Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of De novo assemblers

Background The sequencing, de novo assembly and annotation of transcriptome datasets generated with next generation sequencing (NGS) has enabled biologists to answer genomic questions in non-model species with unprecedented ease. Reliable and accurate de novo assembly and annotation of transcriptomes, however, is a critically important step for transcriptome assemblies generated from short read sequences. Typical benchmarks for assembly and annotation reliability have been performed with model species. To address the reliability and accuracy of de novo transcriptome assembly in non-model species, we generated an RNAseq dataset for an intertidal gastropod mollusc species, Nerita melanotragus, and compared the assembly produced by four different de novo transcriptome assemblers; Velvet, Oases, Geneious and Trinity, for a number of quality metrics and redundancy. Results Transcriptome sequencing on the Ion Torrent PGM™ produced 1,883,624 raw reads with a mean length of 133 base pairs (bp). Both the Trinity and Oases de novo assemblers produced the best assemblies based on all quality metrics including fewer contigs, increased N50 and average contig length and contigs of greater length. Overall the BLAST and annotation success of our assemblies was not high with only 15-19% of contigs assigned a putative function. Conclusions We believe that any improvement in annotation success of gastropod species will require more gastropod genome sequences, but in particular an increase in mollusc protein sequences in public databases. Overall, this paper demonstrates that reliable and accurate de novo transcriptome assemblies can be generated from short read sequencers with the right assembly algorithms. Keywords: Nerita melanotragus; De novo assembly; Transcriptome; Heat shock protein; Ion torrent

Improving the outcomes of foot and ankle surgery through the audit cycle : a case study

The direct costs of managing adverse outcomes from Australian health care are estimated to be $2 billion. The audit cycle is considered an important tool to assist in the preventive management of adverse outcomes.Australian guidelines for audit cycle design allow for comparison of data sets derived from similar surgical specialities. However a lack of data set standardisation inhibits meaningful comparisons of foot and ankle surgical audits. This research will assist development of a best practice model for auditing foot and ankle surgery. Data derived from this model will improve the safety and quality of foot and ankle surgery. The preliminary phase of this process is to identify and understand the attitudes and behaviours of how and why surgeons participate in the audit cycle. A descriptive embedded multiple case study research design is planned to provide an intense focus on a single phenomenon (the audit cycle) within its real life context (clinical governance). The measures to be included in the case study have been identified by the Balanced Patient Safety Measurement Framework. These include: audit and peer review activity, provider attitudes to patient safety, safety learning, action and performance. A purposive sample of 6 to 8 surgeons (units of analysis) from 3 to 4 specialities (cases) will undergo semi-structured interview. This will investigate: current audit tools and processes; attitudes; and behaviours of surgeons to the audit cycle. Similarities in and differences between the units of analysis will indicate which identified measures function as barriers or enablers of the audit cycle. Reliability and validity (external and construct) will be assessed using established methods for case studies. The descriptive embedded multiple case study will reveal how and why foot and ankle surgeons participate in the audit cycle. This will inform further research to improve the outcomes of foot and ankle surgery through development of an audit tool.

Development and validation of the ankle fracture outcome of rehabilitation measure (A-FORM)

Study Design Delphi panel and cohort study. Objective To develop and refine a condition-specific, patient-reported outcome measure, the Ankle Fracture Outcome of Rehabilitation Measure (A-FORM), and to examine its psychometric properties, including factor structure, reliability, and validity, by assessing item fit with the Rasch model. Background To our knowledge, there is no patient-reported outcome measure specific to ankle fracture with a robust content foundation. Methods A 2-stage research design was implemented. First, a Delphi panel that included patients and health professionals developed the items and refined the item wording. Second, a cohort study (n = 45) with 2 assessment points was conducted to permit preliminary maximum-likelihood exploratory factor analysis and Rasch analysis. Results The Delphi panel reached consensus on 53 potential items that were carried forward to the cohort phase. From the 2 time points, 81 questionnaires were completed and analyzed; 38 potential items were eliminated on account of greater than 10% missing data, factor loadings, and uniqueness. The 15 unidimensional items retained in the scale demonstrated appropriate person and item reliability after (and before) removal of 1 item (anxious about footwear) that had a higher-than-ideal outfit statistic (1.75). The “anxious about footwear” item was retained in the instrument, but only the 14 items with acceptable infit and outfit statistics (range, 0.5–1.5) were included in the summary score. Conclusion This investigation developed and refined the A-FORM (Version 1.0). The A-FORM items demonstrated favorable psychometric properties and are suitable for conversion to a single summary score. Further studies utilizing the A-FORM instrument are warranted. J Orthop Sports Phys Ther 2014;44(7):488–499. Epub 22 May 2014. doi:10.2519/jospt.2014.4980

