Chemistry in Bioinformatics

A preprint of an invited submission to BioMedCentral Bioinformatics. This short manuscript is an overview or the current problems and opportunities in publishing chemical information. Full details of technology are given in the sibling manuscript http://www.dspace.cam.ac.uk/handle/1810/34579 The manuscript is the authors' preprint although it has been automatically transformed into this archived PDF by the submission system. The authors are not responsible for the formattingChemical information is now seen as critical for most areas of life sciences. But unlike Bioinformatics, where data is Openly available and freely re−usable, most chemical information is closed and cannot be re−distributed without permission. This has led to a failure to adopt modern informatics and software techniques and therefore paucity of chemistry in bioinformatics. New technology, however, offers the hope of making chemical data (compounds and properties) Free during the authoring process. We argue that the technology is already available; we require a collective agreement to enhance publication protocols

Spatial attention increases the pupillary response to light changes

We measured pupil size in adult human subjects while we manipulated both the luminance of the visual scene and the location of attention. We found that, with central fixation maintained, pupillary constrictions and dilations evoked by peripheral luminance increments and decrements are larger when spatial attention is covertly (i.e., with no eye movements) directed to the stimulus region versus when it is directed to the opposite hemifield. Irrespective of the size of the attended region (focused at the center of the stimulus or spread within and outside the stimulus), the attentional enhancement is large: more than 20% of the response to stimuli in the unattended hemifield. This indicates that a sizable portion of this simple ocular behavior—often considered a subcortical ''reflex''—in fact depends on cortical processing. Together, these features indicate that pupillometry is not only an index of retinal and brainstem function, but also an objective measure of complex constructs such as attention and its effects on sensory processing

Analysis of complex contagions in random multiplex networks

We study the diffusion of influence in random multiplex networks where links can be of $r$ different types, and for a given content (e.g., rumor, product, political view), each link type is associated with a content dependent parameter $c_i$ in $[0,\infty]$ that measures the relative bias type-$i$ links have in spreading this content. In this setting, we propose a linear threshold model of contagion where nodes switch state if their "perceived" proportion of active neighbors exceeds a threshold \tau. Namely, a node connected to $m_i$ active neighbors and $k_i-m_i$ inactive neighbors via type-$i$ links will turn active if $\sum{c_i m_i}/\sum{c_i k_i}$ exceeds its threshold \tau. Under this model, we obtain the condition, probability and expected size of global spreading events. Our results extend the existing work on complex contagions in several directions by i) providing solutions for coupled random networks whose vertices are neither identical nor disjoint, (ii) highlighting the effect of content on the dynamics of complex contagions, and (iii) showing that content-dependent propagation over a multiplex network leads to a subtle relation between the giant vulnerable component of the graph and the global cascade condition that is not seen in the existing models in the literature.Comment: Revised 06/08/12. 11 Pages, 3 figure

Medication supply for people evacuated during disasters.

© 2015 Chinese Cochrane Center, West China Hospital of Sichuan University and Wiley Publishing Asia Pty Ltd.Medication loss is a major problem in disaster settings, and it is crucial for patients to bring their medication and healthcare items with them when they leave their homes during an evacuation. This article is based on a systematic literature review on medication loss, the objectives of which were to identify the extent and implications of medication loss, to identify the burden of prescription refill, and to make recommendations on effective preparedness. The review revealed that medication loss, prescription loss and refills, and the loss of medical aids are a significant burden on the medical relief teams. The medical aids are not limited to drugs, but include routine medications, medical/allergy records, devices for specific care and daily life, and emergency medications. One possible solution is to make a personal emergency pack and for people to carry this with them at all times. To ensure that patients are adequately prepared, stakeholders, especially health professionals, need to be actively involved in the preparation plans. Since our findings have little impact on disaster risk reduction unless shared broadly, we are now taking actions to spread our findings, such as presenting in conferences and via posters, in order to raise awareness among patients and healthcare professionals. As part of these activities, our findings were presented at the Evidence Aid Symposium on 20 September 2014, at Hyderabad, India

The impact of life course exposures to neighbourhood deprivation on health and well-being: a review of the long-term neighbourhood effects literature

