De-Identification of health records using Anonym: Effectiveness and robustness across datasets

Objective Evaluate the effectiveness and robustness of Anonym, a tool for de-identifying free-text health records based on conditional random fields classifiers informed by linguistic and lexical features, as well as features extracted by pattern matching techniques. De-identification of personal health information in electronic health records is essential for the sharing and secondary usage of clinical data. De-identification tools that adapt to different sources of clinical data are attractive as they would require minimal intervention to guarantee high effectiveness. Methods and Materials The effectiveness and robustness of Anonym are evaluated across multiple datasets, including the widely adopted Integrating Biology and the Bedside (i2b2) dataset, used for evaluation in a de-identification challenge. The datasets used here vary in type of health records, source of data, and their quality, with one of the datasets containing optical character recognition errors. Results Anonym identifies and removes up to 96.6% of personal health identifiers (recall) with a precision of up to 98.2% on the i2b2 dataset, outperforming the best system proposed in the i2b2 challenge. The effectiveness of Anonym across datasets is found to depend on the amount of information available for training. Conclusion Findings show that Anonym compares to the best approach from the 2006 i2b2 shared task. It is easy to retrain Anonym with new datasets; if retrained, the system is robust to variations of training size, data type and quality in presence of sufficient training data.

Fatty acid uptake and incorporation into phospholipids in the rat lens

PURPOSE. Phospholipids are a major component of lens fiber cells and influence the activity of membrane proteins. Previous investigations of fatty acid uptake by the lens are limited. The purpose of the present study was thus to determine whether exogenous fatty acids could be taken up by the rat lens and incorporated into molecular phospholipids. METHODS. Lenses were incubated with fluorescently labeled palmitic acid and then analyzed by confocal microscopy. Concurrently, lenses incubated with either fluorescently labeled palmitic acid or the more physiologically relevant (13)C(18)-oleic acid were sectioned into nuclear and cortical regions and analyzed by highly sensitive and structurally selective electrospray ionization tandem mass spectrometry techniques. RESULTS. The detection of fluorescently labeled palmitic acid, even after 16 hours of incubation, was limited to approximately the outer 25% to 30% of the rat lens. Mass spectrometry also revealed the presence of free (13)C(18)-oleic acid in the cortex but not the nucleus. No evidence could be found for incorporation of fluorescently labeled palmitic acid into phospholipids; however, a low level of (13)C(18)-oleic acid incorporation into phosphatidylethanolamine (PE), specifically PE (PE 16:0/(13)C(18) 18:1) was detected in the lens cortex after 16 hours. CONCLUSIONS. These data demonstrate that uptake of exogenous (e.g., dietary fatty acids) by the lens and their incorporation into phospholipids is minimal, most likely occurring only during de novo synthesis in the outermost region of the lens. This finding adds support to the hypothesis that once synthesized there is no active remodeling or turnover of fiber cell phospholipids.

An algebraic analysis of trivium ciphers based on the boolean satisfiability problem

Trivium is a stream cipher candidate of the eStream project. It has successfully moved into phase three of the selection process under the hardware category. No attacks faster than the exhaustive search have so far been reported on Trivium. Bivium-A and Bivium-B are simplified versions of Trivium that are built on the same design principles but with two registers. The simplified design is useful in investigating Trivium type ciphers with a reduced complexity and provides insight into effective attacks which could be extended to Trivium. This paper focuses on an algebraic analysis which uses the boolean satisfiability problem in propositional logic. For reduced variants of the cipher, this analysis recovers the internal state with a minimal amount of keystream observations.

