Full publication of results initially presented in abstracts

BACKGROUND: Abstracts of presentations at scientific meetings are usually available only in conference proceedings. If subsequent full publication of abstract results is based on the magnitude or direction of study results, publication bias may result. Publication bias, in turn, creates problems for those conducting systematic reviews or relying on the published literature for evidence. OBJECTIVES: To determine the rate at which abstract results are subsequently published in full, and the time between meeting presentation and full publication. To assess the association between study characteristics and full publication. SEARCH STRATEGY: We searched MEDLINE, EMBASE, The Cochrane Library, Science Citation Index, reference lists, and author files. Date of most recent search: June 2003. SELECTION CRITERIA: We included all reports that examined the subsequent full publication rate of biomedical results initially presented as abstracts or in summary form. Follow-up of abstracts had to be at least two years. DATA COLLECTION AND ANALYSIS: Two reviewers extracted data. We calculated the weighted mean full publication rate and time to full publication. Dichotomous variables were analyzed using relative risk and random effects models. We assessed time to publication using Kaplan-Meier survival analyses. MAIN RESULTS: Combining data from 79 reports (29,729 abstracts) resulted in a weighted mean full publication rate of 44.5% (95% confidence interval (CI) 43.9 to 45.1). Survival analyses resulted in an estimated publication rate at 9 years of 52.6% for all studies, 63.1% for randomized or controlled clinical trials, and 49.3% for other types of study designs.'Positive' results defined as any 'significant' result showed an association with full publication (RR = 1.30; CI 1.14 to 1.47), as did 'positive' results defined as a result favoring the experimental treatment (RR =1.17; CI 1.02 to 1.35), and 'positive' results emanating from randomized or controlled clinical trials (RR = 1.18, CI 1.07 to 1.30).Other factors associated with full publication include oral presentation (RR = 1.28; CI 1.09 to 1.49); acceptance for meeting presentation (RR = 1.78; CI 1.50 to 2.12); randomized trial study design (RR = 1.24; CI 1.14 to 1.36); and basic research (RR = 0.79; CI 0.70 to 0.89). Higher quality of abstracts describing randomized or controlled clinical trials was also associated with full publication (RR = 1.30, CI 1.00 to 1.71). AUTHORS' CONCLUSIONS: Only 63% of results from abstracts describing randomized or controlled clinical trials are published in full. 'Positive' results were more frequently published than not 'positive' results.

Generalized fuzzy clustering for segmentation of multi-spectral magnetic resonance images.

An integrated approach for multi-spectral segmentation of MR images is presented. This method is based on the fuzzy c-means (FCM) and includes bias field correction and contextual constraints over spatial intensity distribution and accounts for the non-spherical cluster's shape in the feature space. The bias field is modeled as a linear combination of smooth polynomial basis functions for fast computation in the clustering iterations. Regularization terms for the neighborhood continuity of intensity are added into the FCM cost functions. To reduce the computational complexity, the contextual regularizations are separated from the clustering iterations. Since the feature space is not isotropic, distance measure adopted in Gustafson-Kessel (G-K) algorithm is used instead of the Euclidean distance, to account for the non-spherical shape of the clusters in the feature space. These algorithms are quantitatively evaluated on MR brain images using the similarity measures.

3D MPRAGE improves classification of cortical lesions in multiple sclerosis.

BACKGROUND: Gray matter lesions are known to be common in multiple sclerosis (MS) and are suspected to play an important role in disease progression and clinical disability. A combination of magnetic resonance imaging (MRI) techniques, double-inversion recovery (DIR), and phase-sensitive inversion recovery (PSIR), has been used for detection and classification of cortical lesions. This study shows that high-resolution three-dimensional (3D) magnetization-prepared rapid acquisition with gradient echo (MPRAGE) improves the classification of cortical lesions by allowing more accurate anatomic localization of lesion morphology. METHODS: 11 patients with MS with previously identified cortical lesions were scanned using DIR, PSIR, and 3D MPRAGE. Lesions were identified on DIR and PSIR and classified as purely intracortical or mixed. MPRAGE images were then examined, and lesions were re-classified based on the new information. RESULTS: The high signal-to-noise ratio, fine anatomic detail, and clear gray-white matter tissue contrast seen in the MPRAGE images provided superior delineation of lesion borders and surrounding gray-white matter junction, improving classification accuracy. 119 lesions were identified as either intracortical or mixed on DIR/PSIR. In 89 cases, MPRAGE confirmed the classification by DIR/PSIR. In 30 cases, MPRAGE overturned the original classification. CONCLUSION: Improved classification of cortical lesions was realized by inclusion of high-spatial resolution 3D MPRAGE. This sequence provides unique detail on lesion morphology that is necessary for accurate classification.

Improved cerebellar tissue classification on magnetic resonance images of brain.

