Data and Tools Integration in the Canadian Open Neuroscience Platform.

We present the Canadian Open Neuroscience Platform (CONP) portal to answer the research community's need for flexible data sharing resources and provide advanced tools for search and processing infrastructure capacity. This portal differs from previous data sharing projects as it integrates datasets originating from a number of already existing platforms or databases through DataLad, a file level data integrity and access layer. The portal is also an entry point for searching and accessing a large number of standardized and containerized software and links to a computing infrastructure. It leverages community standards to help document and facilitate reuse of both datasets and tools, and already shows a growing community adoption giving access to more than 60 neuroscience datasets and over 70 tools. The CONP portal demonstrates the feasibility and offers a model of a distributed data and tool management system across 17 institutions throughout Canada.

Enhanced Ductility of PEEK thin film with self-assembled fibre-like crystals.

Poly Ether Ether Ketone (PEEK) is a high temperature polymer material known for its excellent chemical resistance, high strength and toughness. As a semi-crystalline polymer, PEEK can become very brittle during long crystallisation times and temperatures helped as well by its high content of rigid benzene rings within its chemical structure. This paper presents a simple quench crystallization method for preparation of PEEK thin films with the formation of a novel fibre-like crystal structure on the surface of the films. These quenched crystallised films show higher elongation at break when compared with conventional melt crystallised thin films incorporating spherulitic crystals, while the tensile strength of both types of films (quenched crystallised and conventional melt) remained the same. The fracture analysis carried out using microscopy revealed an interesting microstructure which evolves as a function of annealing time. Based on these results, a crystal growth mechanism describing the development of the fibre-like crystals on the surface of the quenched crystallised films is proposed.

The comparative effectiveness of electroencephalographic indices in predicting response to escitalopram therapy in depression: A pilot study.

BACKGROUND: This study aims to compare the effectiveness of EEG frequency band activity including interhemispheric asymmetry and prefrontal theta cordance in predicting response to escitalopram therapy at 8-weeks post-treatment, in a multi-site initiative. METHODS: Resting state 64-channel EEG data were recorded from 44 patients with a diagnosis of major depressive disorder (MDD) as part of a larger, multisite discovery study of biomarkers in antidepressant treatment response, conducted by the Canadian Biomarker Integration Network in Depression (CAN-BIND). Clinical response was measured at 8-weeks post-treatment as change from baseline Montgomery-Asberg Depression Rating Scale (MADRS) score of 50% or more. EEG measures were analyzed at (1) pre-treatment baseline (2) 2 weeks post-treatment and (3) as an ''early change" variable defined as change in EEG from baseline to 2 weeks post-treatment. RESULTS: At baseline, treatment responders showed elevated absolute alpha power in the left hemisphere while non-responders showed the opposite. Responders further exhibited a cortical asymmetry in the parietal region. Groups also differed in pre-treatment relative delta power with responders showing greater power in the right hemisphere over the left while non-responders showed the opposite. At 2 weeks post-treatment, responders exhibited greater absolute beta power in the left hemisphere relative to the right and the opposite was noted for non-responders. A reverse pattern was noted for absolute and relative delta power at 2 weeks post-treatment. Responders exhibited early reductions in relative alpha power and early increments in relative theta power. Non-responders showed a significant early increase in prefrontal theta cordance. CONCLUSIONS: Hemispheric asymmetries in the alpha and delta bands at baseline and at 2 weeks post-treatment have moderately strong predictive utility in predicting response to antidepressant treatment.

Exploring high dimensional data with Butterfly: a novel classification algorithm based on discrete dynamical systems.

MOTIVATION: We introduce a novel method for visualizing high dimensional data via a discrete dynamical system. This method provides a 2D representation of the relationship between subjects according to a set of variables without geometric projections, transformed axes or principal components. The algorithm exploits a memory-type mechanism inherent in a certain class of discrete dynamical systems collectively referred to as the chaos game that are closely related to iterative function systems. The goal of the algorithm was to create a human readable representation of high dimensional patient data that was capable of detecting unrevealed subclusters of patients from within anticipated classifications. This provides a mechanism to further pursue a more personalized exploration of pathology when used with medical data. For clustering and classification protocols, the dynamical system portion of the algorithm is designed to come after some feature selection filter and before some model evaluation (e.g. clustering accuracy) protocol. In the version given here, a univariate features selection step is performed (in practice more complex feature selection methods are used), a discrete dynamical system is driven by this reduced set of variables (which results in a set of 2D cluster models), these models are evaluated for their accuracy (according to a user-defined binary classification) and finally a visual representation of the top classification models are returned. Thus, in addition to the visualization component, this methodology can be used for both supervised and unsupervised machine learning as the top performing models are returned in the protocol we describe here. RESULTS: Butterfly, the algorithm we introduce and provide working code for, uses a discrete dynamical system to classify high dimensional data and provide a 2D representation of the relationship between subjects. We report results on three datasets (two in the article; one in the appendix) including a public lung cancer dataset that comes along with the included Butterfly R package. In the included R script, a univariate feature selection method is used for the dimension reduction step, but in the future we wish to use a more powerful multivariate feature reduction method based on neural networks (Kriesel, 2007). AVAILABILITY AND IMPLEMENTATION: A script written in R (designed to run on R studio) accompanies this article that implements this algorithm and is available at http://butterflygeraci.codeplex.com/. For details on the R package or for help installing the software refer to the accompanying document, Supporting Material and Appendix.

