Discovering context-specific relationships from biological literature by using multi-level context terms

<p>Abstract</p> <p>Background</p> <p>The Swanson's ABC model is powerful to infer hidden relationships buried in biological literature. However, the model is inadequate to infer relations with context information. In addition, the model generates a very large amount of candidates from biological text, and it is a semi-automatic, labor-intensive technique requiring human expert's manual input. To tackle these problems, we incorporate context terms to infer relations between AB interactions and BC interactions.</p> <p>Methods</p> <p>We propose 3 steps to discover meaningful hidden relationships between drugs and diseases: 1) multi-level (gene, drug, disease, symptom) entity recognition, 2) interaction extraction (drug-gene, gene-disease) from literature, 3) context vector based similarity score calculation. Subsequently, we evaluate our hypothesis with the datasets of the "Alzheimer's disease" related 77,711 PubMed abstracts. As golden standards, PharmGKB and CTD databases are used. Evaluation is conducted in 2 ways: first, comparing precision of the proposed method and the previous method and second, analysing top 10 ranked results to examine whether highly ranked interactions are truly meaningful or not.</p> <p>Results</p> <p>The results indicate that context-based relation inference achieved better precision than the previous ABC model approach. The literature analysis also shows that interactions inferred by the context-based approach are more meaningful than interactions by the previous ABC model.</p> <p>Conclusions</p> <p>We propose a novel interaction inference technique that incorporates context term vectors into the ABC model to discover meaningful hidden relationships. By utilizing multi-level context terms, our model shows better performance than the previous ABC model.</p

Oxidative Stability of Polyunsaturated Edible Oils Mixed With Microcrystalline Cellulose

The oxidative stability of mixtures of edible oils containing polyunsaturated fatty acids (PUFA) and microcrystalline cellulose (MCC) was investigated. The mixtures studied consisted of oils of either camelina (CAM), cod liver (CLO), or salmon (SO) mixed with either colloidal or powdered MCC. A 50:50 (w/w) ratio of oil:MCC resulted in an applicable mixture containing high levels of PUFA edible oil and dietary fiber. The oxidative stability of the formulated mixtures and the pure oils was investigated over a period of 28 days. The peroxide value (PV) was assessed as a parameter for primary oxidation products and dynamic headspace gas chromatography mass spectrometry (GC/MS) was used to analyze secondary volatile organic compounds (VOC). CAM and the respective mixtures were oxidatively stable at both 4 and 22 °C during the storage period. The marine oils and the respective mixtures were stable at 4 °C. At 22 °C, an increase in hydroperoxides was found, but no increase in VOC was detected during the time-frame investigated. At 42 °C, prominent increases in PV and VOC were found for all oils and mixtures. Hexanal, a common marker for the degradation of n-6 fatty acids, propanal and 2,4-heptadienal (E,E), common indicators for the degradation of n-3 fatty acids, were among the volatiles detected in the headspace of oils and mixtures. This study showed that a mixture containing a 50:50 ratio of oil:MCC can be obtained by a low-tech procedure that does not induce oxidation when stored at low temperatures during a period of 1 month

Cell Pattern in Adult Human Corneal Endothelium

A review of the current data on the cell density of normal adult human endothelial cells was carried out in order to establish some common parameters appearing in the different considered populations. From the analysis of cell growth patterns, it is inferred that the cell aging rate is similar for each of the different considered populations. Also, the morphology, the cell distribution and the tendency to hexagonallity are studied. The results are consistent with the hypothesis that this phenomenon is analogous with cell behavior in other structures such as dry foams and grains in polycrystalline materials. Therefore, its driving force may be controlled by the surface tension and the mobility of the boundaries

A framework for teaching epistemic insight in schools

This paper gives the rationale and a draft outline for a framework for education to teach epistemic insight into schools in England. The motivation to research and propose a strategy to teach and assess epistemic insight followed research that investigated how students and teachers in primary and secondary schools respond to big questions about the nature of reality and human personhood. The research revealed that there are pressures in schools that dampen students’ expressed curiosity in these types of questions and limit their developing epistemic insight into how science, religion and the wider humanities relate. These findings prompted the construction of a framework for education for students aged 5–16 designed to encourage students’ expressed interest in big questions and develop their understanding of the ways that science interacts with other ways of knowing. The centrepiece of the framework is a sequence of learning objectives for epistemic insight, organised into three categories. The categories are, firstly, the nature of science in real world contexts and multidisciplinary arenas; secondly, ways of knowing and how they interact; and thirdly, the relationships between science and religion. Our current version of the Framework is constructed to respond to the way that teaching is organised in England. The key principles and many of the activities could be adopted and tailored to work in many other countries

