Identify disorders in health records using Conditional Random Fields and Metamap: AEHRC at ShARe/CLEF 2013 eHealth Evaluation Lab Task 1

The Australian e-Health Research Centre (AEHRC) recently participated in the ShARe/CLEF eHealth Evaluation Lab Task 1. The goal of this task is to individuate mentions of disorders in free-text electronic health records and map disorders to SNOMED CT concepts in the UMLS metathesaurus. This paper details our participation to this ShARe/CLEF task. Our approaches are based on using the clinical natural language processing tool Metamap and Conditional Random Fields (CRF) to individuate mentions of disorders and then to map those to SNOMED CT concepts. Empirical results obtained on the 2013 ShARe/CLEF task highlight that our instance of Metamap (after ltering irrelevant semantic types), although achieving a high level of precision, is only able to identify a small amount of disorders (about 21% to 28%) from free-text health records. On the other hand, the addition of the CRF models allows for a much higher recall (57% to 79%) of disorders from free-text, without sensible detriment in precision. When evaluating the accuracy of the mapping of disorders to SNOMED CT concepts in the UMLS, we observe that the mapping obtained by our ltered instance of Metamap delivers state-of-the-art e ectiveness if only spans individuated by our system are considered (`relaxed' accuracy).

Low temperature pretreatment of sugarcane bagasse at atmospheric pressure using mixtures of ethylene carbonate and ethylene glycol

A low temperature lignocellulose pretreatment process was developed using acid-catalysed mixtures of alkylene carbonate and alkylene glycol. Pretreatment of sugarcane bagasse with mixtures of ethylene carbonate (EC) and ethylene glycol (EG) was more effective than that with mixtures of propylene carbonate (PC) and propylene glycol (PG). These mixtures were more effective than the individual components in making bagasse cellulose more amenable to cellulase digestion. Glucan digestibilities of ≥87% could be achieved with a wide range of EC to EG ratios from 9:1 to 1:1 (w/w). Pretreatment of bagasse by the EC/EG mixture with a ratio of 4:1 in the presence of 1.2% H2SO4 at 90 °C for 30 min led to the highest glucan enzymatic digestibility of 93%. The high glucan digestibilities obtained under these acidic conditions were due to (a) the ability of alkylene carbonate to cause significant biomass size reduction, (b) the ability of alkylene glycol to cause biomass defibrillation, (c) the ability of alkylene carbonate and alkylene glycol to remove xylan and lignin, and (d) the magnified above attributes in the mixtures of alkylene carbonate and alkylene glycol.

Visualising experimental flow fields through a stormwater gross pollutant trap

Abstract An experimental dataset representing a typical flow field in a stormwater gross pollutant trap (GPT) was visualised. A technique was developed to apply the image-based flow visualisation (IBFV) algorithm to the raw dataset. Particle image velocimetry (PIV) software was previously used to capture the flow field data by tracking neutrally buoyant particles with a high speed camera. The dataset consisted of scattered 2D point velocity vectors and the IBFV visualisation facilitates flow feature characterisation within the GPT. The flow features played a pivotal role in understanding stormwater pollutant capture and retention behaviour within the GPT. It was found that the IBFV animations revealed otherwise unnoticed flow features and experimental artefacts. For example, a circular tracer marker in the IBFV program visually highlighted streamlines to investigate the possible flow paths of pollutants entering the GPT. The investigated flow paths were compared with the behaviour of pollutants monitored during experiments.

Decision making under pressure : a behavioural economics perspective

This research investigates the decision making process of individuals from revealed preferences in extreme environments or life-and-death situations, from a behavioral economics perspective. The empirical analysis of revealed behavioral preferences shows how the individual decision making process can deviate from the standard self-interested or “homo economicus” model in non-standard situations. The environments examined include: elite athletes in FIFA World and Euro Cups; climbing on Everest and the Himalaya; communication during 9/11 and risk seeking after the 2011 Brisbane floods. The results reveal that the interaction of culture and environment has a significant impact on the decision process, as social behaviors and institutions are intimately intertwined, which govern the processes of human behavior and interaction. Additionally, that risk attitudes are not set and that immediate environmental factors can induce a significant shift in an individuals risk seeking behaviors.