Geometric sensitivity of patient-specific finite element models of the spine to variability in user-selected anatomical landmarks

Software to create individualised finite element (FE) models of the osseoligamentous spine using pre-operative computed tomography (CT) data-sets for spinal surgery patients has recently been developed. This study presents a geometric sensitivity analysis of this software to assess the effect of intra-observer variability in user-selected anatomical landmarks. User-selected landmarks on the osseous anatomy were defined from CT data-sets for three scoliosis patients and these landmarks were used to reconstruct patient-specific anatomy of the spine and ribcage using parametric descriptions. The intra-observer errors in landmark co-ordinates for these anatomical landmarks were calculated. FE models of the spine and ribcage were created using the reconstructed anatomy for each patient and these models were analysed for a loadcase simulating clinical flexibility assessment. The intra-observer error in the anatomical measurements was low in comparison to the initial dimensions, with the exception of the angular measurements for disc wedge and zygapophyseal joint (z-joint) orientation and disc height. This variability suggested that CT resolution may influence such angular measurements, particularly for small anatomical features, such as the z-joints, and may also affect disc height. The results of the FE analysis showed low variation in the model predictions for spinal curvature with the mean intra-observer variability substantially less than the accepted error in clinical measurement. These findings demonstrate that intra-observer variability in landmark point selection has minimal effect on the subsequent FE predictions for a clinical loadcase.

Perceived obstacles to multi-storey timber-frame construction : an Australian study

The contemporary default materials for multi-storey buildings – namely concrete and steel – are all significant generators of carbon and the use of timber products provides a technically, economically and environmentally viable alternative. In particular, timber’s sustainability can drive increased use and subsequent evolution of the Blue economy as a new economic model. National research to date, however, indicates a resistance to the uptake of timber technologies in Australia. To investigate this further, a preliminary study involving a convenience sample of 15 experts was conducted to identify the main barriers involved in the use of timber frames in multi-storey buildings. A closed-ended questionnaire survey involving 74 experienced construction industry participants was then undertaken to rate the relative importance of the barriers. The survey confirmed the most significant barriers to be a perceived increase in maintenance costs and fire risk, together with a limited awareness of the emerging timber technologies available. It is expected that the results will benefit government and the timber industry, contributing to environmental improvement by developing strategies to increase the use of timber technologies in multi-storey buildings by countering perceived barriers in the Australian context.

Kinematic models for manoeuvring and seakeeping of marine vessels

The motion of marine vessels has traditionally been studied using two different approaches: manoeuvring and seakeeping. These two approaches use different reference frames and coordinate systems to describe the motion. This paper derives the kinematic models that characterize the transformation of motion variables (position, velocity, accelerations) and forces between the different coordinate systems used in these theories. The derivations hereby presented are done in terms of the formalism adopted in robotics. The advantage of this formulation is the use of matrix notation and operations. As an application, the transformation of linear equations of motion used in seakeeping into body-fixed coordinates is considered for both zero and forward speed.

Evaluation of a pilot-scale oil extraction from microalgae for biodiesel production

Biodiesel derived from microalgae is one of a suite of potential solutions to meet the increasing demand for a renewable, carbon-neutral energy source. However, there are numerous challenges that must be addressed before algae biodiesel can become commercially viable. These challenges include the economic feasibility of harvesting and dewatering the biomass and the extraction of lipids and their conversion into biodiesel. Therefore, it is essential to find a suitable extraction process given these processes presently contribute significantly to the total production costs which, at this stage, inhibit the ability of biodiesel to compete financially with petroleum diesel. This study focuses on pilot-scale (100 kg dried microalgae) solvent extraction of lipids from microalgae and subsequent transesterification to biodiesel. Three different solvents (hexane, isopropanol (IPA) and hexane + IPA (1:1)) were used with two different extraction methods (static and Soxhlet) at bench-scale to find the most suitable solvent extraction process for the pilot-scale. The Soxhlet method extracted only 4.2% more lipid compared to the static method. However, the fatty acid profiles of different extraction methods with different solvents are similar, suggesting that none of the solvents or extraction processes were biased for extraction of particular fatty acids. Considering the cost and availability of the solvents, hexane was chosen for pilot-scale extraction using static extraction. At pilot-scale the lipid yield was found to be 20.3% of total biomass which is 2.5% less than from bench scale. Extracted fatty acids were dominated by polyunsaturated fatty acids (PUFAs) (68.94±0.17%) including 47.7±0.43 and 17.86±0.42% being docosahexaenoic acid (DHA) (C22:6) and docosapentaenoic acid (DPA) (C22:5, ω-3), respectively. These high amounts of long chain poly unsaturated fatty acids are unique to some marine microalgae and protists and vary with environmental conditions, culture age and nutrient status, as well as with cultivation process. Calculated physical and chemical properties of density, viscosity of transesterified fatty acid methyl esters (FAMEs) were within the limits of the biodiesel standard specifications as per ASTM D6751-2012 and EN 14214. The calculated cetane number was, however, significantly lower (17.8~18.6) compared to ASTM D6751-2012 or EN 14214-specified minimal requirements. We conclude that the obtained microalgal biodiesel would likely only be suitable for blending with petroleum diesel to a maximum of 5 to 20%.

