GliomaPredict: A Clinically Useful Tool for Assigning Glioma Patients to Specific Molecular Subtypes

Background: Advances in generating genome-wide gene expression data have accelerated the development of molecular-based tumor classification systems. Tools that allow the translation of such molecular classification schemas from research into clinical applications are still missing in the emerging era of personalized medicine. Results: We developed GliomaPredict as a computational tool that allows the fast and reliable classification of glioma patients into one of six previously published stratified subtypes based on sets of extensively validated classifiers derived from hundreds of glioma transcriptomic profiles. Our tool utilizes a principle component analysis (PCA)-based approach to generate a visual representation of the analyses, quantifies the confidence of the underlying subtype assessment and presents results as a printable PDF file. GliomaPredict tool is implemented as a plugin application for the widely-used GenePattern framework. Conclusions: GliomaPredict provides a user-friendly, clinically applicable novel platform for instantly assigning gene expression-based subtype in patients with gliomas thereby aiding in clinical trial design and therapeutic decisionmaking. Implemented as a user-friendly diagnostic tool, we expect that in time GliomaPredict, and tools like it, will become routinely used in translational/clinical research and in the clinical care of patients with gliomas

Master Regulators, Regulatory Networks, and Pathways of Glioblastoma Subtypes

Glioblastoma multiforme (GBM) is the most common malignant brain tumor. GBM samples are classified into subtypes based on their transcriptomic and epigenetic profiles. Despite numerous studies to better characterize GBM biology, a comprehensive study to identify GBM subtype-specific master regulators, gene regulatory networks, and pathways is missing. Here, we used FastMEDUSA to compute master regulators and gene regulatory networks for each GBM subtype. We also ran Gene Set Enrichment Analysis and Ingenuity Pathway Analysis on GBM expression dataset from The Cancer Genome Atlas Project to compute GBM- and GBM subtype-specific pathways. Our analysis was able to recover some of the known master regulators and pathways in GBM as well as some putative novel regulators and pathways, which will aide in our understanding of the unique biology of GBM subtypes

Anatomical location of the vertebrobasilar junction: computed tomography morphometrics for planning endoscopic transsphenoidal transclival approaches

Background: The aim of this study was to determine the anatomical localisation and morphometry of vertebrobasilar junction (VBJ) by computed tomography (CT) images which may be helpful in planning the correct procedure before surgery such as endoscopic transsphenoidal transclival approach to the retroclival space. Materials and methods: Vertebrobasilar junction level was determined on axial, coronal reformat and sagittal reformat images. Clivus length, the distances of the VBJ to the upper and lower end of the clivus and to the bottom of the sphenoid sinus were measured. In addition, the position and distance of the VBJ relative to the midline were measured. The vertebral artery dominance was determined and the position of VBJ relative to the midline was evaluated. Results: When compared by gender, 1, a, b and c values were significantly longer in males than in females (p < 0.05). The location of the bottom of the sphenoid sinus was higher than the VBJ level in 263 (98.1%) cases, equal to the VBJ level in 1 (0.4%) case, and lower than the VBJ level in 4 (1.5%) cases. There was no statistically significant difference between the distances to the midline when the VBJs with right and left localisation were compared (p > 0.05). A statistically significant relationship was found between vertebral artery predominance and localisation of VBJ relative to the midline (p < 0.001). Conclusions: Careful perusal of CT images and the described VBJ morphometrics can help in accurate procedure planning to avoid basilar artery injury

Electrical spin injection from an organic-based ferrimagnet in a hybrid organic/inorganic heterostructure

We report the successful extraction of spin polarized current from the organic-based room temperature ferrimagnetic semiconductor V[TCNE]x (x~2, TCNE: tetracyanoethylene; TC ~ 400 K, EG ~ 0.5 eV, s ~ 10-2 S/cm) and its subsequent injection into a GaAs/AlGaAs light-emitting diode (LED). The spin current tracks the magnetization of V[TCNE]x~2, is weakly temperature dependent, and exhibits heavy hole / light hole asymmetry. This result has implications for room temperature spintronics and the use of inorganic materials to probe spin physics in organic and molecular systems

Correction to “Master Regulators, Regulatory Networks, and Pathways of Glioblastoma Subtypes”

Roll 184a. Klubertanz / Ginger Lee / Chris Keeler. Image 14 of 42. (19 April, 1955) [PHO 1.184a.20]The Boleslaus Lukaszewski (Father Luke) Photographs contain more than 28,000 images of Saint Louis University people, activities, and events between 1951 and 1970. The photographs were taken by Boleslaus Lukaszewski (Father Luke), a Jesuit priest and member of the University's Philosophy Department faculty

Forensic age estimation based on fast spin-echo proton density (FSE PD)-weighted MRI of the distal radial epiphysis.