A novel method for purification of low grade diatomite powders in centrifugal fields

This study presented a novel method for purification of three different grades of diatomite from China by scrubbing technique using sodiumhexametaphosphate (SHMP) as dispersant combinedwith centrifugation. Effects of pH value and dispersant amount on the grade of purified diatomitewere studied and the optimumexperimental conditions were obtained. The characterizations of original diatomite and derived products after purification were determined by scanning electron microscopy (SEM), X-ray diffraction (XRD), infrared spectroscopy (IR) and specific surface area analyzer (BET). The results indicated that the pore size distribution, impurity content and bulk density of purified diatomite were improved significantly. The dispersive effect of pH and SHMP on the separation of diatomite from clay minerals was discussed systematically through zeta potential test. Additionally, a possible purification mechanism was proposed in the light of the obtained experimental results.

Business value from intelligent fields

The Smart Fields programme has been active in Shell over the last decade and has given large benefits. In order to understand the value and to underpin strategies for the future implementation programme, a study was carried out to quantify the benefits to date. This focused on actually achieved value, through increased production or lower costs. This provided an estimate of the total value achieved to date. Future benefits such as increased reserves or continued production gain were recorded separately. The paper describes the process followed in the benefits quantification. It identifies the key solutions and technologies and describes the mechanism used to understand the relation between solutions and value. Examples have been given of value from various assets around the world, in both existing fields and in green fields. Finally, the study provided the methodology for tracking of value. This helps Shell to estimate and track the benefits of the Smart Fields programme at company scale.

Biomechanical characteristics of peripheral diabetic neuropathy : a systematic review and meta-analysis of findings from the gait cycle, muscle activity and dynamic barefoot plantar pressure

Background: Diabetic peripheral neuropathy is an important cause of foot ulceration and limb loss. This systematic review and meta-analysis investigated the effect of diabetic peripheral neuropathy on gait, dynamic electromyography and dynamic plantar pressures. Methods: Electronic databases were searched systematically for articles reporting the effect of diabetic peripheral neuropathy on gait, dynamic electromyography and plantar pressures. Searches were restricted to articles published between January 2000 and April 2012. Outcome measures assessed included spatiotemporal parameters, lower limb kinematics, kinetics, muscle activation and plantar pressure. Meta-analyses were carried out on all outcome measures reported by ≥3 studies. Findings: Sixteen studies were included consisting of 382 neuropathy participants, 216 diabetes controls without neuropathy and 207 healthy controls. Meta-analysis was performed on 11 gait variables. A high level of heterogeneity was noted between studies. Meta-analysis results suggested a longer stance time and moderately higher plantar pressures in diabetic peripheral neuropathy patients at the rearfoot, midfoot and forefoot compared to controls. Systematic review of studies suggested potential differences in the biomechanical characteristics (kinematics, kinetics, EMG) of diabetic neuropathy patients. However these findings were inconsistent and limited by small sample sizes.; Interpretation: Current evidence suggests that patients with diabetic peripheral neuropathy have elevated plantar pressures and occupy a longer duration of time in the stance-phase during gait. Firm conclusions are hampered by the heterogeneity and small sample sizes of available studies. Interpretation: Current evidence suggests that patients with diabetic peripheral neuropathy have elevated plantar pressures and occupy a longer duration of time in the stance-phase during gait. Firm conclusions are hampered by the heterogeneity and small sample sizes of available studies.

Influence of eye rotation on peripheral eye length measurement obtained with a partial coherence interferometry instrument