PURPOSE: To develop and implement a method for improved cerebellar tissue classification on the MRI of brain by automatically isolating the cerebellum prior to segmentation. MATERIALS AND METHODS: Dual fast spin echo (FSE) and fluid attenuation inversion recovery (FLAIR) images were acquired on 18 normal volunteers on a 3 T Philips scanner. The cerebellum was isolated from the rest of the brain using a symmetric inverse consistent nonlinear registration of individual brain with the parcellated template. The cerebellum was then separated by masking the anatomical image with individual FLAIR images. Tissues in both the cerebellum and rest of the brain were separately classified using hidden Markov random field (HMRF), a parametric method, and then combined to obtain tissue classification of the whole brain. The proposed method for tissue classification on real MR brain images was evaluated subjectively by two experts. The segmentation results on Brainweb images with varying noise and intensity nonuniformity levels were quantitatively compared with the ground truth by computing the Dice similarity indices. RESULTS: The proposed method significantly improved the cerebellar tissue classification on all normal volunteers included in this study without compromising the classification in remaining part of the brain. The average similarity indices for gray matter (GM) and white matter (WM) in the cerebellum are 89.81 (+/-2.34) and 93.04 (+/-2.41), demonstrating excellent performance of the proposed methodology. CONCLUSION: The proposed method significantly improved tissue classification in the cerebellum. The GM was overestimated when segmentation was performed on the whole brain as a single object.

Refinement of experimental design and conduct in laboratory animal research.

The scientific literature of laboratory animal research is replete with papers reporting poor reproducibility of results as well as failure to translate results to clinical trials in humans. This may stem in part from poor experimental design and conduct of animal experiments. Despite widespread recognition of these problems and implementation of guidelines to attenuate them, a review of the literature suggests that experimental design and conduct of laboratory animal research are still in need of refinement. This paper will review and discuss possible sources of biases, highlight advantages and limitations of strategies proposed to alleviate them, and provide a conceptual framework for improving the reproducibility of laboratory animal research.

The business management strategy of Iran's large apparel firms : overview of results from a questionnaire survey and interviews 2009-2011

This paper is an overview of the results from a questionnaire survey and subsequent supplementary interviews of Iran's large apparel firms conducted by the author in 2009-2011. Most of the large apparel firms in Iran are based in Tehran and have been in business for some twenty years. They have a solid business with regular customers, but in general have hesitated to expand the size of their firms. Following the relaxation of restrictions on the procurement of raw materials that existed in the 1990s, the results of survey and interviews show that the firms have developed new channels of procurement although they depend to a considerable degree on imported raw materials and machinery. They have managed to maintain their level of output even with the rapid increase in imports since 2000, although the number of firms has decreased. Low-priced Chinese products have basically not been their rivals; instead, the inflow of foreign name-brand products have hit them heavily.

CFD modelling of the interaction between the Surface Boundary Layer and rotor wake. Comparison of results obtained with different turbulence models and mesh strategies

A simplified CFD wake model based on the actuator disk concept is used to simulate the wind turbine, represented by a disk upon which a distribution of forces, defined as axial momentum sources, are applied on the incoming non-uniform flow. The rotor is supposed to be uniformly loaded, with the exerted forces function of the incident wind speed, the thrust coefficient and the rotor diameter. The model is tested under different parameterizations of turbulence models and validated through experimental measurements downwind of a wind turbine in terms of wind speed deficit and turbulence intensity.

Radiation heat savings in polysilicon production: validation of results through a CVD laboratory prototype

This work aims at a deeper understanding of the energy loss phenomenon in polysilicon production reactors by the so-called Siemens process. Contributions to the energy consumption of the polysilicon deposition step are studied in this paper, focusing on the radiation heat loss phenomenon. A theoretical model for radiation heat loss calculations is experimentally validated with the help of a laboratory CVD prototype. Following the results of the model, relevant parameters that directly affect the amount of radiation heat losses are put forward. Numerical results of the model applied to a state-of-the-art industrial reactor show the influence of these parameters on energy consumption due to radiation per kilogram of silicon produced; the radiation heat loss can be reduced by 3.8% when the reactor inner wall radius is reduced from 0.78 to 0.70 m, by 25% when the wall emissivity is reduced from 0.5 to 0.3, and by 12% when the final rod diameter is increased from 12 to 15 cm.

Enhanced reproducibility of SADI web service workflows with Galaxy and Docke

Background: Semantic Web technologies have been widely applied in the life sciences, for example by data providers such as OpenLifeData and through web services frameworks such as SADI. The recently reported OpenLifeData2SADI project offers access to the vast OpenLifeData data store through SADI services. Findings: This article describes how to merge data retrieved from OpenLifeData2SADI with other SADI services using the Galaxy bioinformatics analysis platform, thus making this semantic data more amenable to complex analyses. This is demonstrated using a working example, which is made distributable and reproducible through a Docker image that includes SADI tools, along with the data and workflows that constitute the demonstration. Conclusions: The combination of Galaxy and Docker offers a solution for faithfully reproducing and sharing complex data retrieval and analysis workflows based on the SADI Semantic web service design patterns.

Effects of the Heartbeat Wales programme over five years on behavioural risks for cardiovascular disease: quasi-experimental comparison of results from Wales and a matched reference area

Objective: To assess the net 5 year effects of intervention of a community based demonstration project, the Heartbeat Wales programme, on modifiable behavioural risks for prevention of cardiovascular disease.