How should sparse marine in situ measurements be compared to a continuous model: an example

This work demonstrates an example of the importance of an adequate method to sub-sample model results when comparing with in situ measurements. A test of model skill was performed by employing a point-to-point method to compare a multi-decadal hindcast against a sparse, unevenly distributed historic in situ dataset. The point-to-point method masked out all hindcast cells that did not have a corresponding in situ measurement in order to match each in situ measurement against its most similar cell from the model. The application of the point-to-point method showed that the model was successful at reproducing the inter-annual variability of the in situ datasets. Furthermore, this success was not immediately apparent when the measurements were aggregated to regional averages. Time series, data density and target diagrams were employed to illustrate the impact of switching from the regional average method to the point-to-point method. The comparison based on regional averages gave significantly different and sometimes contradicting results that could lead to erroneous conclusions on the model performance. Furthermore, the point-to-point technique is a more correct method to exploit sparse uneven in situ data while compensating for the variability of its sampling. We therefore recommend that researchers take into account for the limitations of the in situ datasets and process the model to resemble the data as much as possible.

Exploiting a priori time constant ratio information in difference equation two-thermocouple sensor characterisation

The characterization of thermocouple sensors for temperature measurement in varying-flow environments is a challenging problem. Recently, the authors introduced novel difference-equation-based algorithms that allow in situ characterization of temperature measurement probes consisting of two-thermocouple sensors with differing time constants. In particular, a linear least squares (LS) lambda formulation of the characterization problem, which yields unbiased estimates when identified using generalized total LS, was introduced. These algorithms assume that time constants do not change during operation and are, therefore, appropriate for temperature measurement in homogenous constant-velocity liquid or gas flows. This paper develops an alternative ß-formulation of the characterization problem that has the major advantage of allowing exploitation of a priori knowledge of the ratio of the sensor time constants, thereby facilitating the implementation of computationally efficient algorithms that are less sensitive to measurement noise. A number of variants of the ß-formulation are developed, and appropriate unbiased estimators are identified. Monte Carlo simulation results are used to support the analysis.

A Robust Co-Localisation Measurement Utilising Z-Stack Image Intensity Similarities for Biological Studies

Background: Co-localisation is a widely used measurement in immunohistochemical analysis to determine if fluorescently labelled biological entities, such as cells, proteins or molecules share a same location. However the measurement of co-localisation is challenging due to the complex nature of such fluorescent images, especially when multiple focal planes are captured. The current state-of-art co-localisation measurements of 3-dimensional (3D) image stacks are biased by noise and cross-overs from non-consecutive planes.

Method: In this study, we have developed Co-localisation Intensity Coefficients (CICs) and Co-localisation Binary Coefficients (CBCs), which uses rich z-stack data from neighbouring focal planes to identify similarities between image intensities of two and potentially more fluorescently-labelled biological entities. This was developed using z-stack images from murine organotypic slice cultures from central nervous system tissue, and two sets of pseudo-data. A large amount of non-specific cross-over situations are excluded using this method. This proposed method is also proven to be robust in recognising co-localisations even when images are polluted with a range of noises.

Results: The proposed CBCs and CICs produce robust co-localisation measurements which are easy to interpret, resilient to noise and capable of removing a large amount of false positivity, such as non-specific cross-overs. Performance of this method of measurement is significantly more accurate than existing measurements, as determined statistically using pseudo datasets of known values. This method provides an important and reliable tool for fluorescent 3D neurobiological studies, and will benefit other biological studies which measure fluorescence co-localisation in 3D.

Glycated Hemoglobin and Risk of Death in Diabetic Patients Treated With Hemodialysis: A Meta-analysis