Second-order elastic finite element analysis of structures using a single element per member

Finite element frame analysis programs targeted for design office application necessitate algorithms which can deliver reliable numerical convergence in a practical timeframe with comparable degrees of accuracy, and a highly desirable attribute is the use of a single element per member to reduce computational storage, as well as data preparation and the interpretation of the results. To this end, a higher-order finite element method including geometric non-linearity is addressed in the paper for the analysis of elastic frames for which a single element is used to model each member. The geometric non-linearity in the structure is handled using an updated Lagrangian formulation, which takes the effects of the large translations and rotations that occur at the joints into consideration by accumulating their nodal coordinates. Rigid body movements are eliminated from the local member load-displacement relationship for which the total secant stiffness is formulated for evaluating the large member deformations of an element. The influences of the axial force on the member stiffness and the changes in the member chord length are taken into account using a modified bowing function which is formulated in the total secant stiffness relationship, for which the coupling of the axial strain and flexural bowing is included.

Distamycin A affects the stability of NF-kappaB p50-DNA complexes in a sequence-dependent manner

The effect of two different DNA minor groove binding molecules, Hoechst 33258 and distamycin A, on the binding kinetics of NF-κB p50 to three different specific DNA sequences was studied at various salt concentrations. Distamycin A was shown to significantly increase the dissociation rate constant of p50 from the sequences PRDII (5′-GGGAAATTCC-3′) and Ig-κ B (5′-GGGACTTTCC-3′) but had a negligible effect on the dissociation from the palindromic target-κB binding site (5′-GGGAATTCCC-3′). By comparison, the effect of Hoechst 33258 on binding of p50 to each sequence was found to be minimal. The dissociation rates for the protein–DNA complexes increased at higher potassium chloride concentrations for the PRDII and Ig-κB binding motifs and this effect was magnified by distamycin A. In contrast, p50 bound to the palindromic target-κB site with a much higher intrinsic affinity and exhibited a significantly reduced salt dependence of binding over the ionic strength range studied, retaining a KD of less than 10 pM at 150 mM KCl. Our results demonstrate that the DNA binding kinetics of p50 and their salt dependence is strongly sequence-dependent and, in addition, that the binding of p50 to DNA can be influenced by the addition of minor groove-binding drugs in a sequence-dependent manner.

Transient expression vectors for functional genomics, quantification of promoter activity and RNA silencing in plants

Background We describe novel plasmid vectors for transient gene expression using Agrobacterium, infiltrated into Nicotiana benthamiana leaves. We have generated a series of pGreenII cloning vectors that are ideally suited to transient gene expression, by removing elements of conventional binary vectors necessary for stable transformation such as transformation selection genes. Results We give an example of expression of heme-thiolate P450 to demonstrate effectiveness of this system. We have also designed vectors that take advantage of a dual luciferase assay system to analyse promoter sequences or post-transcriptional regulation of gene expression. We have demonstrated their utility by co-expression of putative transcription factors and the promoter sequence of potential target genes and show how orthologous promoter sequences respond to these genes. Finally, we have constructed a vector that has allowed us to investigate design features of hairpin constructs related to their ability to initiate RNA silencing, and have used these tools to study cis-regulatory effect of intron-containing gene constructs. Conclusion In developing a series of vectors ideally suited to transient expression analysis we have provided a resource that further advances the application of this technology. These minimal vectors are ideally suited to conventional cloning methods and we have used them to demonstrate their flexibility to investigate enzyme activity, transcription regulation and post-transcriptional regulatory processes in transient assays.

