The Cyclin D1 (CCND1) A870G polymorphism predicts clinical outcome to lapatinib and capecitabine in HER2-positive metastatic breast cancer

BACKGROUND: Lapatinib plus capecitabine emerged as an efficacious therapy in metastatic breast cancer (mBC). We aimed to identify germline single-nucleotide polymorphisms (SNPs) in genes involved in capecitabine catabolism and human epidermal receptor signaling that were associated with clinical outcome to assist in selecting patients likely to benefit from this combination.

PATIENTS AND METHODS: DNA was extracted from 240 of 399 patients enrolled in EGF100151 clinical trial (NCT00078572; clinicaltrials.gov) and SNPs were successfully evaluated in 234 patients. The associations between SNPs and clinical outcome were analyzed using Fisher's exact test, Kaplan-Meier curves, log-rank tests, likelihood ratio test within logistic or Cox regression model, as appropriate.

RESULTS: There were significant interactions between CCND1 A870G and clinical outcome. Patients carrying the A-allele were more likely to benefit from lapatinib plus capecitabine versus capecitabine when compared with patients harboring G/G (P = 0.022, 0.024 and 0.04, respectively). In patients with the A-allele, the response rate (RR) was significantly higher with lapatinib plus capecitabine (35%) compared with capecitabine (11%; P = 0.001) but not between treatments in patients with G/G (RR = 24% and 32%, respectively; P = 0.85). Time to tumor progression (TTP) was longer in patients with the A-allele treated with lapatinib plus capecitabine compared with capecitabine (median TTP = 7.9 and 3.4 months; P < 0.001), but not in patients with G/G (median TTP = 6.1 and 6.6 months; P = 0.92).

CONCLUSION: Our findings suggest that CCND1A870G may be useful in predicting clinical outcome in HER2-positive mBC patients treated with lapatinib plus capecitabine.

Statistical Tests for Joint Analysis of Performance Measures

Recently there has been an increasing interest in the development of new methods using Pareto optimality to deal with multi-objective criteria (for example, accuracy and architectural complexity). Once one has learned a model based on their devised method, the problem is then how to compare it with the state of art. In machine learning, algorithms are typically evaluated by comparing their performance on different data sets by means of statistical tests. Unfortunately, the standard tests used for this purpose are not able to jointly consider performance measures. The aim of this paper is to resolve this issue by developing statistical procedures that are able to account for multiple competing measures at the same time. In particular, we develop two tests: a frequentist procedure based on the generalized likelihood-ratio test and a Bayesian procedure based on a multinomial-Dirichlet conjugate model. We further extend them by discovering conditional independences among measures to reduce the number of parameter of such models, as usually the number of studied cases is very reduced in such comparisons. Real data from a comparison among general purpose classifiers is used to show a practical application of our tests.

Joint Analysis of Multiple Algorithms and Performance Measures

There has been an increasing interest in the development of new methods using Pareto optimality to deal with multi-objective criteria (for example, accuracy and time complexity). Once one has developed an approach to a problem of interest, the problem is then how to compare it with the state of art. In machine learning, algorithms are typically evaluated by comparing their performance on different data sets by means of statistical tests. Standard tests used for this purpose are able to consider jointly neither performance measures nor multiple competitors at once. The aim of this paper is to resolve these issues by developing statistical procedures that are able to account for multiple competing measures at the same time and to compare multiple algorithms altogether. In particular, we develop two tests: a frequentist procedure based on the generalized likelihood-ratio test and a Bayesian procedure based on a multinomial-Dirichlet conjugate model. We further extend them by discovering conditional independences among measures to reduce the number of parameters of such models, as usually the number of studied cases is very reduced in such comparisons. Data from a comparison among general purpose classifiers is used to show a practical application of our tests.

