On the Benjamini--Hochberg method

We investigate the properties of the Benjamini--Hochberg method for multiple testing and of a variant of Storey's generalization of it, extending and complementing the asymptotic and exact results available in the literature. Results are obtained under two different sets of assumptions and include asymptotic and exact expressions and bounds for the proportion of rejections, the proportion of incorrect rejections out of all rejections and two other proportions used to quantify the efficacy of the method.Comment: Published at http://dx.doi.org/10.1214/009053606000000425 in the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

Responsiveness: a reinvention of the wheel?

BACKGROUND: Since the mid eighties, responsiveness is considered to be a separate property of health status questionnaires distinct from reliability and validity. The aim of the study was to assess the strength of the relationship between internal consistency reliability, referring to an instrument's sensitivity to differences in health status among subjects at one point in time, and responsiveness referring to sensitivity to health status changes over time. METHODS: We used three different datasets comprising the scores of patients on the Barthel, the SIP and the GO-QoL instruments at two points in time. The internal consistency was reduced stepwise by removing the item that contributed most to a scale's reliability. We calculated the responsiveness expressed by the Standardized Response Mean (SRM) on each set of remaining items. The strength of the relationship between the thus obtained internal consistency coefficients and SRMs was quantified by Spearman rank correlation coefficients. RESULTS: Strong to perfect correlations (0.90 – 1.00) was found between internal consistency coefficients and SRMs for all instruments indicating, that the two can be used interchangeably. CONCLUSION: The results contradict the conviction that responsiveness is a separate psychometric property. The internal consistency coefficient adequately reflects an instrument's potential sensitivity to changes over time

Synovial tissue response to rituximab: mechanism of action and identification of biomarkers of response

OBJECTIVE: To investigate the synovial tissue in patients with rheumatoid arthritis (RA) treated with rituximab and to identify possible predictors of clinical response. METHODS: A total of 24 patients with RA underwent synovial biopsy before, 4 and 16 weeks after initiation of rituximab treatment (without peri-infusional corticosteroids to prevent bias). Immunohistochemical analysis was performed and stained sections were analysed by digital image analysis. Linear regression analysis was used to identify predictors of clinical response. RESULTS: The 28-joint Disease Activity Score (DAS28) was unaltered at 4 weeks, but significantly reduced at 16 and 24 weeks. Serum levels of IgM-rheumatoid factor (RF) decreased significantly at 24 weeks and anti-citrullinated peptide antibody (ACPA) levels at 36 weeks. Peripheral blood B cells were depleted at 4 weeks and started to return at 24 weeks. Synovial B cells were significantly decreased at 4 weeks, but were not completely depleted in all patients; there was a further reduction at 16 weeks in some patients. We found a significant decrease in macrophages at 4 weeks, which was more pronounced at 16 weeks. At that timepoint, T cells were also significantly decreased. The reduction of plasma cells predicted clinical improvement at 24 weeks. CONCLUSIONS: The results support the view that B cells orchestrate local cellular infiltration. The kinetics of the serological as well as the tissue response in clinical responders are consistent with the notion that rituximab exerts its effects in part by an indirect effect on plasma cells associated with autoantibody production, which could help explain the delayed response after rituximab treatmen

Statistical models for quantifying diagnostic accuracy with multiple lesions per patient

We propose random-effects models to summarize and quantify the accuracy of the diagnosis of multiple lesions on a single image without assuming independence between lesions. The number of false-positive lesions was assumed to be distributed as a Poisson mixture, and the proportion of true-positive lesions was assumed to be distributed as a binomial mixture. We considered univariate and bivariate, both parametric and nonparametric mixture models. We applied our tools to simulated data and data of a study assessing diagnostic accuracy of virtual colonography with computed tomography in 200 patients suspected of having one or more polyps

A prospective, randomised, placebo-controlled study to identify biomarkers associated with active treatment in psoriatic arthritis: effects of adalimumab treatment on synovial tissue

OBJECTIVE: To determine which of the changes in synovial tissue correlates best with clinical response associated with effective therapy (adalimumab) to facilitate the planning of future studies with therapeutic agents for psoriatic arthritis (PsA). METHODS: A total of 24 patients with active PsA were randomised to receive adalimumab (n = 12) or placebo (n = 12) for 4 weeks. Synovial biopsies were obtained before and after 4 weeks of treatment. Immunohistochemical analysis was performed to characterise the cell infiltrate, expression of cytokines and matrix metalloproteinases (MMPs) and vascularity. Sections were analysed by digital image analysis. Statistical analysis was performed using covariance analysis. RESULTS: The mean Disease Activity Score in 28 joints (DAS28) after 4 weeks was 1.92 units lower (95% confidence interval (CI) 1.07 to 2.77) after adalimumab therapy compared with placebo. Paired pretreatment and post-treatment synovial samples were available from 19 patients. Many cell types were reduced after adalimumab treatment compared to placebo. After applying a ranked analysis of covariance (ANCOVA) model to correct for baseline imbalances, a significant effect of treatment was observed on CD3-positive cells: there was a median reduction of 248 cells/mm(2) after adalimumab versus placebo treatment (p = 0.035). In addition, the expression of MMP13 was significantly reduced after active treatment: the integrated optical density (IOD)/mm(2) was 18 190 lower after adalimumab treatment as compared to placebo (p = 0.033). CONCLUSION: Adalimumab therapy in PsA is associated with a marked reduction in T cell infiltration and MMP13 expression in synovial tissue, suggesting that these parameters could be used as biomarkers that are sensitive to change after active treatment in small proof of concept studies in Ps