Accelerometer data reduction : a comparison of four reduction algorithms on select outcome variables

Purpose Accelerometers are recognized as a valid and objective tool to assess free-living physical activity. Despite the widespread use of accelerometers, there is no standardized way to process and summarize data from them, which limits our ability to compare results across studies. This paper a) reviews decision rules researchers have used in the past, b) compares the impact of using different decision rules on a common data set, and c) identifies issues to consider for accelerometer data reduction. Methods The methods sections of studies published in 2003 and 2004 were reviewed to determine what decision rules previous researchers have used to identify wearing period, minimal wear requirement for a valid day, spurious data, number of days used to calculate the outcome variables, and extract bouts of moderate to vigorous physical activity (MVPA). For this study, four data reduction algorithms that employ different decision rules were used to analyze the same data set. Results The review showed that among studies that reported their decision rules, much variability was observed. Overall, the analyses suggested that using different algorithms impacted several important outcome variables. The most stringent algorithm yielded significantly lower wearing time, the lowest activity counts per minute and counts per day, and fewer minutes of MVPA per day. An exploratory sensitivity analysis revealed that the most stringent inclusion criterion had an impact on sample size and wearing time, which in turn affected many outcome variables. Conclusions These findings suggest that the decision rules employed to process accelerometer data have a significant impact on important outcome variables. Until guidelines are developed, it will remain difficult to compare findings across studies

Indexes of insulin resistance and secretion in obese children and adolescents : a validation study

OBJECTIVE To assess the concurrent validity of fasting indexes of insulin sensitivity and secretion in - obese prepubertal (Tanner stage 1) children and pubertal (Tanner stages 2-5) glucose tolerance test (FSIVGTT) as a criterion measure. RESEARCH DESIGN AND METHODS Eighteen obese children and adolescents (11 girls and 7 boys, mean age 12.2 +/- 2.4 years, mean BMI 35.4 +/- 6.2 kg/m(2), mean BMI-SDS 3.5 +/- 0.5, 7 prepubertal and I I pubertal) participated in the study. All participants underwent an insulin-modified FSIVGTT on two occasions, and 15 repeated this test a third time (mean 12.9 and 12.0 weeks apart). S-i measured by the FSIVGTT was compared with homeostasis model assessment (HOMA) of insulin resistance (HOMA-IR), quantitative insulin-sensitivity check index (QUICKI), fasting glucose-to-insulin ratio (FGIR), and fasting insulin (estimates of insulin sensitivity derived from fasting samples). The acute insulin response (AIR) measured by the FSIVGTT was compared with HOMA of percent beta-cell function (HOMA-beta%), FGIR, and fasting insulin (estimates of insulin secretion derived from fasting samples). RESULTS There was a significant negative correlation between HOMA-IR and S-i (r = -0.89, r = -0.90, and r = -0.81, P < 0.01) and a significant positive correlation between QUICKI and S-i (r = 0.89, r = 0.90, and r = 0.81, P < 0.01) at each time point. There was a significant positive correlation between FGIR and S-i (r = 0.91, r = 0.91, and r = 0.82, P < 0.01) and a significant negative correlation between fasting insulin and S-i (r = -90, r = -0.90, and r = -0.88, P < 0.01). HOMA-beta% was not as strongly correlated with AIR (r = 0.60, r = 0.54, and r = 0.61, P < 0.05). CONCLUSIONS HOMA-IR, QUICKI, FGIR, and fasting insulin correlate strongly with S-i assessed by the FSIVGTT in obese children and adolescents. Correlations between HOMA-β% FGIR and fasting insulin, and AIR were not as strong. Indexes derived from fasting samples are a valid tool for assessing insulin sensitivity in prepubertal and pubertal obese children.