Purpose The eye rotation approach for measuring peripheral eye length leads to concern about whether the rotation influences results, such as through pressure exerted by eyelids or extra-ocular muscles. This study investigated whether this approach is valid. Methods Peripheral eye lengths were measured with a Lenstar LS 900 biometer for eye rotation and no-eye rotation conditions (head rotation for horizontal meridian and instrument rotation for vertical meridian). Measurements were made for 23 healthy young adults along the horizontal visual field (±30°) and, for a subset of eight participants along the vertical visual field (±25°). To investigate the influence of the duration of eye rotation, for six participants measurements were made at 0, 60, 120, 180 and 210 s after eye rotation to ±30° along horizontal and vertical visual fields. Results Peripheral eye lengths were not significantly different for the conditions along the vertical meridian (F1,7 = 0.16, p = 0.71). The peripheral eye lengths for the conditions were significantly different along the horizontal meridian (F1,22 = 4.85, p = 0.04), although not at individual positions (p ≥ 0.10) and were not important. There were no apparent differences between the emmetropic and myopic groups. There was no significant change in eye length at any position after maintaining position for 210 s. Conclusion Eye rotation and no-eye rotation conditions were similar for measuring peripheral eye lengths along horizontal and vertical visual field meridians at ±30° and ±25°, respectively. Either condition can be used to estimate retinal shape from peripheral eye lengths.

Continuous positive air pressure treatment for obstructive sleep apnoea patients : effects on sleep quality and quantity as measured by actigraphy

Objectives Actigraphy can reliably assess sleep in healthy adults and be used to estimate total sleep time in suspected obstructive sleep apnoea (OSA) patients. We compared sleep quality for Continuous Positive Air Pressure (CPAP) treated OSA patients and controls, evaluating the impact of stopping CPAP for one night. Methods 11 men, aged 51–75 years (m = 65.6 years), compliant CPAP users, treated for 1–19 years (m = 7.8 years) wore Cambridge Neurotechnology Ltd actiwatches for one night while using CPAP and for one night sleeping without CPAP. A control group of 11 healthy men, aged 63–74 years (m = 64.1 years) slept normally whilst wearing an actiwatch. Subsequent daytime sleepiness was recorded using Karolinska sleepiness scores (KSS). Results Actimetry showed no significant differences between actual sleep time, sleep efficiency, sleep disturbance index or number of wake bouts when comparing OSA participants using CPAP, with controls; there was no difference in subsequent daytime sleepiness, control KSS = 4.21, OSA KSS = 4.17. Without CPAP there was no significant difference in sleep length or sleep onset latency compared with using CPAP, but there was a significant impact on sleep quality as shown by: increased sleep disturbance index from 7.9 to 13.8 [t(10) = 3.510, P < 0.05], decreased percent of actual sleep from 92.05% to 86.15% [t(10) = 3.51, P < 0.05], decreased sleep efficiency from 86.6% to 81% [t(10) = 2.204, P < 0.05] and increased number of wake bouts from 29 to 42.5 [t(10) = 3.877, P < 0.05]. Daytime sleepiness became significantly worse increasing from KSS 4.17 to 6.27 [t(10) = )4.96, P < 0.05]. Conclusion There was no disparity in sleep quality or KSS scores between CPAP treated OSA patients and healthy controls of a similar age. Treated OSA patients obtained quality sleep with no elevated day time sleepiness. However, cessation of treatment for one night caused sleep quality to deteriorate despite a comparable sleep time; the deterioration in sleep quality could explain the increase in daytime sleepiness. OSA patients need to know that even short-term noncompliance with CPAP treatment significantly impairs sleep quality, leading to excessive sleepiness during monotonous tasks such as driving. Actigraphy successfully identified nights of non-compliance in treated OSA patients; but did not differentiate between the sleep of CPAP treated OSA patients and healthy controls.

Visual analog scale and pressure pain threshold for delayed onset muscle soreness assessment

Objectives: To investigate the relationship between two assessments to quantify delayed onset muscle soreness [DOMS]: visual analog scale [VAS] and pressure pain threshold [PPT]. Methods: Thirty-one healthy young men [25.8 ± 5.5 years] performed 10 sets of six maximal eccentric contractions of the elbow flexors with their non-dominant arm. Before and one to four days after the exercise, muscle pain perceived upon palpation of the biceps brachii at three sites [5, 9 and 13 cm above the elbow crease] was assessed by VAS with a 100 mm line [0 = no pain, 100 = extremely painful], and PPT of the same sites was determined by an algometer. Changes in VAS and PPT over time were compared amongst three sites by a two-way repeated measures analysis of variance, and the relationship between VAS and PPT was analyzed using a Pearson product-moment correlation. Results: The VAS increased one to four days after exercise and peaked two days post-exercise, while the PPT decreased most one day post-exercise and remained below baseline for four days following exercise [p < 0.05]. No significant difference among the three sites was found for VAS [p = 0.62] or PPT [p = 0.45]. The magnitude of change in VAS did not significantly correlate with that of PPT [r = −0.20, p = 0.28]. Conclusion: These results suggest that the level of muscle pain is not region-specific, at least among the three sites investigated in the study, and VAS and PPT provide different information about DOMS, indicating that VAS and PPT represent different aspects of pain.