Probability of cancer in pulmonary nodules detected on first screening CT.

BACKGROUND: Major issues in the implementation of screening for lung cancer by means of low-dose computed tomography (CT) are the definition of a positive result and the management of lung nodules detected on the scans. We conducted a population-based prospective study to determine factors predicting the probability that lung nodules detected on the first screening low-dose CT scans are malignant or will be found to be malignant on follow-up. METHODS: We analyzed data from two cohorts of participants undergoing low-dose CT screening. The development data set included participants in the Pan-Canadian Early Detection of Lung Cancer Study (PanCan). The validation data set included participants involved in chemoprevention trials at the British Columbia Cancer Agency (BCCA), sponsored by the U.S. National Cancer Institute. The final outcomes of all nodules of any size that were detected on baseline low-dose CT scans were tracked. Parsimonious and fuller multivariable logistic-regression models were prepared to estimate the probability of lung cancer. RESULTS: In the PanCan data set, 1871 persons had 7008 nodules, of which 102 were malignant, and in the BCCA data set, 1090 persons had 5021 nodules, of which 42 were malignant. Among persons with nodules, the rates of cancer in the two data sets were 5.5% and 3.7%, respectively. Predictors of cancer in the model included older age, female sex, family history of lung cancer, emphysema, larger nodule size, location of the nodule in the upper lobe, part-solid nodule type, lower nodule count, and spiculation. Our final parsimonious and full models showed excellent discrimination and calibration, with areas under the receiver-operating-characteristic curve of more than 0.90, even for nodules that were 10 mm or smaller in the validation set. CONCLUSIONS: Predictive tools based on patient and nodule characteristics can be used to accurately estimate the probability that lung nodules detected on baseline screening low-dose CT scans are malignant. (Funded by the Terry Fox Research Institute and others; ClinicalTrials.gov number, NCT00751660.).

Thymoma: a population-based study of the management and outcomes for the province of British Columbia.

INTRODUCTION: Thymomas are rare neoplasms with variable clinical behavior. Our primary study aim was to analyze treatment practices and outcomes in a population-based cohort of thymoma patients. We hypothesized that stage I and II thymomas would have high cure rates with resection and adjuvant radiation, whereas locally advanced cases would benefit from multimodality therapy. METHODS: All patients, diagnosed with thymoma or thymic carcinoma in British Columbia between 1994 and 2009, were identified using the British Columbia Cancer Agency Registry. Chart review was used to collect demographic and treatment data. Detailed pathology review was performed using the World Health Organization classification. RESULTS: One hundred and seventy-one patients were identified for analysis. The 5-year overall survival was 93.3%, 88.7%, 74.6%, 43.4% for stages I, II, III, and IV, respectively. Survival varied significantly among patients with thymoma compared with thymic carcinoma. In patients with stage II disease, adjuvant radiation did not confer an overall survival or recurrence-free survival benefit. Seventy-five patients had locally advanced disease. There was practice variation in treatment of these patients. Patients with thymoma undergoing trimodality treatment had a 5-year median overall survival of 80%, whereas patients with thymic carcinoma had poor outcomes despite aggressive treatment. CONCLUSIONS: Survival rates in this population-based series were comparable to those in previously published reports. The ideal management of thymic tumors involves a multidisciplinary approach, particularly in locally advanced disease and selection of patients for adjuvant radiation therapy.

EMT transcription factors snail and slug directly contribute to cisplatin resistance in ovarian cancer.