Diagnostic accuracy of loop-mediated isothermal amplification as a near-patient test for meningococcal disease in children: An observational cohort study

Background: Diagnosis of meningococcal disease relies on recognition of clinical signs and symptoms that are notoriously non-specific, variable, and often absent in the early stages of the disease. Loop-mediated isothermal amplification (LAMP) has previously been shown to be fast and effective for the molecular detection of meningococcal DNA in clinical specimens. We aimed to assess the diagnostic accuracy of meningococcal LAMP as a near-patient test in the emergency department.

Methods: For this observational cohort study of diagnostic accuracy, children aged 0-13 years presenting to the emergency department of the Royal Belfast Hospital for Sick Children (Belfast, UK) with suspected meningococcal disease were eligible for inclusion. Patients underwent a standard meningococcal pack of investigations testing for meningococcal disease. Respiratory (nasopharyngeal swab) and blood specimens were collected from patients and tested with near-patient meningococcal LAMP and the results were compared with those obtained by reference laboratory tests (culture and PCR of blood and cerebrospinal fluid).

Findings: Between Nov 1, 2009, and Jan 31, 2012, 161 eligible children presenting at the hospital underwent the meningococcal pack of investigations and were tested for meningococcal disease, of whom 148 consented and were enrolled in the study. Combined testing of respiratory and blood specimens with use of LAMP was accurate (sensitivity 89% [95% CI 72-96], specificity 100% [97-100], positive predictive value 100% [85-100]; negative predictive value 98% [93-99]) and diagnostically useful (positive likelihood ratio 213 [95% CI 13-infinity] and negative likelihood ratio 0·11 [0·04-0·32]). The median time required for near-patient testing from sample to result was 1 h 26 min (IQR 1 h 20 min-1 h 32 min).

Interpretation: Meningococcal LAMP is straightforward enough for use in any hospital with basic laboratory facilities, and near-patient testing with this method is both feasible and effective. By contrast with existing UK National Institute of Health and Care Excellence guidelines, we showed that molecular testing of non-invasive respiratory specimens from children is diagnostically accurate and clinically useful.

Monitoring growth in asthmatic children treated with high dose inhaled glucocorticoids does not predict adrenal suppression

Aims: To determine whether routine outpatient monitoring of growth predicts adrenal suppression in prepubertal children treated with high dose inhaled glucocorticoid.

Methods: Observational study of 35 prepubertal children (aged 4–10 years) treated with at least 1000 µg/day of inhaled budesonide or equivalent potency glucocorticoid for at least six months. Main outcome measures were: changes in HtSDS over 6 and 12 month periods preceding adrenal function testing, and increment and peak cortisol after stimulation by low dose tetracosactrin test. Adrenal suppression was defined as a peak cortisol 500 nmol/l.

Results: The areas under the receiver operator characteristic curves for a decrease in HtSDS as a predictor of adrenal insufficiency 6 and 12 months prior to adrenal testing were 0.50 (SE 0.10) and 0.59 (SE 0.10). Prediction values of an HtSDS change of –0.5 for adrenal insufficiency at 12 months prior to testing were: sensitivity 13%, specificity 95%, and positive likelihood ratio of 2.4. Peak cortisol reached correlated poorly with change in HtSDS ( = 0.23, p = 0.19 at 6 months; = 0.33, p = 0.06 at 12 months).

Conclusions: Monitoring growth does not enable prediction of which children treated with high dose inhaled glucocorticoids are at risk of potentially serious adrenal suppression. Both growth and adrenal function should be monitored in patients on high dose inhaled glucocorticoids. Further research is required to determine the optimal frequency of monitoring adrenal function.

The structure of the Statistics Anxiety Rating Scale: A confirmatory factor analysis using UK psychology students

This study aimed to examine the structure of the statistics anxiety rating scale. Responses from 650 undergraduate psychology students throughout the UK were collected through an on-line study. Based on previous research three different models were specified and estimated using confirmatory factor analysis. Fit indices were used to determine if the model fitted the data and a likelihood ratio difference test was used to determine the best fitting model. The original six factor model was the best explanation of the data. All six subscales were intercorrelated and internally consistent. It was concluded that the statistics anxiety rating scale was found to measure the six subscales it was designed to assess in a UK population.