Background: Studies investigating the association between glycated hemoglobin (HbA) level and mortality risk in diabetic patients receiving hemodialysis have shown conflicting results. 
Study Design: We conducted a systematic review and meta-analysis using MEDLINE, EMBASE, Web of Science, and the Cochrane Library. 
Setting & Population: Diabetic patients on maintenance hemodialysis therapy. 
Selection Criteria for Studies: Observational studies or randomized controlled trials investigating the association between HbA values and mortality risk. Study authors were asked to provide anonymized individual patient data or reanalyze results according to a standard template. 
Predictor: Single measurement or mean HbA values. Mean HbA values were calculated using all individual-patient HbA values during the follow-up period of contributing studies. 
Outcome: HR for mortality risk. 
Results: 10 studies (83,684 participants) were included: 9 observational studies and one secondary analysis of a randomized trial. After adjustment for confounders, patients with baseline HbA levels =8.5% (=69 mmol/mol) had increased mortality (7 studies; HR, 1.14; 95% CI, 1.09-1.19) compared with patients with HbA levels of 6.5%-7.4% (48-57 mmol/mol). Likewise, patients with a mean HbA value =8.5% also had a higher adjusted risk of mortality (6 studies; HR,1.29; 95% CI, 1.23-1.35). There was a small but nonsignificant increase in mortality associated with mean HbA levels =5.4% (=36 mmol/mol; 6 studies; HR, 1.09; 95% CI, 0.89-1.34). Sensitivity analyses in incident (=90 days of hemodialysis) and prevalent patients (>90 days of hemodialysis) showed a similar pattern. In incident patients, mean HbA levels =5.4% also were associated with increased mortality risk (4 studies; HR, 1.29; 95% CI, 1.23-1.35). 
Limitations: Observational study data and inability to adjust for diabetes type in all studies. 
Conclusions: Despite concerns about the utility of HbA measurement in hemodialysis patients, high levels (=8.5%) are associated with increased mortality risk. Very low HbA levels (=5.4%) also may be associated with increased mortality risk. 

How secure is a Newtonian paradigm for psychological and educational measurement?

From the early 1900s, some psychologists have attempted to establish their discipline as a quantitative science. In using quantitative methods to investigate their theories, they adopted their own special definition of measurement of attributes such as cognitive abilities, as though they were quantities of the type encountered in Newtonian science. Joel Michell has presented a carefully reasoned argument that psychological attributes lack additivity, and therefore cannot be quantities in the same way as the attributes of classical Newtonian physics. In the early decades of the 20th century, quantum theory superseded Newtonian mechanics as the best model of physical reality. This paper gives a brief, critical overview of the evolution of current measurement practices in psychology, and suggests the need for a transition from a Newtonian to a quantum theoretical paradigm for psychological measurement. Finally, a case study is presented that considers the implications of a quantum theoretical model for educational measurement. In particular, it is argued that, since the OECD’s Programme for International Student Assessment (PISA) is predicated on a Newtonian conception of measurement, this may constrain the extent to which it can make accurate comparisons of the achievements of different education systems.

An Informant Report Behavior Diary for Measuring Temper Outbursts in an Intervention Setting

Temper outbursts are associated with several psychological disorders and comprise a high priority for intervention. However, the low frequency of outbursts presents a challenge for valid measurement. In the present study an informant report behavior diary for measuring temper outbursts was developed and its validity assessed in a case series. Caregivers of 12 individuals with the neurodevelopmental disorder Prader-Willi syndrome (PWS, in which temper outbursts are common) completed a behavior diary over 4 weeks, and a structured interview. Heart rate and movement data were recorded during a sample of the days subject to diary reporting. Individuals with PWS completed self-report ratings of negative emotion experience. Behavior diaries showed high concordance with the component behaviors and duration of temper outbursts reported in structured interviews; but tended to report a lower frequency. For outbursts reported in diaries during physiological recording, heart rate was consistently elevated above a resting state baseline; and was comparable to that recorded during high physical activity. Available self-report data demonstrated correspondence with the diaries but few self-report data were produced. The present results provide critical proof of principle data supporting the concurrent validity of the ecologically valid, resource efficient diaries, which can be exploited in future research.