Reliability in the Parameterization of the Functional Reach Test in Elderly Stroke Patients: A Pilot Study

BACKGROUND: Postural instability is one of the major complications found in stroke survivors. Parameterising the functional reach test (FRT) could be useful in clinical practice and basic research. OBJECTIVES: To analyse the reliability, sensitivity, and specificity in the FRT parameterisation using inertial sensors for recording kinematic variables in patients who have suffered a stroke. DESIGN: Cross-sectional study. While performing FRT, two inertial sensors were placed on the patient's back (lumbar and trunk). PARTICIPANTS: Five subjects over 65 who suffer from a stroke. MEASUREMENTS: FRT measures, lumbosacral/thoracic maximum angular displacement, maximum time of lumbosacral/thoracic angular displacement, time return initial position, and total time. Speed and acceleration of the movements were calculated indirectly. RESULTS: FRT measure is  12.75±2.06 cm. Intrasubject reliability values range from 0.829 (time to return initial position (lumbar sensor)) to 0.891 (lumbosacral maximum angular displacement). Intersubject reliability values range from 0.821 (time to return initial position (lumbar sensor)) to 0.883 (lumbosacral maximum angular displacement). FRT's reliability was 0.987 (0.983-0.992) and 0.983 (0.979-0.989) intersubject and intrasubject, respectively. CONCLUSION: The main conclusion could be that the inertial sensors are a tool with excellent reliability and validity in the parameterization of the FRT in people who have had a stroke.

Factors influencing the provision of end-of-life care in critical care settings : development and testing of a survey instrument

Aim. To develop and psychometrically test a survey instrument to identify the factors influencing the provision of end-of-life care by critical care nurses. Background. Following a decision to withdraw life-sustaining treatment, critical care nurses remain with the patient and their family providing end-of-life care. Identification of factors influencing the provision of this care can give evidence to inform practice development and support nurses. Design. A cross-sectional survey of critical care nurses. Method. An online survey was developed, reviewed by an expert panel and pilot tested to obtain preliminary evidence of its reliability and validity. In May 2011, a convenience sample of critical care nurses (n = 392, response rate 25%) completed the survey. The analytical approach to data obtained from the 58 items measured on a Likert scale included exploratory factor analysis and descriptive statistics. Results. Exploratory factor analysis identified eight factors influencing the provision of end-of-life care: emotional support for nurses, palliative values, patient and family preferences, resources, organizational support, care planning, knowledge and preparedness. Internal consistency of each latent construct was deemed satisfactory. The results of descriptive statistics revealed a strong commitment to the inclusion of families in end-of-life care and the value of this care in the critical care setting. Conclusion. This paper reports preliminary evidence of the psychometric properties of a new survey instrument. The findings may inform practice development opportunities to support critical care nurses in the provision of endof- life care and improve the care that patients and their families receive.

Arabic translation, adaptation and modification of the dialysis symptom index for chronic kidney disease stages four and five

Background Symptom burden in chronic kidney disease (CKD) is poorly understood. To date, the majority of research focuses on single symptoms and there is a lack of suitable multidimensional symptom measures. The purpose of this study was to modify, translate, cross-culturally adapt and psychometrically analyse the Dialysis Symptom Index (DSI). Methods The study methods involved four phases: modification, translation, pilot-testing with a bilingual non-CKD sample and then psychometric testing with the target population. Content validity was assessed using an expert panel. Inter-rater agreement, test-retest reliability and Cronbach’s alpha coefficient were calculated to demonstrate reliability of the modified DSI. Discriminative and convergent validity were assessed to demonstrate construct validity. Results Content validity index during translation was 0.98. In the pilot study with 25 bilingual students a moderate to perfect agreement (Kappa statistic = 0.60-1.00) was found between English and Arabic versions of the modified DSI. The main study recruited 433 patients CKD with stages 4 and 5. The modified DSI was able to discriminate between non-dialysis and dialysis groups (p < 0.001) and demonstrated convergent validity with domains of the Kidney Disease Quality of Life short form. Excellent test-retest and internal consistency (Cronbach’s α = 0.91) reliability were also demonstrated. Conclusion The Arabic version of the modified DSI demonstrated good psychometric properties, measures the multidimensional nature of symptoms and can be used to assess symptom burden at different stages of CKD. The modified instrument, renamed the CKD Symptom Burden Index (CKD-SBI), should encourage greater clinical and research attention to symptom burden in CKD.