Sedentary behaviour and physical activity in bronchiectasis: a cross-sectional study

BACKGROUND: The impact of bronchiectasis on sedentary behaviour and physical activity is unknown. It is important to explore this to identify the need for physical activity interventions and how to tailor interventions to this patient population. We aimed to explore the patterns and correlates of sedentary behaviour and physical activity in bronchiectasis.

METHODS: Physical activity was assessed in 63 patients with bronchiectasis using an ActiGraph GT3X+ accelerometer over seven days. Patients completed: questionnaires on health-related quality-of-life and attitudes to physical activity (questions based on an adaption of the transtheoretical model (TTM) of behaviour change); spirometry; and the modified shuttle test (MST). Multiple linear regression analysis using forward selection based on likelihood ratio statistics explored the correlates of sedentary behaviour and physical activity dimensions. Between-group analysis using independent sample t-tests were used to explore differences for selected variables.

RESULTS: Fifty-five patients had complete datasets. Average daily time, mean(standard deviation) spent in sedentary behaviour was 634(77)mins, light-lifestyle physical activity was 207(63)mins and moderate-vigorous physical activity (MVPA) was 25(20)mins. Only 11% of patients met recommended guidelines. Forced expiratory volume in one-second percentage predicted (FEV1% predicted) and disease severity were not correlates of sedentary behaviour or physical activity. For sedentary behaviour, decisional balance 'pros' score was the only correlate. Performance on the MST was the strongest correlate of physical activity. In addition to the MST, there were other important correlate variables for MVPA accumulated in ≥10-minute bouts (QOL-B Social Functioning) and for activity energy expenditure (Body Mass Index and QOL-B Respiratory Symptoms).

CONCLUSIONS: Patients with bronchiectasis demonstrated a largely inactive lifestyle and few met the recommended physical activity guidelines. Exercise capacity was the strongest correlate of physical activity, and dimensions of the QOL-B were also important. FEV1% predicted and disease severity were not correlates of sedentary behaviour or physical activity. The inclusion of a range of physical activity dimensions could facilitate in-depth exploration of patterns of physical activity. This study demonstrates the need for interventions targeted at reducing sedentary behaviour and increasing physical activity, and provides information to tailor interventions to the bronchiectasis population.

Rarity, pseudodiagnosticity and Bayesian reasoning

Three experiments investigated the effect of rarity on people's selection and interpretation of data in a variant of the pseudodiagnosticity task. For familiar (Experiment 1) but not for arbitrary (Experiment 3) materials, participants were more likely to select evidence so as to complete a likelihood ratio when the initial evidence they received was a single likelihood concerning a rare feature. This rarity effect with familiar materials was replicated in Experiment 2 where it was shown that participants were relatively insensitive to explicit manipulations of the likely diagnosticity of rare evidence. In contrast to the effects for data selection, there was an effect of rarity on confidence ratings after receipt of a single likelihood for arbitrary but not for familiar materials. It is suggested that selecting diagnostic evidence necessitates explicit consideration of the alternative hypothesis and that consideration of the possible consequences of the evidence for the alternative weakens the rarity effect in confidence ratings. Paradoxically, although rarity effects in evidence selection and confidence ratings are in the spirit of Bayesian reasoning, the effect on confidence ratings appears to rely on participants thinking less about the alternative hypothesis.

Background beliefs and evidence interpretation

In this paper we argue that it is often adaptive to use one’s background beliefs when interpreting information that, from a normative point of view, is incomplete. In both of the experiments reported here participants were presented with an item possessing two features and were asked to judge, in the light of some evidence concerning the features, to which of two categories it was more likely that the item belonged. It was found that when participants received evidence relevant to just one of these hypothesised categories (i.e. evidence that did not form a Bayesian likelihood ratio) they used their background beliefs to interpret this information. In Experiment 2, on the other hand, participants behaved in a broadly Bayesian manner when the evidence they received constituted a completed likelihood ratio. We discuss the circumstances under which participants, when making their judgements, consider the alternative hypothesis. We conclude with a discussion of the implications of our results for an understanding of hypothesis testing, belief revision, and categorisation.