The dimensions of travel journalism : exploring new fields for journalism research beyond the news

Much of the existing empirical research on journalism focuses largely on hard-news journalism, at the expense of its less traditional forms, particularly the soft-news areas of lifestyle and entertainment journalism. In focussing on one particular area of lifestyle journalism – the reporting of travel stories – this paper argues for renewed scholarly efforts in this increasingly important field. Travel journalism’s location at the intersection between information and entertainment, journalism and advertising, as well as its increasingly significant role in the representation of foreign cultures makes it a significant site for scholarly research. By reviewing existing research about travel journalism and examining in detail the special exigencies that constrain it, the article proposes a number of dimensions for future research into the production practices of travel journalism. These dimensions include travel journalism’s role in mediating foreign cultures, its market orientation, motivational aspects and its ethical standards.

Chronic activation of the low affinity site of β1-adrenoceptors stimulates haemodynamics but exacerbates pressure-overload cardiac remodelling

Background and Purpose The β1-adrenoceptor has at least two binding sites, high and low affinity sites (β1H and β1L, respectively), which mediate cardiostimulation. While β1H-adrenoceptor can be blocked by all clinically used β-blockers, β1L-adrenoceptor is relatively resistant to blockade. Thus, chronic β1L-adrenoceptor activation may mediate persistent cardiostimulation, despite the concurrent blockade of β1H-adrenoceptors. Hence, it is important to determine the potential significance of β1L-adrenoceptors in vivo, particularly in pathological situations. Experimental Approach C57Bl/6 male mice were used. Chronic (4 or 8 weeks) β1L-adrenoceptor activation was achieved by treatment, via osmotic mini pumps, with (-)-CGP12177 (10 mg·kg−1·day−1). Cardiac function was assessed by echocardiography and micromanometry. Key Results (-)-CGP12177 treatment of healthy mice increased heart rate and left ventricular (LV) contractility. (-)-CGP12177 treatment of mice subjected to transverse aorta constriction (TAC), during weeks 4–8 or 4–12 after TAC, led to a positive inotropic effect and exacerbated fibrogenic signalling while cardiac hypertrophy tended to be more severe. (-)-CGP12177 treatment of mice with TAC also exacerbated the myocardial expression of hypertrophic, fibrogenic and inflammatory genes compared to untreated TAC mice. Washout of (-)-CGP12177 revealed a more pronounced cardiac dysfunction after 12 weeks of TAC. Conclusions and Implications β1L-adrenoceptor activation provides functional support to the heart, in both normal and pathological (pressure overload) situations. Sustained β1L-adrenoceptor activation in the diseased heart exacerbates LV remodelling and therefore may promote disease progression from compensatory hypertrophy to heart failure.

Simultaneous estimation of hunting pressure, harvest and hunter success rates using WinBUGS

The use of hierarchical Bayesian spatial models in the analysis of ecological data is increasingly prevalent. The implementation of these models has been heretofore limited to specifically written software that required extensive programming knowledge to create. The advent of WinBUGS provides access to Bayesian hierarchical models for those without the programming expertise to create their own models and allows for the more rapid implementation of new models and data analysis. This facility is demonstrated here using data collected by the Missouri Department of Conservation for the Missouri Turkey Hunting Survey of 1996. Three models are considered, the first uses the collected data to estimate the success rate for individual hunters at the county level and incorporates a conditional autoregressive (CAR) spatial effect. The second model builds upon the first by simultaneously estimating the success rate and harvest at the county level, while the third estimates the success rate and hunting pressure at the county level. These models are discussed in detail as well as their implementation in WinBUGS and the issues arising therein. Future areas of application for WinBUGS and the latest developments in WinBUGS are discussed as well.

