocabulary, and traditional location change and unexpected contents false belief tasks. Consistent with predictions, the correlation between complement syntax score and location change task performance was significantly stronger within the ASD group than within the comparison group. However, contrary to predictions, complement syntax score was not significantly correlated with unexpected contents task performance within either group. Possible explanations for this pattern of results are considered

Impaired Competence for Pretense in Children with Autism: Exploring Potential Cognitive Predictors.

Lack of pretense in children with autism has been explained by a number of theoretical explanations, including impaired mentalising, impaired response inhibition, and weak central coherence. This study aimed to empirically test each of these theories. Children with autism (n=60) were significantly impaired relative to controls (n=65) when interpreting pretense, thereby supporting a competence deficit hypothesis. They also showed impaired mentalising and response inhibition, but superior local processing indicating weak central coherence. Regression analyses revealed that mentalising significantly and independently predicted pretense. The results are interpreted as supporting the impaired mentalising theory and evidence against competing theories invoking impaired response inhibition or a local processing bias. The results of this study have important implications for treatment and intervention

A graph-search framework for associating gene identifiers with documents

BACKGROUND: One step in the model organism database curation process is to find, for each article, the identifier of every gene discussed in the article. We consider a relaxation of this problem suitable for semi-automated systems, in which each article is associated with a ranked list of possible gene identifiers, and experimentally compare methods for solving this geneId ranking problem. In addition to baseline approaches based on combining named entity recognition (NER) systems with a "soft dictionary" of gene synonyms, we evaluate a graph-based method which combines the outputs of multiple NER systems, as well as other sources of information, and a learning method for reranking the output of the graph-based method. RESULTS: We show that named entity recognition (NER) systems with similar F-measure performance can have significantly different performance when used with a soft dictionary for geneId-ranking. The graph-based approach can outperform any of its component NER systems, even without learning, and learning can further improve the performance of the graph-based ranking approach. CONCLUSION: The utility of a named entity recognition (NER) system for geneId-finding may not be accurately predicted by its entity-level F1 performance, the most common performance measure. GeneId-ranking systems are best implemented by combining several NER systems. With appropriate combination methods, usefully accurate geneId-ranking systems can be constructed based on easily-available resources, without resorting to problem-specific, engineered components

‘Blue boats’ and ‘reef robbers’: A new maritime security threat for the Asia Pacific?

© 2019 The Authors. Asia Pacific Viewpoint published by Victoria University of Wellington and John Wiley & Sons Australia, Ltd Vietnamese ‘blue boats’ – small wooden-hulled fishing boats – are now entering the territorial waters of Pacific Island countries and illegally catching high-value species found on remote coastal reefs. Crossing several international boundaries and traversing a distance of over 5000 km, these intrusions have alarmed Oceanic countries, including Australia. Lacking administrative capacity as well as jurisdictional authority to effectively control the vast stretches of island coastlines individually, governments and intergovernmental bodies in the region have called for strengthened coordination of surveillance efforts while also pressuring Vietnam diplomatically. This paper reviews these latest developments and is the first to provide a focused assessment of the issue. Through the lens of Copenhagen School of securitisation theory, we analyse responses of national and regional actors and their portrayal in online media to understand how blue boats are constructed as a security threat within a narrative of maritime, food and human security. Arguably, Australia together with the Forum Fisheries Agency, who advise on the governance of offshore tuna resources, have so far acted most decisively – in a way that might see them extend their strategic role in the region. We propose a comprehensive empirical research agenda to better understand and manage this nascent, flammable and largely unpredictable inter-regional phenomenon

Do adults with high functioning autism or Asperger Syndrome differ in empathy and emotion recognition?

The present study examined whether adults with high functioning autism (HFA) showed greater difficulties in (i) their self-reported ability to empathise with others and/or (ii) their ability to read mental states in others’ eyes than adults with Asperger syndrome (AS). The Empathy Quotient (EQ) and ‘Reading the Mind in the Eyes’ Test (Eyes Test) were compared in 43 adults with AS and 43 adults with HFA. No significant difference was observed on EQ score between groups, while adults with AS performed significantly better on the Eyes Test than those with HFA. This suggests that adults with HFA may need more support, particularly in mentalizing and complex emotion recognition, and raises questions about the existence of subgroups within autism spectrum conditions

Which activities threaten independent living of elderly when becoming problematic : inspiration for meaningful service robot functionality

Purpose: In light of the increasing elderly population and the growing demand for home care, the potential of robot support is given increasing attention. In this paper, an inventory of activities was made that threaten independent living of elderly when becoming problematic. Results will guide the further development of an existing service robot, the Care-O-bot®. Method: A systematic literature search of PubMed was performed, focused on the risk factors for institutionalization. Additionally, focus group sessions were conducted in the Netherlands, United Kingdom and France. In these focus group sessions, problematic activities threatening the independence of elderly people were discussed. Three separate target groups were included in the focus group sessions: (1) elderly persons (n = 41), (2) formal caregivers (n = 40) and (3) informal caregivers (n = 32). Results: Activities within the International Classification of Functioning domains mobility, self-care, and interpersonal interaction and relationships were found to be the most problematic. Conclusions: A distinct set of daily activities was identified that may threaten independent living, but no single activity could be selected as the main activity causing a loss of independence as it is often a combination of problematic activities that is person-specific. Supporting the problematic activities need not involve a robotic solution Read More: http://informahealthcare.com/doi/abs/10.3109/17483107.2013.840861Peer reviewe

Coherent quantum phase slip

A hundred years after discovery of superconductivity, one fundamental prediction of the theory, the coherent quantum phase slip (CQPS), has not been observed. CQPS is a phenomenon exactly dual to the Josephson effect: whilst the latter is a coherent transfer of charges between superconducting contacts, the former is a coherent transfer of vortices or fluxes across a superconducting wire. In contrast to previously reported observations of incoherent phase slip, the CQPS has been only a subject of theoretical study. Its experimental demonstration is made difficult by quasiparticle dissipation due to gapless excitations in nanowires or in vortex cores. This difficulty might be overcome by using certain strongly disordered superconductors in the vicinity of the superconductor-insulator transition (SIT). Here we report the first direct observation of the CQPS in a strongly disordered indium-oxide (InOx) superconducting wire inserted in a loop, which is manifested by the superposition of the quantum states with different number of fluxes. Similarly to the Josephson effect, our observation is expected to lead to novel applications in superconducting electronics and quantum metrology.Comment: 14 pages, 3 figure