Measuring critical thinking skills and dispositions in undergraduate students

This thesis investigates critical thinking with a particular focus on measurement in undergraduate students. A higher education context was chosen because many regard critical thinking development as a primary goal for third level education. Nine studies, both cross-sectional and longitudinal in design, were conducted with undergraduate psychology students (N=387), using the California Critical Thinking Disposition Inventory (CCTDI) and the California Critical Thinking Skills Test (CCTST). Studies 1-3 revealed psychometric weaknesses in the CCTDI and revised the scale with factor analysis and reliability analysis to form the CCTDI United Kingdom revision (CCTDI-UK). Study 4 investigated convergent validity and showed significant inter-correlation between the sub-scales of the CCTDI-UK, and significant correlations with the Openness scale of the NEO Personality Inventory (NEO PI-R). The study also provided evidence for improvement in scores on three of the six sub-scales in the CCTDI-UK (Truth-Seeking, Inquisitiveness, Open-Mindedness) during the course of an undergraduate degree. Study 5 explored a two factor structure for critical thinking dispositions. Study 6 used reliability analysis to revise the CCTST to produce the CCTST-UK. Study 7 showed that the CCTST-UK had a moderate correlation with degree attainment and a slightly higher correlation with a test of non-verbal intelligence (Raven’s Advanced Progressive Matrices short form); in addition, the study showed that scores on the CCTST-UK improved during the course of the degree. Studies 8 and 9 investigated the potential of critical thinking for predicting degree attainment. A-levels predicted approximately 10% of the variance of degree attainment while entry level scores on the CCTST-UK predicted an additional 5%. Exit level scores on the CCTST-UK and the Inquisitive sub-scale of the CCTDI-UK were found to be predictors of degree attainment The main conclusions of the thesis were that these tests had significant potential for predicting degree attainment and that they measured a substantial proportion of the theoretical constructs identified by the major authors in critical thinking.

Automated tumor analysis for molecular profiling in lung cancer

The discovery and clinical application of molecular biomarkers in solid tumors, increasingly relies on nucleic acid extraction from FFPE tissue sections and subsequent molecular profiling. This in turn requires the pathological review of haematoxylin & eosin (H&E) stained slides, to ensure sample quality, tumor DNA sufficiency by visually estimating the percentage tumor nuclei and tumor annotation for manual macrodissection. In this study on NSCLC, we demonstrate considerable variation in tumor nuclei percentage between pathologists, potentially undermining the precision of NSCLC molecular evaluation and emphasising the need for quantitative tumor evaluation. We subsequently describe the development and validation of a system called TissueMark for automated tumor annotation and percentage tumor nuclei measurement in NSCLC using computerized image analysis. Evaluation of 245 NSCLC slides showed precise automated tumor annotation of cases using Tissuemark, strong concordance with manually drawn boundaries and identical EGFR mutational status, following manual macrodissection from the image analysis generated tumor boundaries. Automated analysis of cell counts for % tumor measurements by Tissuemark showed reduced variability and significant correlation (p < 0.001) with benchmark tumor cell counts. This study demonstrates a robust image analysis technology that can facilitate the automated quantitative analysis of tissue samples for molecular profiling in discovery and diagnostics.

An integrated 256-point complex FFT processor for real-time spectrum analysis and measurement

This paper describes in detail the design of a custom CMOS Fast Fourier Transform (FFT) processor for computing 256-point complex FFT. The FFT is well suited for real-time spectrum analysis in instrumentation and measurement applications. The FFT butterfly processor consists of one parallel-parallel multiplier and two adders. It is capable of computing one butterfly computation every 100 ns thus it can compute 256-complex point FFT in 25.6 μs excluding data input and output processes.

Quantification of aortic flow by phase-contrast magnetic resonance in patients with bicuspid aortic valve.

AIMS: Bicuspid aortic valve (BAV) causes complex flow patterns in the ascending aorta (AAo), which may compromise the accuracy of flow measurement by phase-contrast magnetic resonance (PC-MR). Therefore, we aimed to assess and compare the accuracy of forward flow measurement in the AAo, where complex flow is more dominant in BAV patients, with flow quantification in the left ventricular outflow tract (LVOT) and the aortic valve orifice (AV), where complex flow is less important, in BAV patients and controls. METHODS AND RESULTS: Flow was measured by PC-MR in 22 BAV patients and 20 controls at the following positions: (i) LVOT, (ii) AV, and (iii) AAo, and compared with the left ventricular stroke volume (LVSV). The correlation between the LVSV and the forward flow in the LVOT, the AV, and the AAo was good in BAV patients (r = 0.97/0.96/0.93; P < 0.01) and controls (r = 0.96/0.93/0.93; P < 0.01). However, in relation with the LVSV, the forward flow in the AAo was mildly underestimated in controls and much more in BAV patients [median (inter-quartile range): 9% (4%/15%) vs. 22% (8%/30%); P < 0.01]. This was not the case in the LVOT and the AV. The severity of flow underestimation in the AAo was associated with flow eccentricity. CONCLUSION: Flow measurement in the AAo leads to an underestimation of the forward flow in BAV patients. Measurement in the LVOT or the AV, where complex flow is less prominent, is an alternative means for quantifying the systolic forward flow in BAV patients.