Novel biomarkers in early diagnosis of acute myocardial infarction compared with cardiac troponin T

Aims: To evaluate the role of novel biomarkers in early detection of acute myocardial infarction (MI) in patients admitted with acute chest pain.
Methods and results: A prospective study of 664 patients presenting to two coronary care units with chest pain was conducted over 3 years from 2003. Patients were assessed on admission: clinical characteristics, ECG (electrocardiogram), renal function, cardiac troponin T (cTnT), heart fatty acid binding protein (H-FABP), glycogen phosphorylase-BB, NT-pro-brain natriuretic peptide, D-dimer, hsCRP (high sensitivity C-reactive protein), myeloperoxidase, matrix metalloproteinase-9, pregnancy associated plasma protein-A, soluble CD40 ligand. A =12 h cTnT sample was also obtained. MI was defined as cTnT = 0.03 µg/L. In patients presenting <4 h of symptom onset, sensitivity of H-FABP for MI was significantly higher than admission cTnT (73 vs. 55%; P = 0.043). Specificity of H-FABP was 71%. None of the other biomarkers challenged cTnT. Combined use of H-FABP and cTnT (either one elevated initially) significantly improved the sensitivities of H-FABP or cTnT (85%; P = 0.004). This combined approach also improved the negative predictive value, negative likelihood ratio, and the risk ratio.
Conclusion: Assessment of H-FABP within the first 4 h of symptoms is superior to cTnT for detection of MI, and is a useful additional biomarker for patients with acute chest pain.

Observational tests of interstellar methanol formation

Context. It has been established that the classical gas-phase production of interstellar methanol (CH3OH) cannot explain observed abundances. Instead it is now generally thought that the main formation path has to be by successive hydrogenation of solid CO on interstellar grain surfaces. Aims. While theoretical models and laboratory experiments show that methanol is efficiently formed from CO on cold grains, our aim is to test this scenario by astronomical observations of gas associated with young stellar objects (YSOs). Methods. We have observed the rotational transition quartets J = 2K – 1K of 12CH3OH and 13CH3OH at 96.7 and 94.4 GHz, respectively, towards a sample of massive YSOs in different stages of evolution. In addition, the J = 1-0 transitions of 12C18O and 13C18O were observed towards some of these sources. We use the 12C/13C ratio to discriminate between gas-phase and grain surface origin: If methanol is formed from CO on grains, the ratios should be similar in CH3OH and CO. If not, the ratio should be higher in CH3OH due to 13C fractionation in cold CO gas. We also estimate the abundance ratios between the nuclear spin types of methanol (E and A). If methanol is formed on grains, this ratio is likely to have been thermalized at the low physical temperature of the grain, and therefore show a relative over-abundance of A-methanol. Results. We show that the 12C/13C isotopic ratio is very similar in gas-phase CH3OH and C18O, on the spatial scale of about 40 arcsec, towards four YSOs. For two of our sources we find an overabundance of A-methanol as compared to E-methanol, corresponding to nuclear spin temperatures of 10 and 16 K. For the remaining five sources, the methanol E/A ratio is less than unity. Conclusions. While the 12C/13C ratio test is consistent with methanol formation from hydrogenation of CO on grain surfaces, the result of the E/A ratio test is inconclusive.