Genome-wide methylation patterns in Marfan syndrome

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Aortic distensibility in Marfan syndrome:a potential predictor of aortic events?

Contains fulltext : 239962.pdf (Publisher’s version ) (Open Access

Nasopharyngeal Myoepithelial Carcinoma Mimicking Nasopharyngeal Carcinoma

AbstractMyoepithelial carcinoma (malignant myoepithelioma) (MC) is a rare tumor, defined as a malignant salivary neoplasm composed almost exclusively of tumor cells with myoepithelial differentiation. It can arise in unusual location sites, such as the nasopharynx, and may be difficult to approach. Nasopharyngeal MC can sometimes present as a nasopharyngeal mass which may be mistaken for primary nasopharyngeal carcinoma (NPC). The treatment strategy for nasopharyngeal MC is different from NPC, and maximal surgical resection of the main lesion is still considered as the mainstay of therapy. Herein we present a 32-year-old man with a nasopharyngeal mass which was initially mistaken as NPC, and which was later confirmed as MC after a comprehensive review of the pathology

Validation of prediction models based on lasso regression with multiply imputed data

BACKGROUND: In prognostic studies, the lasso technique is attractive since it improves the quality of predictions by shrinking regression coefficients, compared to predictions based on a model fitted via unpenalized maximum likelihood. Since some coefficients are set to zero, parsimony is achieved as well. It is unclear whether the performance of a model fitted using the lasso still shows some optimism. Bootstrap methods have been advocated to quantify optimism and generalize model performance to new subjects. It is unclear how resampling should be performed in the presence of multiply imputed data. METHOD: The data were based on a cohort of Chronic Obstructive Pulmonary Disease patients. We constructed models to predict Chronic Respiratory Questionnaire dyspnea 6 months ahead. Optimism of the lasso model was investigated by comparing 4 approaches of handling multiply imputed data in the bootstrap procedure, using the study data and simulated data sets. In the first 3 approaches, data sets that had been completed via multiple imputation (MI) were resampled, while the fourth approach resampled the incomplete data set and then performed MI. RESULTS: The discriminative model performance of the lasso was optimistic. There was suboptimal calibration due to over-shrinkage. The estimate of optimism was sensitive to the choice of handling imputed data in the bootstrap resampling procedure. Resampling the completed data sets underestimates optimism, especially if, within a bootstrap step, selected individuals differ over the imputed data sets. Incorporating the MI procedure in the validation yields estimates of optimism that are closer to the true value, albeit slightly too larger. CONCLUSION: Performance of prognostic models constructed using the lasso technique can be optimistic as well. Results of the internal validation are sensitive to how bootstrap resampling is performed

Robotic Ultrasound Guidance by B-scan Plane Positioning Control

AbstractUltrasound is indispensable imaging modality for clinical diagnosis such as fetus assessment and heart assessment. Moreover, many ultrasound applications for image guided procedures have been proposed and attempted because US is less invasive, less cost, and high portability. However, to obtain US images, a US imaging probe has to be held manually and contacted with a patient body. To address the issue, we have proposed a robotic system for automatic probe scanning. The system consists of a probe scanning robot, navigation software, an optical tracking device, and an ultrasound imaging device. The robot, that is six degrees of freedom, is composed of a frame mechanism and a probe holding mechanism. The frame mechanism has six pneumatic actuators to reduce its weight, and the probe holding mechanism has one DC motor. The probe holding mechanism is connected with the pneumatic actuators using wires. Moreover, the robot can control the position and orientation of the B-scan plane based on the transformation between an optical tracker attached to the US probe and the B-scan plane. The navigation system, which is connected with the tracking device and an US imaging device via a VGA cable, computes the relative position between the positions of a therapeutic tool and the B-scan plane, and sends it to the robot. Then the position of the B-scan plane can be controlled based on the tool position. Also, the navigation system displays the plane with a texture of an actual echogram and a tool model three-dimensionally to monitor the relative position of the tool and the B-scan plane. To validate the basic system performance, phantom tests were conducted. The phantom was made of gelatin and poly(ethylene glycol). In the tests, the needle was inserted into the phantom, and the B-scan plane was controlled to contain a tracked needle in real-time. From the results, the needle was continuously visualized during needle insertion. Therefore, it is confirmed that the system has a great potential for automatic US image guided procedures