Background In this review article, we detail a small but growing literature in the field of health geography that uses longitudinal data to determine a life course component to the neighbourhood effects thesis. For too long, there has been reliance on cross-sectional data to test the hypothesis that where you live has an effect on your health and well-being over and above your individual circumstances. Methods We identified 53 articles that demonstrate how neighbourhood deprivation measured at least 15 years prior affects health and well-being later in life using the databases Scopus and Web of Science. Results We find a bias towards US studies, the most common being the Panel Study of Income Dynamics. Definition of neighbourhood and operationalization of neighbourhood deprivation across most of the included articles relied on data availability rather than a priori hypothesis. Conclusions To further progress neighbourhood effects research, we suggest that more data linkage to longitudinal datasets is required beyond the narrow list identified in this review. The limited literature published to date suggests an accumulation of exposure to neighbourhood deprivation over the life course is damaging to later life health, which indicates improving neighbourhoods as early in life as possible would have the greatest public health improvement

Radiation exposure awareness from patients undergoing nuclear medicine diagnostic 99mTc-MDP bone scans and 2-deoxy-2-(18F) fluoro-D-glucose PET/computed tomography scans

INTRODUCTION: Medical imaging is on average the largest source of artificial radiation exposure worldwide. This study seeks to understand patient's awareness of radiation exposure derived from nuclear medicine diagnostic scans and assess if current information provided by leaflets is adequate. METHODS: Single-centre cross-sectional questionnaire study applied to bone scan and FDG PET/computed tomography patients, at a nuclear medicine and PET/computed tomography department over a 15-week period in 2018. Questionnaires on dose comparators were designed in collaboration with patients, public, and experts in radiation exposure. Qualitative data were analysed using thematic analysis and quantitative data using SPSS (V. 24). RESULTS: A total of 102 questionnaires were completed (bone scan = 50; FDG PET/computed tomography = 52). Across both groups, 33/102 (32.4%) patients reported having a reasonable understanding of nuclear medicine and 21/102 (20.6%) reported a reasonable knowledge of ionising radiations. When asked to compare the exposure dose of respective scans with common comparators 8/50 (16%) of bone scan patients and 11/52 (21.2%) FDG PET/computed tomography answered correctly. On leaflet information, 15/85 (17.6%) patients reported the leaflets do not provide enough information on radiation exposure and of these 10/15 (66.7%) commented the leaflets should incorporate more information on radiation exposure dose. CONCLUSION: More observational and qualitative studies in collaboration with patients are warranted to evaluate patients' understanding and preferences in communication of radiation exposure from nuclear medicine imaging. This will ensure communication tools and guidelines developed to comply with ionising radiation (medical exposure) regulation 2017 are according to patients needs and preferences

Disaster-driven evacuation and medication loss: a systematic literature review

AIM: The aim of this systematic literature review was to identify the extent and implications of medication loss and the burden of prescription refill on medical relief teams following extreme weather events and other natural hazards. METHOD: The search strategy followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). Key health journal databases (Medline, Embase, PsycINFO, Maternity and Infant Care, and Health Management Information Consortium (HMIC)) were searched via the OvidSP search engine. Search terms were identified by consulting MeSH terms. The inclusion criteria comprised articles published from January 2003 to August 2013, written in English and containing an abstract. The exclusion criteria included abstracts for conferences or dissertations, book chapters and articles written in a language other than English. A total of 70 articles which fulfilled the inclusion criteria were included in this systematic review. RESULTS: All relevant information was collated regarding medication loss, prescription loss and refills, and medical aids loss which indicated a significant burden on the medical relief teams. Data also showed the difficulty in filling prescriptions due to lack of information from the evacuees. People with chronic conditions are most at risk when their medication is not available. This systematic review also showed that medical aids such as eye glasses, hearing aids as well as dental treatment are a high necessity among evacuees. DISCUSSION: This systematic review revealed that a considerable number of patients lose their medication during evacuation, many lose essential medical aids such as insulin pens and many do not bring prescriptions with them when evacuated.. Since medication loss is partly a responsibility of evacuees, understanding the impact of medication loss may lead to raising awareness and better preparations among the patients and health care professionals. People who are not prepared could have worse outcomes and many risk dying when their medication is not available