Development and validation of 'AutoRIF': Software for the automated analysis of radiation-induced foci

Copyright @ 2012 McVean et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.This article has been made available through the Brunel Open Access Publishing Fund.Background: The quantification of radiation-induced foci (RIF) to investigate the induction and subsequent repair of DNA double strands breaks is now commonplace. Over the last decade systems specific for the automatic quantification of RIF have been developed for this purpose, however to ask more mechanistic questions on the spatio-temporal aspects of RIF, an automated RIF analysis platform that also quantifies RIF size/volume and relative three-dimensional (3D) distribution of RIF within individual nuclei, is required. Results: A java-based image analysis system has been developed (AutoRIF) that quantifies the number, size/volume and relative nuclear locations of RIF within 3D nuclear volumes. Our approach identifies nuclei using the dynamic Otsu threshold and RIF by enhanced Laplacian filtering and maximum entropy thresholding steps and, has an application ‘batch optimisation’ process to ensure reproducible quantification of RIF. AutoRIF was validated by comparing output against manual quantification of the same 2D and 3D image stacks with results showing excellent concordance over a whole range of sample time points (and therefore range of total RIF/nucleus) after low-LET radiation exposure. Conclusions: This high-throughput automated RIF analysis system generates data with greater depth of information and reproducibility than that which can be achieved manually and may contribute toward the standardisation of RIF analysis. In particular, AutoRIF is a powerful tool for studying spatio-temporal relationships of RIF using a range of DNA damage response markers and can be run independently of other software, enabling most personal computers to perform image analysis. Future considerations for AutoRIF will likely include more complex algorithms that enable multiplex analysis for increasing combinations of cellular markers.This article is made available through the Brunel Open Access Publishing Fund

Retrieval-induced forgetting as motivated cognition

Recalling information from a particular category can reduce one's memory capability for related, non-retrieved information. This is known as the retrieval-induced forgetting effect (RIF; Anderson et al., 1994). The present paper reviews studies that show that the RIF effect is motivated. More specifically, we describe research showing that the need for closure (NFC; the motivation to attain epistemic certainty; Kruglanski and Webster, 1996) generally enhances the RIF, because this prevents uncertainty and confusion from the intrusion of unwanted memories during selective-retrieval. However, when the content of the to-be-forgotten information serves the retriever's goals, NFC reduces RIF. Overall, the present findings are consistent with the view that motivation can affect the magnitude of RIF effects which, in turn, can serve as a mechanism for reaching preferred conclusion

Labiatae checklist for Andalusia (Southern Spain) and Rif (Northern Morocco)

. Labiatae checklist for Andalusia (Southern Spain) and the Rif (Northern Morocco). The taxa of Labiatae from Andalusia (Southern Iberian Peninsula) and the Rif (Northern Morocco) are included in a checklist, which has about 262 taxa, belonging to 28 genera and 5 subfamilies, representing almost 25% of total Mediterranean Labiatae taxa and c. 70% of total strict Labiatae Mediterranean genera. Nepetoideae with 17 genera is the richest subfamily; Ajugoideae (Ajuga genus), Teucrioideae (Teucrium genus) and Scutellarioideae (Scutellaria genus) are monogenerics. In this biogeographical region, 23 genera and about 70 species are common to both Andalusia and the Rif (about 88% of all genera and 30% of all taxa). Teucrium, Sideritis Satureja and allied genera, Salvia and Mentha, are the most widespread, representing almost 50% of the total taxa. The importance of the Labiatae family in the Andalusia and the Rif regions is reflected by the fact that they make up c. 20% of all taxa, while 25 of the total number of genera are distributed in the Betic-Rif Mountains. In addition, these mountains, are themselves the richest and best endowed regions of the Andalusia and the Rif, with the greatest concentration of endemic species (c. 65% of total endemisms)

Evaluation of Xpert® MTB/RIF and ustar easyNAT™ TB IAD for diagnosis of tuberculous lymphadenitis of children in Tanzania : a prospective descriptive study

Fine needle aspiration biopsy has become a standard approach for diagnosis of peripheral tuberculous lymphadenitis. The aim of this study was to compare the performance of Xpert MTB/RIF and Ustar EasyNAT TB IAD nucleic acid amplification assays, against acid-fast bacilli microscopy, cytology and mycobacterial culture for the diagnosis of TB lymphadenitis in children from a TB-endemic setting in Tanzania.; Children of 8 weeks to 16 years of age, suspected of having TB lymphadenitis, were recruited at a district hospital in Tanzania. Fine needle aspirates of lymph nodes were analysed using acid-fast bacilli microscopy, liquid TB culture, cytology, Xpert MTB/RIF and EasyNAT. Latent class analysis and comparison against a composite reference standard comprising "culture and/or cytology" was done, to assess the performance of Xpert MTB/RIF and EasyNAT for the diagnosis of TB lymphadenitis.; Seventy-nine children were recruited; 4 were excluded from analysis. Against a composite reference standard of culture and/or cytology, Xpert MTB/RIF and EasyNAT had a sensitivity and specificity of 58 % and 93 %; and 19 % and 100 % respectively. Relative to latent class definitions, cytology had a sensitivity of 100 % and specificity of 94.7 %.; Combining clinical assessment, cytology and Xpert MTB/RIF may allow for a rapid and accurate diagnosis of childhood TB lymphadenitis. Larger diagnostic evaluation studies are recommended to validate these findings and on Xpert MTB/RIF to assess its use as a solitary initial test for TB lymphadenitis in children