Second-to-Fourth Digit Ratio and Impulsivity: A Comparison between Offenders and Nonoffenders

Personality characteristics, particularly impulsive tendencies, have long been conceived as the primary culprit in delinquent behavior. One crucial question to emerge from this line of work is whether impulsivity has a biological basis. To test this possibility, 44 male offenders and 46 nonoffenders completed the Eysenck Impulsivity Questionnaire, and had their 2D:4D ratio measured. Offenders exhibited smaller right hand digit ratio measurements compared to non-offenders, but higher impulsivity scores. Both impulsivity and 2D:4D ratio measurements significantly predicted criminality (offenders vs. nonoffenders). Controlling for education level, the 2D:4D ratio measurements had remained a significant predictor of criminality, while impulsivity scores no longer predicted criminality significantly. Our data, thus, indicates that impulsivity but not 2D:4D ratio measurements relate to educational attainment. As offenders varied in their number of previous convictions and the nature of their individual crimes, we also tested for differences in 2D:4D ratio and impulsivity among offenders. Number of previous convictions did not correlate significantly with the 2D:4D ratio measurements or impulsivity scores. Our study established a link between a biological marker and impulsivity among offenders (and lack thereof among non-offenders), which emphasise the importance of studying the relationship between biological markers, impulsivity and criminal behavior.

Detectability of bovine TB using the tuberculin skin test does not vary significantly according to pathogen genotype within Northern Ireland

Strains of many infectious diseases differ in parameters that influence epidemic spread, for example virulence, transmissibility, detectability and host specificity. Knowledge of inter-strain variation can be exploited to improve management and decrease disease incidence. Bovine tuberculosis (bTB) is increasingly prevalent among farmed cattle in the UK, exerting a heavy economic burden on the farming industry and government. We aimed to determine whether strains of Mycobacterium bovis (the causative agent of bTB) identified and classified using genetic markers (spoligotyping and multi-locus VNTR analysis) varied in response to the tuberculin skin test; this being the primary method of bTB detection used in the UK. Inter-strain variation in detectability of M. bovis could have important implications for disease control. The skin test is based on a differential delayed type hypersensitivity (DTH) response to intradermal injections of purified protein derivative (PPD) from M. bovis (PPD-B) and Mycobacterium avium (PPD-A). We searched for an association between skin test response (PPD-B skin rise minus PPD-A skin rise) and M. bovis genotype at the disclosing test in culture-confirmed cases using a field dataset consisting of 21,000 isolates belonging to 63 genotypes of M. bovis from cattle in Northern Ireland. We found no substantial variation among genotypes (estimated responses clustered tightly around the mean) controlling for animal sex, breed and test effects. We also estimated the ratio of skin test detected to undetected cases (i.e. cases only detected at abattoir). The skin test detection ratio varied among abattoirs with some detecting a greater proportion of cases than others but this variation was unrelated to the community composition of genotypes within each abattoir catchment. These two lines of evidence indicate that M. bovis genotypes in Northern Ireland have similar detectability using the skin test.

Optical coherence tomography for the diagnosis, monitoring and guiding of treatment for neovascular age-related macular degeneration:a systematic review and economic evaluation

BACKGROUND: Age-related macular degeneration is the most common cause of sight impairment in the UK. In neovascular age-related macular degeneration (nAMD), vision worsens rapidly (over weeks) due to abnormal blood vessels developing that leak fluid and blood at the macula.

OBJECTIVES: To determine the optimal role of optical coherence tomography (OCT) in diagnosing people newly presenting with suspected nAMD and monitoring those previously diagnosed with the disease.

DATA SOURCES: Databases searched: MEDLINE (1946 to March 2013), MEDLINE In-Process & Other Non-Indexed Citations (March 2013), EMBASE (1988 to March 2013), Biosciences Information Service (1995 to March 2013), Science Citation Index (1995 to March 2013), The Cochrane Library (Issue 2 2013), Database of Abstracts of Reviews of Effects (inception to March 2013), Medion (inception to March 2013), Health Technology Assessment database (inception to March 2013).

REVIEW METHODS: Types of studies: direct/indirect studies reporting diagnostic outcomes.

INDEX TEST: time domain optical coherence tomography (TD-OCT) or spectral domain optical coherence tomography (SD-OCT).