Radiation exposure is a crucial factor to consider in forensic age estimation. The various magnetic resonance imaging (MRI) modalities used in forensic age estimation avoid radiation exposure. This study examined the reliability of distal radius ossification using fast spin-echo proton density (FSE PD)-weighted MRI to estimate age. Left wrist MRI findings of 532 patients aged 10-29 years were evaluated retrospectively using the five-stage system of Dedouit et al. The intra- and interobserver reliability values were κ = 0.906 and 0.869, respectively. Based on the results, the respective minimum ages estimated for stages 4 and 5 were 13.4 and 16.1 years for females, and 15.1 and 17.3 years for males; the method could not estimate an age of 18 years in any case. FSE PD MRI analysis of the distal radius epiphysis provides supportive data and can be used when evaluating the distal radius for forensic age estimation

Exploring the functionality of mesh-to-mesh value comparison in pair-matching and its application to fragmentary remains

SIMPLE SUMMARY: Forensic anthropologists often face the task of analysing a mixed group of skeletal remains or matching a solitary bone with the rest of a skeleton to determine if it belongs to the same individual. One of the best ways to do this is by pair-matching left and right bones of the same type. Common pair-matching methods experience issues such as high levels of subjectivity, lack of reliability, or expensive cost of implementation. This study explores the application of the relatively new method, mesh-to-mesh value comparison (MVC), which matches paired bones based on morphological shape to determine the likelihood that they derive from the same individual. This study sought to expand on the success found in past publications using MVC and to see how well it performed on a sample of clavicles, a bone known for having a high degree of bilateral variability, of 80 modern Turkish individuals. This study also explored whether MVC can reliably match fragmented bones to their intact counterpart. Results show MVC successfully matched 88.8% of paired clavicles and suggest the method continues to be a promising avenue for pair-matching that is not affected by ancestry and may be applicable to fragmented remains with further study. ABSTRACT: Many cases encountered by forensic anthropologists involve commingled remains or isolated elements. Common methods for analysing these contexts are characterised by limitations such as high degrees of subjectivity, high cost of application, or low proven accuracy. This study sought to test mesh-to-mesh value comparison (MCV), a relatively new method for pair-matching skeletal elements, to validate the claims that the technique is unaffected by age, sex and pathology. The sample consisted of 160 three-dimensional clavicle models created from computed tomography (CT) scans of a contemporary Turkish population. Additionally, this research explored the application of MVC to match fragmented elements to their intact counterparts by creating a sample of 480 simulated fragments, consisting of three different types based on the region of the bone they originate from. For comparing whole clavicles, this resulted in a sensitivity value of 87.6% and specificity of 90.9% using ROC analysis comparing clavicles. For the fragment comparisons, each type was compared to the entire clavicles of the opposite side. The results included a range of sensitivity values from 81.3% to 87.6%. Overall results are promising and the MVC technique seems to be a useful technique for matching paired elements that can be accurately applied to a Modern Turkish sample

Micro-Environment Causes Reversible Changes in DNA Methylation and mRNA Expression Profiles in Patient-Derived Glioma Stem Cells

In vitro and in vivo models are widely used in cancer research. Characterizing the similarities and differences between a patient\u27s tumor and corresponding in vitro and in vivo models is important for understanding the potential clinical relevance of experimental data generated with these models. Towards this aim, we analyzed the genomic aberrations, DNA methylation and transcriptome profiles of five parental tumors and their matched in vitro isolated glioma stem cell (GSC) lines and xenografts generated from these same GSCs using high-resolution platforms. We observed that the methylation and transcriptome profiles of in vitro GSCs were significantly different from their corresponding xenografts, which were actually more similar to their original parental tumors. This points to the potentially critical role of the brain microenvironment in influencing methylation and transcriptional patterns of GSCs. Consistent with this possibility, ex vivo cultured GSCs isolated from xenografts showed a tendency to return to their initial in vitro states even after a short time in culture, supporting a rapid dynamic adaptation to the in vitro microenvironment. These results show that methylation and transcriptome profiles are highly dependent on the microenvironment and growth in orthotopic sites partially reverse the changes caused by in vitro culturing

Corpora in Text-Based Russian Studies

This chapter focuses on textual data that are collected for a specific purpose, which are usually referred to as corpora. Scholars use corpora when they examine existing instances of a certain phenomenon or to conduct systematic quantitative analyses of occurrences, which in turn reflect habits, attitudes, opinions, or trends. For these contexts, it is extremely useful to combine different approaches. For example, a linguist might analyze the frequency of a certain buzzword, whereas a scholar in the political, cultural, or sociological sciences might attempt to explain the change in language usage from the data in question.Peer reviewe