Extracting protein-protein interactions from MEDLINE using the hidden vector state model

A major challenge in text mining for biomedicine is automatically extracting protein-protein interactions from the vast amount of biomedical literature. We have constructed an information extraction system based on the Hidden Vector State (HVS) model for protein-protein interactions. The HVS model can be trained using only lightly annotated data whilst simultaneously retaining sufficient ability to capture the hierarchical structure. When applied in extracting protein-protein interactions, we found that it performed better than other established statistical methods and achieved 61.5% in F-score with balanced recall and precision values. Moreover, the statistical nature of the pure data-driven HVS model makes it intrinsically robust and it can be easily adapted to other domains.

Semantic sentiment analysis of Twitter

Sentiment analysis over Twitter offer organisations a fast and effective way to monitor the publics' feelings towards their brand, business, directors, etc. A wide range of features and methods for training sentiment classifiers for Twitter datasets have been researched in recent years with varying results. In this paper, we introduce a novel approach of adding semantics as additional features into the training set for sentiment analysis. For each extracted entity (e.g. iPhone) from tweets, we add its semantic concept (e.g. Apple product) as an additional feature, and measure the correlation of the representative concept with negative/positive sentiment. We apply this approach to predict sentiment for three different Twitter datasets. Our results show an average increase of F harmonic accuracy score for identifying both negative and positive sentiment of around 6.5% and 4.8% over the baselines of unigrams and part-of-speech features respectively. We also compare against an approach based on sentiment-bearing topic analysis, and find that semantic features produce better Recall and F score when classifying negative sentiment, and better Precision with lower Recall and F score in positive sentiment classification.

Steps and bumps:precision extraction of discrete states of molecular machines

We report statistical time-series analysis tools providing improvements in the rapid, precision extraction of discrete state dynamics from time traces of experimental observations of molecular machines. By building physical knowledge and statistical innovations into analysis tools, we provide techniques for estimating discrete state transitions buried in highly correlated molecular noise. We demonstrate the effectiveness of our approach on simulated and real examples of steplike rotation of the bacterial flagellar motor and the F1-ATPase enzyme. We show that our method can clearly identify molecular steps, periodicities and cascaded processes that are too weak for existing algorithms to detect, and can do so much faster than existing algorithms. Our techniques represent a step in the direction toward automated analysis of high-sample-rate, molecular-machine dynamics. Modular, open-source software that implements these techniques is provided.

Visual stress symptoms secondary to stroke alleviated with spectral filters and precision tinted ophthalmic lenses:a case report

Visual stress is a condition characterised by symptoms of eyestrain, headaches and distortions of visual perception when reading text. The symptoms are frequently alleviated with spectral filters and precision tinted ophthalmic lenses. Visual stress is thought to arise due to cortical hyperexcitability and is associated with a range of neurological conditions. Cortical hyperexcitability is known to occur following stroke. The case presented describes visual stress symptoms resulting from stroke, subsequently managed with spectral filters and precision tinted ophthalmic lenses. The case also highlights that the spectral properties of the tint may need to be modified if the disease course alters.

IT as enabler of sustainable farming:an empirical analysis of farmers' adoption decision of precision agriculture technology

Precision agriculture (PA) describes a suite of IT based tools which allow farmers to electronically monitor soil and crop conditions and analyze treatment options. This study tests a model explaining the difficulties of PA technology adoption. The model draws on theories of technology acceptance and diffusion of innovation and is validated using survey data from farms in Canada. Findings highlight the importance of compatibility among PA technology components and the crucial role of farmers' expertise. The model provides the theoretical and empirical basis for developing policies and initiatives to support PA technology adoption.

Issues in learning an ontology from text

Ontology construction for any domain is a labour intensive and complex process. Any methodology that can reduce the cost and increase efficiency has the potential to make a major impact in the life sciences. This paper describes an experiment in ontology construction from text for the animal behaviour domain. Our objective was to see how much could be done in a simple and relatively rapid manner using a corpus of journal papers. We used a sequence of pre-existing text processing steps, and here describe the different choices made to clean the input, to derive a set of terms and to structure those terms in a number of hierarchies. We describe some of the challenges, especially that of focusing the ontology appropriately given a starting point of a heterogeneous corpus. Results - Using mainly automated techniques, we were able to construct an 18055 term ontology-like structure with 73% recall of animal behaviour terms, but a precision of only 26%. We were able to clean unwanted terms from the nascent ontology using lexico-syntactic patterns that tested the validity of term inclusion within the ontology. We used the same technique to test for subsumption relationships between the remaining terms to add structure to the initially broad and shallow structure we generated. All outputs are available at http://thirlmere.aston.ac.uk/~kiffer/animalbehaviour/ webcite. Conclusion - We present a systematic method for the initial steps of ontology or structured vocabulary construction for scientific domains that requires limited human effort and can make a contribution both to ontology learning and maintenance. The method is useful both for the exploration of a scientific domain and as a stepping stone towards formally rigourous ontologies. The filtering of recognised terms from a heterogeneous corpus to focus upon those that are the topic of the ontology is identified to be one of the main challenges for research in ontology learning.