COMPARATORS: clinical evaluation, visual acuity, Amsler grid, colour fundus photographs, infrared reflectance, red-free images/blue reflectance, fundus autofluorescence imaging, indocyanine green angiography, preferential hyperacuity perimetry, microperimetry. Reference standard: fundus fluorescein angiography (FFA). Risk of bias was assessed using quality assessment of diagnostic accuracy studies, version 2. Meta-analysis models were fitted using hierarchical summary receiver operating characteristic curves. A Markov model was developed (65-year-old cohort, nAMD prevalence 70%), with nine strategies for diagnosis and/or monitoring, and cost-utility analysis conducted. NHS and Personal Social Services perspective was adopted. Costs (2011/12 prices) and quality-adjusted life-years (QALYs) were discounted (3.5%). Deterministic and probabilistic sensitivity analyses were performed.

RESULTS: In pooled estimates of diagnostic studies (all TD-OCT), sensitivity and specificity [95% confidence interval (CI)] was 88% (46% to 98%) and 78% (64% to 88%) respectively. For monitoring, the pooled sensitivity and specificity (95% CI) was 85% (72% to 93%) and 48% (30% to 67%) respectively. The FFA for diagnosis and nurse-technician-led monitoring strategy had the lowest cost (£39,769; QALYs 10.473) and dominated all others except FFA for diagnosis and ophthalmologist-led monitoring (£44,649; QALYs 10.575; incremental cost-effectiveness ratio £47,768). The least costly strategy had a 46.4% probability of being cost-effective at £30,000 willingness-to-pay threshold.

LIMITATIONS: Very few studies provided sufficient information for inclusion in meta-analyses. Only a few studies reported other tests; for some tests no studies were identified. The modelling was hampered by a lack of data on the diagnostic accuracy of strategies involving several tests.

CONCLUSIONS: Based on a small body of evidence of variable quality, OCT had high sensitivity and moderate specificity for diagnosis, and relatively high sensitivity but low specificity for monitoring. Strategies involving OCT alone for diagnosis and/or monitoring were unlikely to be cost-effective. Further research is required on (i) the performance of SD-OCT compared with FFA, especially for monitoring but also for diagnosis; (ii) the performance of strategies involving combinations/sequences of tests, for diagnosis and monitoring; (iii) the likelihood of active and inactive nAMD becoming inactive or active respectively; and (iv) assessment of treatment-associated utility weights (e.g. decrements), through a preference-based study.

STUDY REGISTRATION: This study is registered as PROSPERO CRD42012001930.

FUNDING: The National Institute for Health Research Health Technology Assessment programme.

The effect of variability in the powder/liquid ratio on the strength of zinc phosphate cement

Aim. To investigate (a) variability in powder/liquid proportioning and (b) effect of variability on diametral tensile strength (DTS), in a zinc phosphate cement. Statistical analyses (α = 0.05) were by Student's t-test in the case of powder/liquid ratio and one-way ANOVA and Tukey HSD for pair-wise comparisons of mean DTS. The Null hypotheses were that (a) the powder-liquid mixing ratios would not differ from the manufacturer's recommended ratio (b) DTS of the set cement samples using the extreme powder/liquid ratios would not differ from those made using the recommended ratio. 

Methodology. 34 dental students dispensed the components according to the manufacturer's instructions. The maximum and minimum powder/liquid ratios, together with the manufacturer's recommended ratio, were used to prepare samples for DTS testing. 

Results. Powder/liquid ratios ranged from 2.386 to 1.018. The mean ratio (1.644) was not significantly different from the recommended value of 1.718 (P = 0.189). DTS values for the maximum and minimum ratios were both significantly different from each other (P < 0.001) and from the mean value obtained from the recommended ratio (P < 0.001). 

Conclusions. Variability exists in powder/liquid ratio for hand dispensed zinc phosphate cement. This variability can affect the DTS of the set material.