Identification of an Efficient Gene Expression Panel for Glioblastoma Classification.

We present here a novel genetic algorithm-based random forest (GARF) modeling technique that enables a reduction in the complexity of large gene disease signatures to highly accurate, greatly simplified gene panels. When applied to 803 glioblastoma multiforme samples, this method allowed the 840-gene Verhaak et al. gene panel (the standard in the field) to be reduced to a 48-gene classifier, while retaining 90.91% classification accuracy, and outperforming the best available alternative methods. Additionally, using this approach we produced a 32-gene panel which allows for better consistency between RNA-seq and microarray-based classifications, improving cross-platform classification retention from 69.67% to 86.07%. A webpage producing these classifications is available at http://simplegbm.semel.ucla.edu

Maternal embryonic leucine zipper kinase (MELK) regulates multipotent neural progenitor proliferation.

Maternal embryonic leucine zipper kinase (MELK) was previously identified in a screen for genes enriched in neural progenitors. Here, we demonstrate expression of MELK by progenitors in developing and adult brain and that MELK serves as a marker for self-renewing multipotent neural progenitors (MNPs) in cultures derived from the developing forebrain and in transgenic mice. Overexpression of MELK enhances (whereas knockdown diminishes) the ability to generate neurospheres from MNPs, indicating a function in self-renewal. MELK down-regulation disrupts the production of neurogenic MNP from glial fibrillary acidic protein (GFAP)-positive progenitors in vitro. MELK expression in MNP is cell cycle regulated and inhibition of MELK expression down-regulates the expression of B-myb, which is shown to also mediate MNP proliferation. These findings indicate that MELK is necessary for proliferation of embryonic and postnatal MNP and suggest that it regulates the transition from GFAP-expressing progenitors to rapid amplifying progenitors in the postnatal brain

Bandwidth Control and Symmetry Breaking in a Mott-Hubbard Correlated Metal

In Mott materials strong electron correlation yields a spectrum of complex electronic structures. Recent synthesis advancements open realistic opportunities for harnessing Mott physics to design transformative devices. However, a major bottleneck in realizing such devices remains the lack of control over the electron correlation strength. This stems from the complexity of the electronic structure, which often veils the basic mechanisms underlying the correlation strength. Here, we present control of the correlation strength by tuning the degree of orbital overlap using picometer-scale lattice engineering. We illustrate how bandwidth control and concurrent symmetry breaking can govern the electronic structure of a correlated $SrVO_3$ model system. We show how tensile and compressive biaxial strain oppositely affect the $SrVO_3$ in-plane and out-of-plane orbital occupancy, resulting in the partial alleviation of the orbital degeneracy. We derive and explain the spectral weight redistribution under strain and illustrate how high tensile strain drives the system towards a Mott insulating state. Implementation of such concepts will drive correlated electron phenomena closer towards new solid state devices and circuits. These findings therefore pave the way for understanding and controlling electron correlation in a broad range of functional materials, driving this powerful resource for novel electronics closer towards practical realization

Cytoplasmic p53 couples oncogene-driven glucose metabolism to apoptosis and is a therapeutic target in glioblastoma.

Cross-talk among oncogenic signaling and metabolic pathways may create opportunities for new therapeutic strategies in cancer. Here we show that although acute inhibition of EGFR-driven glucose metabolism induces only minimal cell death, it lowers the apoptotic threshold in a subset of patient-derived glioblastoma (GBM) cells. Mechanistic studies revealed that after attenuated glucose consumption, Bcl-xL blocks cytoplasmic p53 from triggering intrinsic apoptosis. Consequently, targeting of EGFR-driven glucose metabolism in combination with pharmacological stabilization of p53 with the brain-penetrant small molecule idasanutlin resulted in synthetic lethality in orthotopic glioblastoma xenograft models. Notably, neither the degree of EGFR-signaling inhibition nor genetic analysis of EGFR was sufficient to predict sensitivity to this therapeutic combination. However, detection of rapid inhibitory effects on [18F]fluorodeoxyglucose uptake, assessed through noninvasive positron emission tomography, was an effective predictive biomarker of response in vivo. Together, these studies identify a crucial link among oncogene signaling, glucose metabolism, and cytoplasmic p53, which may potentially be exploited for combination therapy in GBM and possibly other malignancies

Rpair: Rescaling RePair with Rsync

Data compression is a powerful tool for managing massive but repetitive datasets, especially schemes such as grammar-based compression that support computation over the data without decompressing it. In the best case such a scheme takes a dataset so big that it must be stored on disk and shrinks it enough that it can be stored and processed in internal memory. Even then, however, the scheme is essentially useless unless it can be built on the original dataset reasonably quickly while keeping the dataset on disk. In this paper we show how we can preprocess such datasets with context-triggered piecewise hashing such that afterwards we can apply RePair and other grammar-based compressors more easily. We first give our algorithm, then show how a variant of it can be used to approximate the LZ77 parse, then leverage that to prove theoretical bounds on compression, and finally give experimental evidence that our approach is competitive in practice

Biometrically linking document leakage to the individuals responsible

Insider threats are a significant security issue. The last decade has witnessed countless instances of data loss and exposure in which data has become publicly available and easily accessible. Losing or disclosing sensitive data or confidential information may cause substantial financial and reputational damage to a company. Whilst more recent research has specifically focused on the insider misuse problem, it has tended to focus on the information itself – either through its protection or approaches to detect leakage. In contrast, this paper presents a proactive approach to the attribution of misuse via information leakage using biometrics and a locality-sensitive hashing scheme. The hash digest of the object (e.g. a document) is mapped with the given biometric information of the person who interacted with it and generates a digital imprint file that represents the correlation between the two parties. The proposed approach does not directly store or preserve any explicit biometric information nor document copy in a repository. It is only the established correlation (imprint) is kept for the purpose of reconstructing the mapped information once an incident occurred. Comprehensive experiments for the proposed approach have shown that it is highly possible to establish this correlation even when the original version has undergone significant file modification. In many scenarios, such as changing the file format r removing parts of the document, including words and sentences, it was possible to extract and reconstruct the correlated biometric information out of a modified document (e.g. 100 words were deleted) with an average success rate of 89.31%

Assessing stimulus–stimulus (semantic) conflict in the Stroop task using saccadic two-to-one color response mapping and preresponse pupillary measures

© 2015, The Psychonomic Society, Inc. Conflict in the Stroop task is thought to come from various stages of processing, including semantics. Two-to-one response mappings, in which two response-set colors share a common response location, have been used to isolate stimulus–stimulus (semantic) from stimulus–response conflict in the Stroop task. However, the use of congruent trials as a baseline means that the measured effects could be exaggerated by facilitation, and recent research using neutral, non-color-word trials as a baseline has supported this notion. In the present study, we sought to provide evidence for stimulus–stimulus conflict using an oculomotor Stroop task and an early, preresponse pupillometric measure of effort. The results provided strong (Bayesian) evidence for no statistical difference between two-to-one response-mapping trials and neutral trials in both saccadic response latencies and preresponse pupillometric measures, supporting the notion that the difference between same-response and congruent trials indexes facilitation in congruent trials, and not stimulus–stimulus conflict, thus providing evidence against the presence of semantic conflict in the Stroop task. We also demonstrated the utility of preresponse pupillometry in measuring Stroop interference, supporting the idea that pupillary effects are not simply a residue of making a response