BACKGROUND: The epithelial to mesenchymal transition (EMT) is a molecular process through which an epithelial cell undergoes transdifferentiation into a mesenchymal phenotype. The role of EMT in embryogenesis is well-characterized and increasing evidence suggests that elements of the transition may be important in other processes, including metastasis and drug resistance in various different cancers. METHODS: Agilent 4 × 44 K whole human genome arrays and selected reaction monitoring mass spectrometry were used to investigate mRNA and protein expression in A2780 cisplatin sensitive and resistant cell lines. Invasion and migration were assessed using Boyden chamber assays. Gene knockdown of snail and slug was done using targeted siRNA. Clinical relevance of the EMT pathway was assessed in a cohort of primary ovarian tumours using data from Affymetrix GeneChip Human Genome U133 plus 2.0 arrays. RESULTS: Morphological and phenotypic hallmarks of EMT were identified in the chemoresistant cells. Subsequent gene expression profiling revealed upregulation of EMT-related transcription factors including snail, slug, twist2 and zeb2. Proteomic analysis demonstrated up regulation of Snail and Slug as well as the mesenchymal marker Vimentin, and down regulation of E-cadherin, an epithelial marker. By reducing expression of snail and slug, the mesenchymal phenotype was largely reversed and cells were resensitized to cisplatin. Finally, gene expression data from primary tumours mirrored the finding that an EMT-like pathway is activated in resistant tumours relative to sensitive tumours, suggesting that the involvement of this transition may not be limited to in vitro drug effects. CONCLUSIONS: This work strongly suggests that genes associated with EMT may play a significant role in cisplatin resistance in ovarian cancer, therefore potentially leading to the development of predictive biomarkers of drug response or novel therapeutic strategies for overcoming drug resistance.

Assessment of cognitive symptoms in prodromal and early huntington disease.

The Functional Rating Scale Taskforce for pre-Huntington Disease (FuRST-pHD) is a multinational, multidisciplinary initiative with the goal of developing a data-driven, comprehensive, psychometrically sound, rating scale for assessing symptoms and functional ability in prodromal and early Huntington disease (HD) gene expansion carriers. The process involves input from numerous sources to identify relevant symptom domains, including HD individuals, caregivers, and experts from a variety of fields, as well as knowledge gained from the analysis of data from ongoing large-scale studies in HD using existing clinical scales. This is an iterative process in which an ongoing series of field tests in prodromal (prHD) and early HD individuals provides the team with data on which to make decisions regarding which questions should undergo further development or testing and which should be excluded. We report here the development and assessment of the first iteration of interview questions aimed to assess cognitive symptoms in prHD and early HD individuals.

Assessment of Day-to-Day Functioning in Prodromal and Early Huntington Disease.

The Functional Rating Scale Taskforce for pre-Huntington Disease (FuRST-pHD) is a multinational, multidisciplinary initiative with the goal of developing a data-driven, comprehensive, psychometrically sound, rating scale for assessing symptoms and functional ability in prodromal and early Huntington disease (HD) gene expansion carriers. The process involves input from numerous sources to identify relevant symptom domains, including HD individuals, caregivers, and experts from a variety of fields, as well as knowledge gained from the analysis of data from ongoing large-scale studies in HD using existing clinical scales. This is an iterative process in which an ongoing series of field tests in prodromal (prHD) and early HD individuals provides the team with data on which to make decisions regarding which questions should undergo further development or testing and which should be excluded. We report here the development and assessment of the first iteration of interview questions aimed to assess functional impact in day-to-day activities in prHD and early HD individuals.

Assessing behavioural manifestations prior to clinical diagnosis of huntington disease: "anger and irritability" and "obsessions and compulsions".

The Functional Rating Scale Taskforce for pre-Huntington Disease (FuRST-pHD) is a multinational, multidisciplinary initiative with the goal of developing a data-driven, comprehensive, psychometrically sound, rating scale for assessing symptoms and functional ability in prodromal and early Huntington disease (HD) gene expansion carriers. The process involves input from numerous sources to identify relevant symptom domains, including HD individuals, caregivers, and experts from a variety of fields, as well as knowledge gained from the analysis of data from ongoing large-scale studies in HD using existing clinical scales. This is an iterative process in which an ongoing series of field tests in prodromal (prHD) and early HD individuals provides the team with data on which to make decisions regarding which questions should undergo further development or testing and which should be excluded. We report here the development and assessment of the first iteration of interview questions aimed to assess "Anger and Irritability" and "Obsessions and Compulsions" in prHD individuals.

Assessment of depression, anxiety and apathy in prodromal and early huntington disease.