Design Pressure Test 2013 Workshop

Design Pressure Test 2013 was a full-day intensive design immersion creative event run on Saturday 3 August 2013, at the QUT Faculty of Creative Industries J Block Design Lab Workshop in Brisbane, Australia, for 25 self-selected high-achieving junior and middle school (year 5-9) students, as part of the Queensland Academies ‘Young Scholars’ Program. Facilitated by tertiary interior design, fashion design and industrial design educators, technicians and six tertiary interior design and fashion design students, the workshop explored design process, environmental impact, the material properties and structural integrity of cardboard, construction techniques, and the production and evaluation of furniture design prototypes. This action research study aimed to facilitate an awareness in young people, of the role and scope of design within our society, the environmental ramifications of design decisions, and the value of design thinking skills in generating strategies to solve basic to complex challenges. It also aimed to investigate the value of collaboration between junior and middle school students, tertiary design educators and students and industry professionals in design awareness, and inspiring post-secondary pathways and idea generation for education. During the creative event, students utilised mathematics skills and developed sketching, making, communication, presentation and collaboration skills to improve their design process, while considering social, cultural and environmental opportunities. Through a series of hands-on collaborative design experiments, participants explored in teams of five, the opportunities available using cardboard as a material – inspiring both functional and aesthetic design solutions. Underpinned by the State Library of Queensland Design Minds Website ‘inquire, ideate and implement’ model of design thinking, the experiments culminated in the development of a detailed client brief, the design and fabrication of a furniture item for seating, and then a team presentation of prototypes to a panel of judges from the professions of architecture, interior design and industrial design, viewed also by parents. The final test for structural integrity was measured by the hoisting down of an adult body weight onto the fabricated seat. The workshop was filmed for the television program ‘Totally Wild’ for dissemination nationally (over 200,000 viewing audience) of the value of design and the Design Minds model to a wider target youth audience.

High pressure in situ diffraction studies of metal–hydrogen systems

“Hybrid” hydrogen storage, where hydrogen is stored in both the solid material and as a high pressure gas in the void volume of the tank can improve overall system efficiency by up to 50% compared to either compressed hydrogen or solid materials alone. Thermodynamically, high equilibrium hydrogen pressures in metal–hydrogen systems correspond to low enthalpies of hydrogen absorption–desorption. This decreases the calorimetric effects of the hydride formation–decomposition processes which can assist in achieving high rates of heat exchange during hydrogen loading—removing the bottleneck in achieving low charging times and improving overall hydrogen storage efficiency of large hydrogen stores. Two systems with hydrogenation enthalpies close to −20 kJ/mol H2 were studied to investigate the hydrogenation mechanism and kinetics: CeNi5–D2 and ZrFe2−xAlx (x = 0.02; 0.04; 0.20)–D2. The structure of the intermetallics and their hydrides were studied by in situ neutron powder diffraction at pressures up to 1000 bar and complementary X-ray diffraction. The deuteration of the hexagonal CeNi5 intermetallic resulted in CeNi5D6.3 with a volume expansion of 30.1%. Deuterium absorption filled three different types of interstices, Ce2Ni2 and Ni4 tetrahedra, and Ce2Ni3 half-octahedra and was accompanied by a valence change for Ce. Significant hysteresis was observed between deuterium absorption and desorption which profoundly decreased on a second absorption cycle. For the Al-modified Laves-type C15 ZrFe2−xAlx intermetallics, deuteration showed very fast kinetics of H/D exchange and resulted in a volume increase of the FCC unit cells of 23.5% for ZrFe1.98Al0.02D2.9(1). Deuterium content, hysteresis of H/D uptake and release, unit cell expansion and stability of the hydrides systematically change with the amount of Al content. In the deuteride D atoms exclusively occupy the Zr2(Fe,Al)2 tetrahedra. Observed interatomic distances are Zr–D = 1.98–2.11; (Fe, Al)–D = 1.70–1.75A˚ . Hydrogenation slightly increases the magnetic moment of the Fe atoms in ZrFe1.98Al0.02 and ZrFe1.96Al0.04 from 1.9 �B at room temperature for the alloy to 2.2 �B for its deuteride.