UIMA in the Biocuration Workflow: A coherent framework for cooperation between biologists and computational linguists

As collaborating partners, Barcelona Media Innovation Centre and GRIB (Universitat Pompeu Fabra) seek to combine strengths from Computational Linguistics and Biomedicine to produce a robust Text Mining system to generate data that will help biocurators in their daily work. The first version of this system will focus on the discovery of relationships between genes, SNPs (Single Nucleotide Polymorphisms) and diseases from the literature.

A first challenge that we were faced with during the setup of this project is the fact that most current tools that support the curation workflow are complex, ad-hoc built applications which sometimes make difficult the interoperability and results sharing between research groups from different and unrelated expert fields. Often, biologists (even computer-savvy ones) are hard pressed to use and adapt sophisticated Natural Language Processing systems, and computational linguists are challenged by the intricacies of biology in applying their processing pipelines to elicit knowledge from texts. The flow of knowledge (needed to develop a usable, practical tool) to and from the parties involved in the development of such systems is not always easy or straightforward.

The modular and versatile architecture of UIMA (Unstructed Information Management Architecture) provides a framework to address these challenges. UIMA is a component architecture and software framework implementation (including a UIMA SDK) to develop applications that analyse large volumes of unstructured information, and has been increasingly adopted by a significant part of the BioNLP community that needs industrial-grade and robust applications to exploit the whole bibliome. The use of UIMA to develop Text Mining applications useful for curation purposes allows the combination of diverse expertises which is beyond the individual know-how of biologists, computer scientists or linguists in isolation. A good synergy and circulation of knowledge between these experts is fundamental to the development of a successful curation tool

Flying down the track

World-class athletes of both sexes cover 100 metres in about 10 seconds. What percentage of this is spent not touching the ground? And what's the figure for a 2-hour marathon

Evolution of the measurement of body segment inertial parameters since the 1970s

Since the development of biomechanics as a sub-discipline within movement science in the last 35 to 40 years (1), analysis techniques have evolved rapidly. To attain the goals of sports biomechanics - performance enhancement, comfort, injury prevention and safety (2) - it has been necessary to further develop techniques to both quantify and analyse data. Research questions have evolved from quantification of movement to questioning how and why movement occurs, and optimisation of performance. Methods of reconstruction such as the 3D Direct Linear Transformation (DLT) (3) and 2D-DLT (4) have evolved from creation to determination of the most accurate reconstruction method (5). Motion analysis has evolved from force-time data (6) to online systems and real-time feedback (7). Errors from soft tissue motion are now investigated to quantify and correct (8-9). Data smoothing has evolved from Winter et al.’s original paper on removal of kinematic noise (10) to modern work by Robertson and Dowling (11) investigating optimal filter design. Computer modelling has evolved from simplistic models of the 70s and 80s investigating simple locomotion (12) to sophisticated modern models of high bar gymnastics (13), high jump (14) and muscle stiffness of the horse (15). Initial work on co-ordination by Bernstein (16) has now evolved into a distinct field of motor control (17-18), with its own measurement issues (19). The focus of this article, however, is on the evolution of measurement techniques for determination of body segment inertial parameters (BSIP) with particular emphasis on development of mathematical models and scanning and imaging techniques

ASSESSMENT OF LOWER LIMB ASYMMETRY: DIFFERENCES DURING ISOMETRIC AND STRETCH-SHORTENING CYCLE TASKS

Assessment of limb function asymmetry is of interest to practitioners due to its role in return to play guidelines and reported links to injury. Dynamometry is one of the most commonly used methods of assessing muscle function, but the mode of contraction used is different to the stretch-shortening cycles experienced during real-life activities. The aim of this study was to compare measures of limb function asymmetry during isometric and stretch-shortening cycle tasks and investigate agreement between the methods. Different between-limb effect sizes were observed between limbs dependent on test used, with different ranges of asymmetry observed. Agreement between methods was very poor. These results show the importance of assessing asymmetry in a condition that is as similar as possible to the task of interest