The Functional Rating Scale Taskforce for pre-Huntington Disease (FuRST-pHD) is a multinational, multidisciplinary initiative with the goal of developing a data-driven, comprehensive, psychometrically sound, rating scale for assessing symptoms and functional ability in prodromal and early Huntington disease (HD) gene expansion carriers. The process involves input from numerous sources to identify relevant symptom domains, including HD individuals, caregivers, and experts from a variety of fields, as well as knowledge gained from the analysis of data from ongoing large-scale studies in HD using existing clinical scales. This is an iterative process in which an ongoing series of field tests in prodromal (prHD) and early HD individuals provides the team with data on which to make decisions regarding which questions should undergo further development or testing and which should be excluded. We report here the development and assessment of the first iteration of interview questions aimed to assess Depression, Anxiety and Apathy in prHD and early HD individuals.

Assessment of motor symptoms and functional impact in prodromal and early huntington disease.

The Functional Rating Scale Taskforce for pre-Huntington Disease (FuRST-pHD) is a multinational, multidisciplinary initiative with the goal of developing a data-driven, comprehensive, psychometrically sound, rating scale for assessing symptoms and functional ability in prodromal and early Huntington disease (HD) gene expansion carriers. The process involves input from numerous sources to identify relevant symptom domains, including HD individuals, caregivers, and experts from a variety of fields, as well as knowledge gained from the analysis of data from ongoing large-scale studies in HD using existing clinical scales. This is an iterative process in which an ongoing series of field tests in prodromal (prHD) and early HD individuals provides the team with data on which to make decisions regarding which questions should undergo further development or testing and which should be excluded. We report here the development and assessment of the first iteration of interview questions aimed to assess functional impact of motor manifestations in prHD and early HD individuals.

Applying mass spectrometry based proteomic technology to advance the understanding of multiple myeloma.

Multiple myeloma (MM) is the second most common hematological malignancy in adults. It is characterized by clonal proliferation of terminally differentiated B lymphocytes and over-production of monoclonal immunoglobulins. Recurrent genomic aberrations have been identified to contribute to the aggressiveness of this cancer. Despite a wealth of knowledge describing the molecular biology of MM as well as significant advances in therapeutics, this disease remains fatal. The identification of biomarkers, especially through the use of mass spectrometry, however, holds great promise to increasing our understanding of this disease. In particular, novel biomarkers will help in the diagnosis, prognosis and therapeutic stratification of MM. To date, results from mass spectrometry studies of MM have provided valuable information with regards to MM diagnosis and response to therapy. In addition, mass spectrometry was employed to study relevant signaling pathways activated in MM. This review will focus on how mass spectrometry has been applied to increase our understanding of MM.

Biochip arrays for the discovery of a biomarker surrogate in a phase I/II study assessing a novel anti-metastasis agent.

OBJECTIVE: Can biochip arrays identify which individuals with metastatic disease will respond to an anti-metastatic agent? DESIGN AND METHODS: Cytokine and cell adhesion arrays (Randox Ltd) were measured over 1 month in 9 research participants receiving CTCE-9908 in a Phase I/II study. RESULTS: Research participants with stable disease (n=2) had significantly higher soluble VCAM-1 as compared to those that progressed. DISCUSSION: VCAM-1 measurement early during CTCE-9908 treatment might be used as a surrogate for response.

Lung nodules: CT-guided placement of microcoils to direct video-assisted thoracoscopic surgical resection.

PURPOSE: To prospectively assess the safety and effectiveness of computed tomography (CT)-guided placement of fiber-coated microcoils used to guide video-assisted thoracoscopic surgical (VATS) excision of small peripheral lung nodules, with successful excision as the primary outcome and successful CT-guided microcoil placement and procedural complications as secondary outcomes. MATERIALS AND METHODS: The institutional review board approved the study protocol. Informed consent was obtained from all 69 enrolled patients (30 men, 39 women; mean age, 60.7 years +/- 10.1 [standard deviation]) with 75 nodules. At CT, one end of an 80-mm long, 0.018-inch-diameter fiber-coated microcoil was placed deep to the small peripheral lung nodule, and the other end was coiled in the pleural space. VATS excision of lung tissue, nodules, and the microcoil was performed with fluoroscopic guidance. RESULTS: Seventy-three (97%) 4-24-mm nodules were successfully removed at fluoroscopically guided VATS excision; two nodules could not be removed. CT-guided microcoil placement was successful in all cases; however, two (3%) of 75 coils were displaced at VATS excision. Pneumothorax requiring chest tube placement occurred in two (3%) patients, and asymptomatic hemothorax occurred in one (1%) patient. The microcoil did not impede intraoperative frozen-section histopathologic analysis, which facilitated accurate clinical management in all patients. For 19 (28%) patients, the preoperative treatment plan based on bronchoscopy, needle biopsy, and positron emission tomography findings changed after VATS excision. CONCLUSION: Microcoil localization of small peripheral lung nodules enabled fluoroscopically guided VATS resection of 97% of the nodules, with a low rate of intervention (3%) for procedural complications.

