Guidelines and considerations for conducting experiments using tissue microarrays

Tissue microarrays (TMAs) represent a powerful method for undertaking large‐scale tissue‐based biomarker studies. While TMAs offer several advantages, there are a number of issues specific to their use which need to be considered when employing this method. Given the investment in TMA‐based research, guidance on design and execution of experiments will be of benefit and should help researchers new to TMA‐based studies to avoid known pitfalls. Furthermore, a consensus on quality standards for TMA‐based experiments should improve the robustness and reproducibility of studies, thereby increasing the likelihood of identifying clinically useful biomarkers. In order to address these issues, the National Cancer Research Institute Biomarker and Imaging Clinical Studies Group organized a 1‐day TMA workshop held in Nottingham in May 2012. The document herein summarizes the conclusions from the workshop. It includes guidance and considerations on all aspects of TMA‐based research, including the pre‐analytical stages of experimental design, the analytical stages of data acquisition, and the postanalytical stages of data analysis. A checklist is presented which can be used both for planning a TMA experiment and interpreting the results of such an experiment. For studies of cancer biomarkers, this checklist could be used as a supplement to the REMARK guidelines.     

Performance of Older Depressed Patients on Two Cognitive Malingering Tests: False Positive Rates for the Rey 15-item Memorization and Dot Counting Tests

To our knowledge, no investigations have been undertaken to determine whether depression impacts performance on two commonly used tests to detect malingering of cognitive symptoms, the Rey 15-item Memorization Test and the Rey Dot Counting Test. This is a critical issue because of the high rate of depressive symptoms in patients with neurological conditions. It was hypothesized that depressed individuals, especially those with more severe depression, might be at risk for failing the tests, because these patients exhibit mild deficits in mental speed, visual perceptual/spatial skills, and visual memory, abilities required for successful completion of the malingering tests. However, examination of test performance in 64 older participants with major depression generally revealed very low false positive rates for most test scores, and severity of depression was unrelated to test scores. These results add to accumulating data supporting the validity of these cognitive malingering tests by documenting few false positive identifications.     

Predicting prostate tumour location from multiparametric MRI using Gaussian kernel support vector machines: a preliminary study

The performance of a support vector machine (SVM) algorithm was investigated to predict prostate tumour location using multi-parametric MRI (mpMRI) data. The purpose was to obtain information of prostate tumour location for the implementation of bio-focused radiotherapy. In vivo mpMRI data were collected from 16 patients prior to radical prostatectomy. Sequences included T2-weighted imaging, diffusion-weighted imaging and dynamic contrast enhanced imaging. In vivo mpMRI was registered with ‘ground truth’ histology, using ex vivo MRI as an intermediate registration step to improve accuracy. Prostate contours were delineated by a radiation oncologist and tumours were annotated on histology by a pathologist. Five patients with minimal imaging artefacts were selected for this study. A Gaussian kernel SVM was trained and tested on different patient data subsets. Parameters were optimised using leave-oneout cross validation. Signal intensities of mpMRI were used as features and histology annotations as true labels. Prediction accuracy, as well as area under the curve (AUC) of the receiver operating characteristics (ROC) curve, were used to assess performance. Results demonstrated the prediction accuracy ranged from 70.4 to 87.1% and AUC of ROC ranged from 0.81 to 0.94. Additional investigations showed the apparent diffusion coefficient map from diffusion weighted imaging was the most important imaging modality for predicting tumour location. Future work will incorporate additional patient data into the framework to increase the sensitivity and specificity of the model, and will be extended to incorporate predictions of biological characteristics of the tumour which will be used in bio-focused radiotherapy optimisation.     

Elevated lactoferrin is associated with moderate to severe Clostridium difficile disease, stool toxin, and 027 infection

We evaluated blood and fecal biomarkers as indicators of severity in symptomatic patients with confirmed Clostridium difficile infection (CDI). Recruitment included patients with CDI based on clinical symptoms and supporting laboratory findings. Disease severity was defined by physician’s assessment and blood and fecal biomarkers were measured. Toxigenic culture done using spore enrichment and toxin B detected by tissue culture were done as confirmatory tests. Polymerase chain reaction (PCR) ribotyping was performed on each isolate. There were 98 patients recruited, with 85 (87 %) confirmed cases of toxigenic CDI (21 severe, 57 moderate, and seven mild), of which 68 (80 %) were also stool toxin-positive. Elevated lactoferrin (p?=?0.01), increased white blood cell (WBC) count (p?=?0.08), and low serum albumin (p?=?0.03) were all associated with the more severe cases of CDI. Ribotype 027 infection accounted for 71 % of severe cases (p?<?0.01) and patients with stool toxin had significantly higher lactoferrin levels and WBC counts (p?<?0.05). Our findings show that elevated fecal lactoferrin, along with increased WBC count and low serum albumin, were associated with more severe CDI. In addition, patients infected with ribotype 027 and those with stool toxin had significantly higher fecal lactoferrin and WBC counts.     

Isoarenarol,A New Protein Kinase Inhibitor from the Marine Sponge Dysidea arenaria

The novel sesquiterpene hydroquinone isoarenarol (1) and the known compound arenarol (2) were isolated from extracts of the marine sponge Dysidea arenaria Bergquist as part of a search for new protein kinase inhibitors. Both 1 and 2 showed potent and selective protein kinase inhibition in vitro.