Finding qualitative research: an evaluation of search strategies

Background Qualitative research makes an important contribution to our understanding of health and healthcare. However, qualitative evidence can be difficult to search for and identify, and the effectiveness of different types of search strategies is unknown. Methods Three search strategies for qualitative research in the example area of support for breast-feeding were evaluated using six electronic bibliographic databases. The strategies were based on using thesaurus terms, free-text terms and broad-based terms. These strategies were combined with recognised search terms for support for breast-feeding previously used in a Cochrane review. For each strategy, we evaluated the recall (potentially relevant records found) and precision (actually relevant records found). Results A total yield of 7420 potentially relevant records was retrieved by the three strategies combined. Of these, 262 were judged relevant. Using one strategy alone would miss relevant records. The broad-based strategy had the highest recall and the thesaurus strategy the highest precision. Precision was generally poor: 96% of records initially identified as potentially relevant were deemed irrelevant. Searching for qualitative research involves trade-offs between recall and precision. Conclusions These findings confirm that strategies that attempt to maximise the number of potentially relevant records found are likely to result in a large number of false positives. The findings also suggest that a range of search terms is required to optimise searching for qualitative evidence. This underlines the problems of current methods for indexing qualitative research in bibliographic databases and indicates where improvements need to be made.

Within-site variation in lichen growth rates and its implications for direct lichenometry

Variation in lichen growth rates poses a significant challenge for the application of direct lichenometry, i.e. the construction of lichen dating curves from direct measurement of growth rates. To examine the magnitude and possible causes of within-site growth variation, radial growth rates (RaGRs) of thalli of the fast-growing foliose lichen Melanelia fuliginosa ssp. fuliginosa (Fr. ex Duby) Essl. and the slow-growing crustose lichen Rhizocarpon geographicum (L.) DC. were studied on two S-facing slate rock surfaces in north Wales, UK using digital photography and an image analysis system (Image-J). RaGRs of M. fuliginosa ssp. fuliginosa varied from 0.44 to 2.63 mmyr-1 and R. geographicum from 0.10 to 1.50 mmyr-1.5. Analysis of variance suggested no significant variation in RaGRs with vertical or horizontal location on the rock, thallus diameter, aspect, slope, light intensity, rock porosity, rock surface texture, distance to nearest lichen neighbour or distance to vegetation on the rock surface. The frequency distribution of RaGR did not deviate from a normal distribution. It was concluded that despite considerable growth rate variation in both species studied, growth curves could be constructed with sufficient precision to be useful for direct lichenometry. © 2014 Swedish Society for Anthropology and Geography.

Is randomisation necessary for measuring defocus curves in pre-presbyopes?

Purpose: Defocus curves are used to evaluate the subjective range of clear vision of presbyopic corrections such as in eyes implanted with accommodating intraocular lenses (IOLs). This study determines whether letter sequences and/or lens presentation order ought to be randomised when measuring defocus curves. Methods: Defocus curves (range +2.00DS to -2.00DS) were measured on 18 pre-presbyopic subjects (mean age 24.1 ± 4.2 years) for six combinations of sequential or randomised positive or negative lens progression and non-randomised or randomised letter sequences. The letters were presented on a computerised logMAR chart at 6 m. Results: Overall there was a statistically significant difference between the six combinations (ANOVA, p < 0.05) attributable to the combination of non-randomised letters with non-randomised lens progression from negative to positive defocus (p < 0.01). There was no statistically significant difference in defocus curve measurements if both letters and lens order were randomised compared to if only one of these variables was randomised (p > 0.05). Non-randomised letters, with a sequential lens progression from negative to positive, was significantly different to all other combinations when compared individually (Student's T-test, p < 0.003 on all comparisons), and was confirmed as the sole source of the overall significant difference. There was no statistically significant difference if both lens presentation order and letter sequences were randomised compared to if only one or the other of these variables was randomised. Conclusion: Non-randomised letters and non-randomised lens progression on their own did not affect the subjective amplitude of accommodation as measured by defocus curves, although their combination should be avoided. © 2007 British Contact Lens Association.

Precision emulsification for droplet and capsule production

Emulsions and microcapsules are typical structures in various dispersion formulations for pharmaceutical, food, personal and house care applications. Precise control over size and size distribution of emulsion droplets and microcapsules are important for effective use and delivery of active components and better product quality. Many emulsification technologies have been developed to meet different formulation and processing requirements. Among them, membrane and microfluidic emulsification as emerging technologies have the feature of being able to precisely manufacture droplets in a drop-by-drop manner to give subscribed sizes and size distributions with lower energy consumption. This paper reviews fundamental sciences and engineering aspects of emulsification, membrane and microfluidic emulsification technologies and their use for precision manufacture of emulsions for intensified processing. Generic application examples are given for single and double emulsions and microcapsules with different structure features. © 2013 The Society of Powder Technology Japan. Published by Elsevier B.V.

