Structured Multi-Label Biomedical Text Tagging via Attentive Neural Tree Decoding

We propose a model for tagging unstructured texts with an arbitrary number of terms drawn from a tree-structured vocabulary (i.e., an ontology). We treat this as a special case of sequence-to-sequence learning in which the decoder begins at the root node of an ontological tree and recursively elects to expand child nodes as a function of the input text, the current node, and the latent decoder state. We demonstrate that this method yields state-of-the-art results on the important task of assigning MeSH terms to biomedical abstracts

Collecting Information on Participant Reactions.

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Probiotic Supplementation and Gastrointestinal Endotoxemia Before and After the Marathon Des Sables.

Whilst evidence of increased gastrointestinal endotoxemia (GE) has been previously demonstrated during single-day ultra-endurance events, less is known on the prevalence of GE following extreme ultra-events such as the Marathon Des Sables (MDS). The potential benefit of probiotic formulas on gut integrity during ultra-endurance events also requires further investigation. PURPOSE: To assess the impact of probiotic supplementation with or without glutamine on GE prevalence in runners competing in a multi-day ultra-run (MDS). METHODS: Thirty four healthy participants from the 2015 MDS UK cohort volunteered for a 12 week pre-race intervention and were randomly assigned to either: probiotic (PRO; 100mg.d-1 lactobacillus acidophilus) (age 40 ±3 yrs., weight 79.4 ±2.0kg, VO2max 4.2 ±0.1 L.min-1), probiotic with glutamine (PROglut; 40.5mg.d-1 lactobacillus acidophilus and 900mg.d-1L-glutamine) (age 39 ±2 yrs., weight 70.6 ±4.8 kg, VO2max 4.0 ±0.2 L.min-1) and control (CON) (age 42±3 yrs., weight 79.2 ±3.8 kg, VO2max 4.0 ±0.3 L.min-1). Plasma lipopolysaccharides (LPS) (via Limulus Amebocyte Lysate chromogenic endotoxin quantification) were assessed at weeks 0, 12, post-race and 7 days post-race. Performance data was collated from official timing chips. Data presented as mean ±SE. RESULTS: Mild to moderate GE was prevalent in all groups at baseline (PRO 9.71 ±0.85pg.ml-1, PROglut 9.89 ±1.43 pg.ml-1, CON 9.40 ±0.57 pg.ml-1; P>0.05). Whilst LPS, post intervention, was lower in PROglut there was no significance between groups (9.81 ±1.47pg.ml-1 vs 12.80 ±0.93pg.ml-1 (PRO) vs 11.72 ±1.08 pg.mol-1 (CON); P>0.05). LPS were evidently reduced 6hrs post-race, but not different between groups (PRO: 7.29 ±1.41 pg.ml-1, PROglut: 6.95 ±0.94 pg.ml-1, CON: 9.73 ±1.39 pg.ml-1; P>0.05).Plasma LPS returned to baseline levels 7 days post-race (PRO 7.60 ±0.95 pg.ml-1, PROglut 10.41 ±1.04 pg.ml-1, CON 8.57 ±0.75 pg.ml-1; P>0.05). Race performance (hrs:mins) was not significant between groups, despite PRO and PROglut being ~9hrs faster than CON (41:28±2:31 vs 41:58±4:02 vs 50:43±4:38; P>0.05). CONCLUSION: Moderate GE was prevalent in all groups pre-race and fell significantly during the short-term recovery period. Despite promising results neither probiotic formula had a significant impact on GE or race performance

Problems and Aspects of Energy-Driven Wavefunction Collapse Models

Four problematic circumstances are considered, involving models which describe dynamical wavefunction collapse toward energy eigenstates, for which it is shown that wavefunction collapse of macroscopic objects does not work properly. In one case, a common particle position measuring situation, the apparatus evolves to a superposition of macroscopically distinguishable states (does not collapse to one of them as it should) because each such particle/apparatus/environment state has precisely the same energy spectrum. Second, assuming an experiment takes place involving collapse to one of two possible outcomes which is permanently recorded, it is shown in general that this can only happen in the unlikely case that the two apparatus states corresponding to the two outcomes have disjoint energy spectra. Next, the progressive narrowing of the energy spectrum due to the collapse mechanism is considered. This has the effect of broadening the time evolution of objects as the universe evolves. Two examples, one involving a precessing spin, the other involving creation of an excited state followed by its decay, are presented in the form of paradoxes. In both examples, the microscopic behavior predicted by standard quantum theory is significantly altered under energy-driven collapse, but this alteration is not observed by an apparatus when it is included in the quantum description. The resolution involves recognition that the statevector describing the apparatus does not collapse, but evolves to a superposition of macroscopically different states.Comment: 17 page