Use of Xpert MTB/RIF in Decentralized Public Health Settings and Its Effect on Pulmonary TB and DR-TB Case Finding in India

Background Xpert MTB/RIF, the first automated molecular test for tuberculosis, is transforming the diagnostic landscape in high-burden settings. This study assessed the impact of up-front Xpert MTB/RIF testing on detection of pulmonary tuberculosis (PTB) and rifampicin-resistant PTB (DR-TB) cases in India. Methods This demonstration study was implemented in 18 sub-district level TB programme units (TUs) in India in diverse geographic and demographic settings covering a population of 8.8 million. A baseline phase in 14 TUs captured programmatic baseline data, and an intervention phase in 18 TUs had Xpert MTB/RIF offered to all presumptive TB patients. We estimated changes in detection of TB and DR-TB, the former using binomial regression models to adjust for clustering and covariates. Results In the 14 study TUs, which participated in both phases, 10,675 and 70,556 presumptive TB patients were enrolled in the baseline and intervention phase, respectively, and 1,532 (14.4%) and 14,299 (20.3%) bacteriologically confirmed PTB cases were detected. The implementation of Xpert MTB/RIF was associated with increases in both notification rates of bacteriologically confirmed TB cases (adjusted incidence rate ratio [aIRR] 1.39; CI 1.18-1.64), and proportion of bacteriological confirmed TB cases among presumptive TB cases (adjusted risk ratio (aRR) 1.33; CI 1.6-1.52). Compared with the baseline strategy of selective drug-susceptibility testing only for PTB cases at high risk of drug-resistant TB, Xpert MTB/RIF implementation increased rifampicin resistant TB case detection by over fivefold. Among, 2765 rifampicin resistance cases detected, 1055 were retested with conventional drug susceptibility testing (DST). Positive predictive value (PPV) of rifampicin resistance detected by Xpert MTB/RIF was 94.7% (CI 91.3-98.1), in comparison to conventional DST. Conclusion Introduction of Xpert MTB/RIF as initial diagnostic test for TB in public health facilities significantly increased case-notification rates of all bacteriologically confirmed TB by 39% and rifampicin-resistant TB case notification by fivefold

A Generalization of Moufang and Steiner Loops

We study a variety of loops, RIF, which arise naturally from considering inner mapping groups, and a somewhat larger variety, ARIF. All Steiner and Moufang loops are RIF, and all flexible C-loops are ARIF. We show that all ARIF loops are diassociative, thus generalizing Moufang's Theorem.Comment: 19 pp., 1 fig., uses amsart.cls, pifont.sty; to appear in Algebra Universali

Imaging Right Iliac Fossa (RIF) pain

Abdominal pain is one of the most common causes for referral to the emergency department coming second only after chest pain. The RIF is the most common location for abdominal pain. Clinical assessment offers little to as aid the diagnosis of RIF pain. With developments in ultrasound (US) and both spiral and multidetector computed tomography (CT), an accurate diagnosis can be made and unnecessary surgery and potentially lethal complications may be avoided.peer-reviewe

Workflows, processes and technical solutions for seeding the research data commons

Queensland University of Technology (QUT) completed an Australian National Data Service (ANDS) funded “Seeding the Commons Project” to contribute metadata to Research Data Australia. The project employed two Research Data Librarians from October 2009 through to July 2010. Technical support for the project was provided by QUT’s High Performance Computing and Research Support Specialists. ---------- The project identified and described QUT’s category 1 (ARC / NHMRC) research datasets. Metadata for the research datasets was stored in QUT’s Research Data Repository (Architecta Mediaflux). Metadata which was suitable for inclusion in Research Data Australia was made available to the Australian Research Data Commons (ARDC) in RIF-CS format. ---------- Several workflows and processes were developed during the project. 195 data interviews took place in connection with 424 separate research activities which resulted in the identification of 492 datasets. ---------- The project had a high level of technical support from QUT High Performance Computing and Research Support Specialists who developed the Research Data Librarian interface to the data repository that enabled manual entry of interview data and dataset metadata, creation of relationships between repository objects. The Research Data Librarians mapped the QUT metadata repository fields to RIF-CS and an application was created by the HPC and Research Support Specialists to generate RIF-CS files for harvest by the Australian Research Data Commons (ARDC). ---------- This poster will focus on the workflows and processes established for the project including: ---------- • Interview processes and instruments • Data Ingest from existing systems (including mapping to RIF-CS) • Data entry and the Data Librarian interface to Mediaflux • Verification processes • Mapping and creation of RIF-CS for the ARD