Moral vitalism: Seeing good and evil as real, agentic forces

Moral vitalism refers to a tendency to view good and evil as actual forces that can influence people and events. We introduce a scale designed to assess the belief in moral vitalism. High scorers on the scale endorse items such as “There are underlying forces of good and evil in this world”. After establishing the reliability and criterion validity of the scale (Studies 1, 2a, 2b), we examined the predictive validity of the moral vitalism scale, showing that “moral vitalists” worry about being possessed by evil (Study 3), being contaminated through contact with evil people (Study 4), and forfeiting their own mental purity (Study 5). We discuss the nature of moral vitalism and the implications of the construct for understanding the role of metaphysical lay theories about the nature of good and evil in moral reasoning.

Kinematics and kinetics of the Nordic hamstring curl

This thesis describes, for the first time, the forces involved in the Nordic hamstring exercise, its reliability and the biomechanical effects of extra loading during the movement. The results provide practitioners with valuable information to enhance hamstring injury prevention and rehabilitation programs.

Inventory of pedagogy and practice: Confirmatory factor analysis of multiple facets of teaching

Student perceptions of teaching have often been used in tertiary education for evaluation purposes. However, there is a paucity of research on the validity, reliability, and applicability of instruments that cover a wide range of student perceptions of pedagogies and practices in high school settings for descriptive purposes. The study attempts to validate an inventory of pedagogy and practice (IPP) that provides researchers and practitioners with a psychometrically sound instrument that covers the most salient factors related to teaching. Using a sample of students (N = 1515) from 39 schools in Singapore, 14 factors about teaching in English lessons from the students’ perspective were tested with confirmatory factor analysis (classroom task goal, structure and clarity, curiosity and interest, positive class climate, feedback, questioning, quality homework, review of students’ work, conventional teaching, exam preparation, behaviour management, maximizing learning time, student-centred pedagogy, and subject domain teaching). Two external criterion factors were used to further test the IPP factor structure. The inventory will enable teachers to understand more about their teaching and researchers to examine how teaching may be related to learning outcomes.

Extending the validity of the Feeding Practices and Structure Questionnaire

Background Feeding practices are commonly examined as potentially modifiable determinants of children’s eating behaviours and weight status. Although a variety of questionnaires exist to assess different feeding aspects, many lack thorough reliability and validity testing. The Feeding Practices and Structure Questionnaire (FPSQ) is a tool designed to measure early feeding practices related to non-responsive feeding and structure of the meal environment. Face validity, factorial validity, internal reliability and cross-sectional correlations with children’s eating behaviours have been established in mothers with 2-year-old children. The aim of the present study was to further extend the validity of the FPSQ by examining factorial, construct and predictive validity, and stability. Methods Participants were from the NOURISH randomised controlled trial which evaluated an intervention with first-time mothers designed to promote protective feeding practices. Maternal feeding practices (FP) and child eating behaviours were assessed when children were aged 2 years and 3.7 years (n=388). Confirmatory Factor analysis, group differences, predictive relationships, and stability were tested. Results The original 9-factor structure was confirmed when children were aged 3.7±0.3 years. Cronbach’s alpha was above the recommended 0.70 cut-off for all factors except Structured Meal Timing, Over Restriction and Distrust in Appetite which were 0.58, 0.67 and 0.66 respectively. Allocated group differences reflected behaviour consistent with intervention content and all feeding practices were stable across both time points (range of r= 0.45-0.70). There was some evidence for the predictive validity of factors with 2 FP showing expected relationships, 2 FP showing expected and unexpected relationships and 5 FP showing no relationship. Conclusions Reliability and validity was demonstrated for most subscales of the FPSQ. Future validation is warranted with culturally diverse samples and with fathers and other caregivers. The use of additional outcomes to further explore predictive validity is recommended as well as testing construct validity and test-retest reliability of the questionnaire.

Translation and psychometric properties of the Chinese version of the Leeds Attitudes to Concordance II scale