PRELIMINARY ANALYSIS OF SLEDGE REACTION FORCES DURING CYCLICAL LOADING OF THE TRICEPS SURAE

To date, no methodology exists that can measure Achilles tendon stiffness in a controlled dynamic situation while simultaneously investigating tendon and joint stiffness interactions. Stiffness refers to the ratio between force and elongation, and the aim of this preliminary study was to establish an analysis protocol for sledge reaction forces during cyclical loading of the triceps surae. Results indicated the magnitude of forces was just under 50% of body weight, which was expected. Removal of the first two trials from analysis reduced standard deviation and 95% confidence interval of plantarflexor force, contact time and contact time-flight time ratio, suggesting this protocol is suitable to ensure data gathered is repeatable and consistent. Future work using inverse dynamics and ultrasound shall provide information on Achilles tendon loading and stiffness

Injury incidence in elite youth field hockey players at the 2016 European Championships

Despite being an essential consideration when deciding rule changes, injury prevention strategies, and athlete development models, there is little epidemiological data of U18 field hockey player injuries–something explicitly referred to in the 2015 International Olympic Committee’s Consensus Statement on Youth Athlete Development. The aim of this study was to quantify incidence and characteristics of injuries in elite youth field hockey players during a major international tournament. Standardized reporting forms detailing time, location on pitch, mechanism and anatomical location of injury were completed for new musculoskeletal conditions resulting in a time stoppage by the umpire and where a player was noticeably affected by an injury for up to 20 s regardless of time stoppage. Injury incidence was 1.35 and 2.20 injuries/match or 53 and 86 injuries per 1000 player match hours for boys (B) and girls (G) respectively; girls were over three times more likely to have a minor injury. Most injuries were contusions due to being hit by the ball or stick (B: 12, G: 27), with high numbers of injuries to the torso (B: 8) and head/face (G: 7). Injuries during the penalty corner (B: 3, G: 4) were to the lower limb and hand, and boys were less likely to wear facial protection (B: 65.9%, G: 86.4%). Results form an essential initial dataset of injuries in U18 field hockey players. Current reporting protocols under-report injuries and must be addressed by the international governing body. The high number of head/face injuries, particularly in females, requires further investigation

THE EFFECT OF INCREASED LOADING ON PLANTARFLEXOR FUNCTION DURING A STRETCH-SHORTENING CYCLE TASK

Increasing loading is one of the most common methods used to increase exercise intensity but it is important to consider the influence of the increase on subsequent force output, rate of force development and, in the case of plyometric exercise, contact time. The aim of this study was to investigate the effect of altering loading on plantarflexor force and force production during a fast stretch-shortening cycle task. Results showed load increased force production and contact time and decreased flight time and reactive strength index. These results have important implications for practitioners in determining the optimal method of increasing training intensity in order to avoid negative training effects

DO FLEXIBILITY SCREENING TESTS REFLECT JOINT RANGE OF MOTION DURING DYNAMIC TASKS?

The aim of this study was to investigate if ankle joint range of motion (ROM) during a functional screen test was related to ankle ROM and plantarflexor reactive strength index (RSI) during a dynamic task. The three measures were correlated for the dominant and non-dominant legs to identify what relationship, if any, existed between the three measures. Results showed that there was no relationship between the two measures of ROM, and ROM during the sledge task was positively related to plantarflexor RSI. This is in contrast to other work, possibly due to the isolation of the plantarflexor muscles in the sledge task. Interestingly, between-leg relationships were lower in the dynamic task, suggesting increased variability in the movement strategies used or underlying training differences

PLANTARFLEXOR FORCE PRODUCTION IN ISOMETRIC AND STRETCH-SHORTENING CYCLE TASKS

The ankle joint and its surrounding musculature are vital in sprinting, and recent work has developed a method to isolate the plantarflexor muscle group for analysis of its force-producing capabilities. The aim of this study was to compare values for plantarflexor force obtained using isometric dynamometry and an adapted force sledge in twenty healthy subjects. Results showed low relationships between isometric and dynamic strength measures, probably because the dynamic test utilises a stretch-shortening cycle. No relationship was observed between isometric strength and the sledge foot plate height during the task with a moderate relationship observed between dynamic strength and plate height. This highlights the important role the Achilles tendon plays in dynamic tasks