Exploring the optimum step size for defocus curves

Purpose: To evaluate the effect of reducing the number of visual acuity measurements made in a defocus curve on the quality of data quantified. Setting: Midland Eye, Solihull, United Kingdom. Design: Evaluation of a technique. Methods: Defocus curves were constructed by measuring visual acuity on a distance logMAR letter chart, randomizing the test letters between lens presentations. The lens powers evaluated ranged between +1.50 diopters (D) and -5.00 D in 0.50 D steps, which were also presented in a randomized order. Defocus curves were measured binocularly with the Tecnis diffractive, Rezoom refractive, Lentis rotationally asymmetric segmented (+3.00 D addition [add]), and Finevision trifocal multifocal intraocular lenses (IOLs) implanted bilaterally, and also for the diffractive IOL and refractive or rotationally asymmetric segmented (+3.00 D and +1.50 D adds) multifocal IOLs implanted contralaterally. Relative and absolute range of clear-focus metrics and area metrics were calculated for curves fitted using 0.50 D, 1.00 D, and 1.50 D steps and a near add-specific profile (ie, distance, half the near add, and the full near-add powers). Results: A significant difference in simulated results was found in at least 1 of the relative or absolute range of clear-focus or area metrics for each of the multifocal designs examined when the defocus-curve step size was increased (P<.05). Conclusion: Faster methods of capturing defocus curves from multifocal IOL designs appear to distort the metric results and are therefore not valid. Financial Disclosure: No author has a financial or proprietary interest in any material or method mentioned. © 2013 ASCRS and ESCRS.

Recall, verbatim memory and remembered narratives

Memory is central to investigative interviews with witnesses and suspects, yet decades of research have shown that remembering is subject to constructive and reconstructive processes that can adversely impact the reliability of accounts that are elicited at interview. In this chapter we first outline research concerning our memory for events (‘episodic memory’) before moving on to discuss the ways in which our attempts to validate and communicate those memories can bias what is eventually reported. We then focus on some of the implications this can have for investigative interviews, specifically the problem of ‘skill fade’ in interviewing, the impact of implicit beliefs about memory and issues surrounding the reliability of recollections of direct speech. We conclude that appropriately structuring the retrieval context is the key to achieving best memory evidence.

Responsive fixture design using dynamic product inspection and monitoring technologies for the precision machining of large-scale aerospace parts

When machining a large-scale aerospace part, the part is normally located and clamped firmly until a set of features are machined. When the part is released, its size and shape may deform beyond the tolerance limits due to stress release. This paper presents the design of a new fixing method and flexible fixtures that would automatically respond to workpiece deformation during machining. Deformation is inspected and monitored on-line, and part location and orientation can be adjusted timely to ensure follow-up operations are carried out under low stress and with respect to the related datum defined in the design models.

Comparison of the measurement performance of high precision multi-axis metal cutting machine tools

High precision manufacturers continuously seek out disruptive technologies to improve the quality, cost, and delivery of their products. With the advancement of machine tool and measurement technology many companies are ready to capitalise on the opportunity of on-machine measurement (OMM). Coupled with business case, manufacturing engineers are now questioning whether OMM can soon eliminate the need for post-process inspection systems. Metrologists will however argue that the machining environment is too hostile and that there are numerous process variables which need consideration before traceable measurement on-the-machine can be achieved. In this paper we test the measurement capability of five new multi-axis machine tools enabled as OMM systems via on-machine probing. All systems are tested under various operating conditions in order to better understand the effects of potentially significant variables. This investigation has found that key process variables such as machine tool warm-up and tool-change cycles can have an effect on machine tool measurement repeatability. New data presented here is important to many manufacturers whom are considering utilising their high precision multi-axis machine tools for both the creation and verification of their products.

Long-range and high-precision correlation optical time-domain reflectometry utilizing an all-fiber chaotic source

We propose a long range, high precision optical time domain reflectometry (OTDR) based on an all-fiber supercontinuum source. The source simply consists of a CW pump laser with moderate power and a section of fiber, which has a zero dispersion wavelength near the laser's central wavelength. Spectrum and time domain properties of the source are investigated, showing that the source has great capability in nonlinear optics, such as correlation OTDR due to its ultra-wide-band chaotic behavior, and mm-scale spatial resolution is demonstrated. Then we analyze the key factors limiting the operational range of such an OTDR, e. g., integral Rayleigh backscattering and the fiber loss, which degrades the optical signal to noise ratio at the receiver side, and then the guideline for counter-act such signal fading is discussed. Finally, we experimentally demonstrate a correlation OTDR with 100km sensing range and 8.2cm spatial resolution (1.2 million resolved points), as a verification of theoretical analysis.