Patient factors associated with non-attendance at colonoscopy after a positive screening faecal occult blood test

BACKGROUND: Screening participants with abnormal faecal occult blood test results who do not attend further testing are at high risk of colorectal cancer, yet little is known about their reasons for non-attendance. METHODS: We conducted a medical record review of 170 patients from two English Bowel Cancer Screening Programme centres who had abnormal guaiac faecal occult blood test screening tests between November 2011 and April 2013 but did not undergo colonoscopy. Using information from patient records, we coded and categorized reasons for non-attendance. RESULTS: Of the 170 patients, 82 were eligible for review, of whom 66 had at least one recorded reason for lack of colonoscopy follow-up. Reasons fell into seven main categories: (i) other commitments, (ii) unwillingness to have the test, (iii) a feeling that the faecal occult blood test result was a false positive, (iv) another health issue taking priority, (v) failing to complete bowel preparation, (vi) practical barriers (e.g. lack of transport), and (vii) having had or planning colonoscopy elsewhere. The most common single reasons were unwillingness to have a colonoscopy and being away. CONCLUSIONS: We identify a range of apparent reasons for colonoscopy non-attendance after a positive faecal occult blood test screening. Education regarding the interpretation of guaiac faecal occult blood test findings, offer of alternative confirmatory test options, and flexibility in the timing or location of subsequent testing might decrease non-attendance of diagnostic testing following positive faecal occult blood test

A mapping approach to synchronization in the "Zajfman trap": stability conditions and the synchronization mechanism

We present a two particle model to explain the mechanism that stabilizes a bunch of positively charged ions in an "ion trap resonator" [Pedersen etal, Phys. Rev. Lett. 87 (2001) 055001]. The model decomposes the motion of the two ions into two mappings for the free motion in different parts of the trap and one for a compressing momentum kick. The ions' interaction is modelled by a time delay, which then changes the balance between adjacent momentum kicks. Through these mappings we identify the microscopic process that is responsible for synchronization and give the conditions for that regime.Comment: 12 pages, 9 figures; submitted to Phys Rev

A Neural Candidate-Selector Architecture for Automatic Structured Clinical Text Annotation

We consider the task of automatically annotating free texts describing clinical trials with concepts from a controlled, structured medical vocabulary. Specifically, we aim to build a model to infer distinct sets of (ontological) concepts describing complementary clinically salient aspects of the underlying trials: the populations enrolled, the interventions administered and the outcomes measured, i.e., the PICO elements. This important practical problem poses a few key challenges. One issue is that the output space is vast, because the vocabulary comprises many unique concepts. Compounding this problem, annotated data in this domain is expensive to collect and hence sparse. Furthermore, the outputs (sets of concepts for each PICO element) are correlated: specific populations (e.g., diabetics) will render certain intervention concepts likely (insulin therapy) while effectively precluding others (radiation therapy). Such correlations should be exploited. We propose a novel neural model that addresses these challenges. We introduce a Candidate-Selector architecture in which the model considers setes of candidate concepts for PICO elements, and assesses their plausibility conditioned on the input text to be annotated. This relies on a 'candidate set' generator, which may be learned or relies on heuristics. A conditional discriminative neural model then jointly selects candidate concepts, given the input text. We compare the predictive performance of our approach to strong baselines, and show that it outperforms them. Finally, we perform a qualitative evaluation of the generated annotations by asking domain experts to assess their quality

Calcitization of aragonitic bryozoans in Cenozoic tropical carbonates from East Kalimantan, Indonesia

© The Author(s) 2016. Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The file attached is the published version of the article