Evaluation of Reducibility of Trunk Asymmetry in Lateral Bending

The value of the lateral bending test is important in the assessment of spinal curve mobility and prediction of surgical outcome in the treatment of adolescent idiopathic scoliosis (AIS). However, radiographic bending tests are unable to assess the reducibility of trunk asymmetry. This study aims to exploit surface topography measurement in order to evaluate the changes in shape of the trunk (a) between bending and neutral standing positions, and (b) between standing pre- and post-operative visits, in a cohort of adolescents with AIS having undergone surgical correction; and to correlate the differences measured in cases (a) and (b). Our cohort includes 13 patients with right thoracic AIS. Each patient had their 3D trunk surface digitized with a multi-head InSpeck system in standing posture (at the pre-op and post-op visits) and in maximum voluntary right and left bending (at the pre-op visit). We developed a novel trunk shape analysis method which produces a set of inclined trunk cross-sections allowing comparison between different postures. Two asymmetry indices, trunk rotation (TR) and back surface rotation (BSR), were computed in all cases and a statistical analysis was performed. Our correlation study (Pearson test) showed fair correlations in most cases between the changes in side-bending and those post-surgery, with the strongest relationship (p-value < 0.01) when combining the TR measurements from both bendings. These results provide evidence that the bending test can be used to assess trunk asymmetry reducibility. The proposed approach could provide a non-invasive trunk asymmetry reducibility test for routine clinical use in AIS surgery planning.

Characterization of human and instrument related measurement errors

Measurement is the act or the result of a quantitative comparison between a given quantity and a quantity of the same kind chosen as a unit. It is generally agreed that all measurements contain errors. In a measuring system where both a measuring instrument and a human being taking the measurement using a preset process, the measurement error could be due to the instrument, the process or the human being involved. The first part of the study is devoted to understanding the human errors in measurement. For that, selected person related and selected work related factors that could affect measurement errors have been identified. Though these are well known, the exact extent of the error and the extent of effect of different factors on human errors in measurement are less reported. Characterization of human errors in measurement is done by conducting an experimental study using different subjects, where the factors were changed one at a time and the measurements made by them recorded. From the pre‐experiment survey research studies, it is observed that the respondents could not give the correct answers to questions related to the correct values [extent] of human related measurement errors. This confirmed the fears expressed regarding lack of knowledge about the extent of human related measurement errors among professionals associated with quality. But in postexperiment phase of survey study, it is observed that the answers regarding the extent of human related measurement errors has improved significantly since the answer choices were provided based on the experimental study. It is hoped that this work will help users of measurement in practice to better understand and manage the phenomena of human related errors in measurement.

Bacterial, SCFA and gas profiles of a range of food ingredients following in vitro fermentation by human colonic microbiota.

It is now apparent that there is a strong link between health and nutrition and this can be seen clearly when we talk of obesity. The food industry is trying to capitalise on this by adapting high sugar/fat foods to become healthier alternatives. In confectionery food ingredients can be used for a range of purposes including sucrose replacement. Many of these ingredients may also evade digestion in the upper gut and be fermented by the gut microbiota upon entering the colon. This study was designed to screen a range of ingredients and their activities on the gut microbiota. In this study we screened a range of these ingredients in triplicate batch culture fermentations with known prebiotics as controls. Changes in bacteriology were monitored using FISH. SCFA were measured by GC and gas production was assessed during anaerobic batch fermentations. Bacterial enumeration showed significant increases (P ≤ 0.05) in bifidobacteria and lactobacilli with polydextrose and most polyols with no significant increases in Clostridium histolyticum/perfringens. SCFA and gas formation indicated that the substrates added to the fermenters were being utilised by the gut microbiota. It therefore appears these ingredients exert some prebiotic activity in vitro. Further studies, particularly in human volunteers, are necessary.

Suspended and bed load sediment transport dynamics in two lowland UK streams—storm integrated monitoring

A great deal of work recently has focused on suspended and bedload sediment transport, driven primarily by interest in contaminant transfer. However, uncertainties regarding the role of storm events, macrophyte beds and interactions between the two phases of sediment still exist. This paper compares two study sites within the same catchment whose geology varies significantly. The differences in hydrology, suspended sediment (SS) transport and bed load transport that this causes are examined. In addition, a method to predict the mobilization of different size fractions of sediment during given flows is investigated using critical entrainment thresholds.