Background Concordance is characterised as a negotiation-like health communication approach based on an equal and collaborative partnership between patients and health professionals. The Leeds Attitudes to Concordance II (LATCon II) scale was developed to measure the attitudes towards concordance. The purpose of this study was to translate the LATCon II into Chinese and psychometrically test the Chinese version of LATCon II (C-LATCon II). Methods The study involved three phases: i) translation and cross-cultural adaptation; ii) pilot study, and; iii) a cross-sectional survey (n = 366). Systematic random sampling was used to recruit hypertensive patients from nine communities covering around 78,000 residents in China. Tests of psychometric properties included content validity, construct validity, criteria-related validity (correlation between the C-LATCon II and the Therapeutic Adherence Scale for Hypertensive Patients (TASHP)), internal reliability, and test-retest reliability (n = 30). Results The study found that the C-LATCon II had a satisfactory content validity (item-level Content Validity Index (CVI) = 0.83-1, scale-level CVI/universal agreement = 0.89, and scale-level CVI/averaging calculation = 0.98), construct validity (four components extracted explained 56.66% of the total variance), internal reliability (Cronbach’s alpha of overall scale and four components was 0.78 and 0.66-0.84, respectively), and test-retest reliability (Pearson’s correlation coefficient = 0.82, p < 0.001; interclass correlation coefficient = 0.82, p < 0.001; linear weighted kappa3 statistic for each item = 0.40-0.65, p < 0.05). Criteria-related validity showed a weak association (Pearson’s correlation coefficient = 0.11, p < 0.05) between patients’ attitudes towards concordance during health communication and their health behaviours for hypertension management. Conclusions The C-LATCon II is a validated and reliable instrument which can be used to evaluate the attitudes to concordance in Chinese populations. Four components (health professionals’ attitudes, partnership between two parties, therapeutic decision making, and patients’ involvement) describe the attitudes towards concordance during health communication.

Agreement between physiotherapists rating scapular posture in multiple planes in patients with neck pain: Reliability study

Objective Evaluation of scapular posture is an integral component of the clinical assessment of painful neck disorders. The aim of this study was to evaluate agreement between therapist judgements of scapula posture in multiple biomechanical planes in individuals with neck pain. Design Inter-therapist reliability study. Setting Research laboratory. Participants Fifteen participants with chronic neck pain. Main outcome measures Four physiotherapists recorded ratings of scapular orientation (relative to the thorax) in five different scapula postural planes (plane of scapula, sagittal plane, transverse plane, horizontal plane, and vertical plane) under four test conditions (at rest, and during three isometric shoulder conditions) in all participants. Inter-therapist reliability was expressed using both generalized and paired kappa coefficient. Results Following adjustment for expected agreement and the high prevalence of neutral ratings (81%), on average both the generalised kappa (0.37) as well as Cohen's Kappa for the two therapist pairs (0.45 and 0.42) demonstrated only slight to moderate inter-therapist reliability. Conclusions The findings suggest that ratings of scapular posture in individuals with neck pain by visual inspection has only slight to moderate reliability and should only be used in conjunction with other clinical tests when judging scapula function in these patients.

Ship Seakeeping Operability, Motion Control, and Autonomy - A Bayesian Perspective

Ship seakeeping operability refers to the quantification of motion performance in waves relative to mission requirements. This is used to make decisions about preferred vessel designs, but it can also be used as comprehensive assessment of the benefits of ship-motion-control systems. Traditionally, operability computation aggregates statistics of motion computed over over the envelope of likely environmental conditions in order to determine a coefficient in the range from 0 to 1 called operability. When used for assessment of motion-control systems, the increase of operability is taken as the key performance indicator. The operability coefficient is often given the interpretation of the percentage of time operable. This paper considers an alternative probabilistic approach to this traditional computation of operability. It characterises operability not as a number to which a frequency interpretation is attached, but as a hypothesis that a vessel will attain the desired performance in one mission considering the envelope of likely operational conditions. This enables the use of Bayesian theory to compute the probability of that this hypothesis is true conditional on data from simulations. Thus, the metric considered is the probability of operability. This formulation not only adheres to recent developments in reliability and risk analysis, but also allows incorporating into the analysis more accurate descriptions of ship-motion-control systems since the analysis is not limited to linear ship responses in the frequency domain. The paper also discusses an extension of the approach to the case of assessment of increased levels of autonomy for unmanned marine craft.

The effect of row configuration on yield reliability in grain sorghum: II. Modelling the effects of row configuration

In recent years many sorghum producers in the more marginal (<600 mm annual rainfall) cropping areas of Qld and northern NSW have utilised skip row configurations in an attempt to improve yield reliability and reduce sorghum production risk. But will this work in the long run? What are the trade-offs between productivity and risk of crop failure? This paper describes a modelling and simulation approach to study the long-term effects of skip row configurations. Detailed measurements of light interception and water extraction from sorghum crops grown in solid, single and double skip row configurations were collected from three on-farm participatory research trials established in southern Qld and northern NSW. These measurements resulted in changes to the model that accounted for the elliptical water uptake pattern below the crop row and reduced total light interception associated with the leaf area reduction of the skip configuration. Following validation of the model, long-term simulation runs using historical weather data were used to determine the value of skip row sorghum production as a means of maintaining yield reliability in the dryland cropping regions of southern Qld and northern NSW.