Reliability and validity of physical fitness field tests for adults aged 55 to 70 years

The aim of this study was to examine the reliability and validity of field tests for assessing physical function in mid-aged and young-old people (55-70 y). Tests were selected that required minimal space and equipment and could be implemented in multiple field settings such as a general practitioner's office. Nineteen participants completed 2 field and I laboratory testing sessions. Intra-class correlations showed good reliability for the tests of upper body strength (lift and reach, R=.66), lower body strength (sit to stand, R=.80) and functional capacity (Canadian Step Test, R=.92), but not for leg power (single timed chair rise, R=.28). There was also good reliability for the balance test during 3 stances: parallel (94.7% agreement), semi-tandem (73.7%), and tandem (52.6%). Comparison of field test results with objective laboratory measures found good validity for the sit to stand (cf 1RM leg press, Pearson r=.68, p <.05), and for the step test (cf PWC140, r = -.60, p <.001), but not for the lift and reach (cf 1RM bench press, r=.43, p >.05), balance (r=-.13, -.18, .23) and rate of force development tests (r=-.28). It was concluded that the lower body strength and cardiovascular function tests were appropriate for use in field settings with mid-aged and young-old adults.

Securing medical devices Part A : what’s available for endotracheal tubes?

Oral endotracheal tubes (ETTs) and nasogastric tubes (NGT) are common devices used in adult intensive care and numerous options exist for safe and comfortable securement of these devices. The aim of this project was to identify the available range of ETT and NGT securement devices in Australia as a resource for clinicians seeking to explore options for tube stabilisation. This article reports part A of this project: ETT securement options. Part B will report NGT device fixation options. Securing ETTs to ensure a patent airway with minimal ETT movement, promotion of patient comfort and absence of adverse events such as ETT dislodgement, unplanned extubation and device-related injury1, are essential critical care nursing actions. The ETT requires a fixation method that is robust yet does not traumatise or injure the mucosal tissues of the mouth and soft tissue of the lips.2,3 Choice of a securement apparatus is often determined by product availability in our units or hospitals but is also driven by evidence-based practice and clinician preference. Trying to put this information together can be difficult and time-consuming for the bedside clinician...

Using objective physical activity measures with youth : How many days of monitoring are needed?

Purpose The purpose of this study was to establish the minimal number of days of monitoring required for accelerometers to assess usual physical activity in children. Methods A total of 381 students (189 M, 192 F) wore a CSA 7164 uniaxial accelerometer for seven consecutive days. To examine age-related trends students were grouped as follows: Group I: grades 1-3 (N = 92); Group II: grades 4-6 (N = 98); Group III: grades 7-9 (N = 97); Group IV: grades 10-12 (N = 94). Average daily time spent in moderate-to-vigorous physical activity (MVPA) was calculated from minute-by-minute activity counts using the regression equation developed by Freedson et al. (1997). Results Compared with adolescents in grades 7 to 12, children in grades 1 to 6 exhibited less day-to-day variability in MVPA behavior. Spearman-Brown analysts indicated that between 4 and 5 d of monitoring would be necessary to a achieve a reliability of 0.80 in children, and between 8 and 9 d of monitoring would be necessary to achieve a reliability of 0.80 in adolescents. Within all grade levels, the 7-d monitoring protocol produced acceptable estimates of daily participation in MVPA (R = 0.76 (0.71-0.81) to 0.87 (0.84-0.90)). Compared with weekdays, children exhibited significantly higher levels of MVPA on weekends, whereas adolescents exhibited significantly lower levels of MVPA on weekends. Principal components analysis revealed two distinct time components for MVPA during the day for children (early morning, rest of the day), and three distinct time components for MVPA during the day for adolescents (morning, afternoon, early evening). Conclusions These results indicate that a 7-d monitoring protocol provides reliable estimates of usual physical activity behavior in children and adolescents and accounts for potentially important differences in weekend versus weekday activity behavior as well as differences in activity patterns within a given day.