The GRID-HAMD: standardization of the Hamilton Depression Rating Scale.

This report describes the GRID-Hamilton Depression Rating Scale (GRID-HAMD), an improved version of the Hamilton Depression Rating Scale that was developed through a broad-based international consensus process. The GRID-HAMD separates the frequency of the symptom from its intensity for most items, refines several problematic anchors, and integrates both a structured interview guide and consensus-derived conventions for all items. Usability was established in a small three-site sample of convenience, evaluating 29 outpatients, with most evaluators finding the scale easy to use. Test-retest (4-week) and interrater reliability were established in 34 adult outpatients with major depressive disorder, as part of an ongoing clinical trial. In a separate study, interrater reliability was found to be superior to the Guy version of the HAMD, and as good as the Structured Interview Guide for the Hamilton Depression Rating Scale (SIGH-D), across 30 interview pairs. Finally, using the SIGH-D as the criterion standard, the GRID-HAMD demonstrated high concurrent validity. Overall, these data suggest that the GRID-HAMD is an improvement over the original Guy version as well as the SIGH-D in its incorporation of innovative features and preservation of high reliability and validity.

Peripheral lung nodules: fluoroscopically guided video-assisted thoracoscopic resection after computed tomography-guided localization using platinum microcoils.

OBJECTIVES: We sought to test the safety and efficacy of fluoroscopically guided, video-assisted, thoracoscopic resection after computed tomography (CT)-guided localization using platinum microcoils. SUMMARY BACKGROUND DATA: Video-assisted thoracoscopic (VATS) resection of small pulmonary nodules >5 mm deep to the visceral pleura fails to locate the nodule and requires conversion to open thoracotomy in two thirds of cases. Therefore, we developed a new technique for intraoperative localization of these nodules using CT-guided placement of platinum microcoils. This study tests the safety and efficacy of this technique in a Phase I human study. METHODS: Twelve patients with undiagnosed growing pulmonary nodules <20 mm were marked preoperatively using percutaneously placed CT-guided platinum microcoils. The coil was deployed adjacent to the nodule with the distal end of the coil placed deep to the nodule and the superficial end coiled on the pleural surface. The nodule and coil were excised using endostaplers guided by VATS and fluoroscopy. Histopathologic diagnosis was performed immediately after resection. RESULTS: CT-guided microcoil localization was successful in all patients. A small hemothorax and a pneumothorax requiring a chest tube occurred in 2 patients. Mean distance from visceral pleura to the deep edge of the nodule was 30.9 +/- 15.4 mm. VATS resection of the nodules (size = 11.8 +/- 3.2 mm) was successful in all patients. Mean microcoil localization, fluoroscopy, and operative times were 42 +/- 14, 3.1 +/- 2.0, and 67 +/- 27 minutes. A diagnosis of primary nonsmall cell bronchogenic carcinoma was made in 6 patients who then received a completion lobectomy. Six patients (hamartoma: 2, reactive lymph node: 1, bronchoalveolar cell carcinoma: 2, metastatic sarcoma: 1) did not receive further resections. CONCLUSIONS: Preoperative localization of pulmonary nodules using percutaneous CT-guided platinum microcoil insertion combined with operative fluoroscopic visualization is a safe, effective technique that increases the success rate of VATS excision.

Site-specific management of nematodes pitfalls and practicalities.

The greatest constraint to potato production in the United Kingdom (UK) is damage by the potato cyst nematodes (PCN) Globodera pallida and G. rostochiensis. Management of PCN depends heavily on nematicides, which are costly. Of all the inputs in UK agriculture, nematicides offer the largest potential cost savings from spatially variable application, and these savings would be accompanied by environmental benefits. We mapped PCN infestations in potato fields and monitored the changes in population density and distribution that occurred when susceptible potato crops were grown. The inverse relationship between population density before planting and multiplication rate of PCN makes it difficult to devise reliable spatial nematicide application procedures, especially when the pre-planting population density is just less than the detection threshold. Also, the spatial dependence found suggests that the coarse sampling grids used commercially are likely to produce misleading distribution maps.