Evaluation of guided imagery as treatment for recurrent abdominal pain in children: a randomized controlled trial

BACKGROUND: Because of the paucity of effective evidence-based therapies for children with recurrent abdominal pain, we evaluated the therapeutic effect of guided imagery, a well-studied self-regulation technique. METHODS: 22 children, aged 5 – 18 years, were randomized to learn either breathing exercises alone or guided imagery with progressive muscle relaxation. Both groups had 4-weekly sessions with a therapist. Children reported the numbers of days with pain, the pain intensity, and missed activities due to abdominal pain using a daily pain diary collected at baseline and during the intervention. Monthly phone calls to the children reported the number of days with pain and the number of days of missed activities experienced during the month of and month following the intervention. Children with ≤ 4 days of pain/month and no missed activities due to pain were defined as being healed. Depression, anxiety, and somatization were measured in both children and parents at baseline. RESULTS: At baseline the children who received guided imagery had more days of pain during the preceding month (23 vs. 14 days, P = 0.04). There were no differences in the intensity of painful episodes or any baseline psychological factors between the two groups. Children who learned guided imagery with progressive muscle relaxation had significantly greater decrease in the number of days with pain than those learning breathing exercises alone after one (67% vs. 21%, P = 0.05), and two (82% vs. 45%, P < 0.01) months and significantly greater decrease in days with missed activities at one (85% vs. 15%, P = 0.02) and two (95% vs. 77%. P = 0.05) months. During the two months of follow-up, more children who had learned guided imagery met the threshold of ≤ 4 day of pain each month and no missed activities (RR = 7.3, 95%CI [1.1,48.6]) than children who learned only the breathing exercises. CONCLUSION: The therapeutic efficacy of guided imagery with progressive muscle relaxation found in this study is consistent with our present understanding of the pathophysiology of recurrent abdominal pain in children. Although unfamiliar to many pediatricians, guided imagery is a simple, noninvasive therapy with potential benefit for treating children with RAP

Intertwining personal and reward relevance: evidence from the drift-diffusion model.

In their seminal paper 'Is our self nothing but reward', Northoff and Hayes (Biol Psychiatry 69(11):1019-1025, Northoff, Hayes, Biological Psychiatry 69(11):1019-1025, 2011) proposed three models of the relationship between self and reward and opened a continuing debate about how these different fields can be linked. To date, none of the proposed models received strong empirical support. The present study tested common and distinct effects of personal relevance and reward values by de-componenting different stages of perceptual decision making using a drift-diffusion approach. We employed a recently developed associative matching paradigm where participants (N = 40) formed mental associations between five geometric shapes and five labels referring personal relevance in the personal task, or five shape-label pairings with different reward values in the reward task and then performed a matching task by indicating whether a displayed shape-label pairing was correct or incorrect. We found that common effects of personal relevance and monetary reward were manifested in the facilitation of behavioural performance for high personal relevance and high reward value as socially important signals. The differential effects between personal and monetary relevance reflected non-decisional time in a perceptual decision process, and task-specific prioritization of stimuli. Our findings support the parallel processing model (Northoff & Hayes, Biol Psychiatry 69(11):1019-1025, Northoff, Hayes, Biological Psychiatry 69(11):1019-1025, 2011) and suggest that self-specific processing occurs in parallel with high reward processing. Limitations and further directions are discussed

Deformation quantisation for unshifted symplectic structures on derived Artin stacks

We prove that every $0$-shifted symplectic structure on a derived Artin $n$-stack admits a curved $A_{\infty}$ deformation quantisation. The classical method of quantising smooth varieties via quantisations of affine space does not apply in this setting, so we develop a new approach. We construct a map from DQ algebroid quantisations of unshifted symplectic structures on a derived Artin $n$-stack to power series in de Rham cohomology, depending only on a choice of Drinfeld associator. This gives an equivalence between even power series and certain involutive quantisations, which yield anti-involutive curved $A_{\infty}$ deformations of the dg category of perfect complexes. In particular, there is a canonical quantisation associated to every symplectic structure on such a stack, which agrees for smooth varieties with the Kontsevich--Tamarkin quantisation for even associators.Comment: 27pp.; v2 Propositions 1.23 and 3.10 added; v3 several small additions; v4 several changes following referee's comments, to appear in Select