Volumetric growth rates of meningioma and its correlation with histological diagnosis and clinical outcome: a systematic review.

INTRODUCTION: Tumour growth has been used to successfully predict progression-free survival in low-grade glioma. This systematic review sought to establish the evidence base regarding the correlation of volumetric growth rates with histological diagnosis and potential to predict clinical outcome in patients with meningioma. METHODS: This systematic review was conducted according to the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. Databases were searched for full text English articles analysing volumetric growth rates in patients with a meningioma. RESULTS: Four retrospective cohort studies were accepted, demonstrating limited evidence of significantly different tumour doubling rates and shapes of growth curves between benign and atypical meningiomas. Heterogeneity of patient characteristics and timing of volumetric assessment, both pre- and post-operatively, limited pooled analysis of the data. No studies performed statistical analysis to demonstrate the clinical utility of growth rates in predicting clinical outcome. CONCLUSION: This systematic review provides limited evidence in support of the use of volumetric growth rates in meningioma to predict histological diagnosis and clinical outcome to guide future monitoring and treatment

Design of plasma shutters for improved heavy ion acceleration by ultra-intense laser pulses

In this work, we investigate the application of the plasma shutters for heavy ion acceleration driven by a high-intensity laser pulse. We use particle-in-cell (PIC) and hydrodynamic simulations. The laser pulse, transmitted through the opaque shutter, gains a steep-rising front and its peak intensity is locally increased at the cost of losing part of its energy. These effects have a direct influence on subsequent ion acceleration from the ultrathin target behind the shutter. In our 3D simulations of silicon nitride plasma shutter and a silver target, the maximal energy of high-Z ions increases significantly when the shutter is included for both linearly and circularly polarized laser pulses. Moreover, application of the plasma shutter for linearly polarized pulse results in focusing of ions towards the laser axis in the plane perpendicular to the laser polarization. The generated high energy ion beam has significantly lower divergence compared to the broad ion cloud, generated without the shutter. The effects of prepulses are also investigated assuming a double plasma shutter. The first shutter can withstand the assumed sub-ns prepulse (treatment of ns and ps prepulses by other techniques is assumed) and the pulse shaping occursvia interaction with the second shutter. On the basis of our theoretical findings, we formulated an approach towards designing a double plasma shutter for high-intensity and high-power laser pulses and built a prototype.Comment: 30 pages 13 figure

On the origin of interface states at oxide/III-nitride heterojunction interfaces

The energy spectrum of interface state density, D-it(E), was determined at oxide/III-N heterojunction interfaces in the entire band gap, using two complementary photo-electric methods: (i) photo-assisted capacitance-voltage technique for the states distributed near the midgap and the conduction band (CB) and (ii) light intensity dependent photo-capacitance method for the states close to the valence band (VB). In addition, the Auger electron spectroscopy profiling was applied for the characterization of chemical composition of the interface region with the emphasis on carbon impurities, which can be responsible for the interface state creation. The studies were performed for the AlGaN/GaN metal-insulator-semiconductor heterostructures (MISH) with Al2O3 and SiO2 dielectric films and AlxGa1-x layers with x varying from 0.15 to 0.4 as well as for an Al2O3/InAlN/GaN MISH structure. For all structures, it was found that: (i) D-it(E) is an U-shaped continuum increasing from the midgap towards the CB and VB edges and (ii) interface states near the VB exhibit donor-like character. Furthermore, D-it(E) for SiO2/AlxGa1-x/GaN structures increased with rising x. It was also revealed that carbon impurities are not present in the oxide/III-N interface region, which indicates that probably the interface states are not related to carbon, as previously reported. Finally, it was proven that the obtained D-it(E) spectrum can be well fitted using a formula predicted by the disorder induced gap state model. This is an indication that the interface states at oxide/III-N interfaces can originate from the structural disorder of the interfacial region. Furthermore, at the oxide/barrier interface we revealed the presence of the positive fixed charge (Q(F)) which is not related to D-it(E) and which almost compensates the negative polarization charge (Q(pol)(-))

UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein–DNA interactions

The Universal PBM Resource for Oligonucleotide-Binding Evaluation (UniPROBE) database is a centralized repository of information on the DNA-binding preferences of proteins as determined by universal protein-binding microarray (PBM) technology. Each entry for a protein (or protein complex) in UniPROBE provides the quantitative preferences for all possible nucleotide sequence variants (‘words’) of length k (‘k-mers’), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. In this update, we describe >130% expansion of the database content, incorporation of a protein BLAST (blastp) tool for finding protein sequence matches in UniPROBE, the introduction of UniPROBE accession numbers and additional database enhancements. The UniPROBE database is available at http://uniprobe.org.National Institutes of Health (U.S.) (grant number R01 HG003985

UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein–DNA interactions

The Universal PBM Resource for Oligonucleotide-Binding Evaluation (UniPROBE) database is a centralized repository of information on the DNA-binding preferences of proteins as determined by universal protein-binding microarray (PBM) technology. Each entry for a protein (or protein complex) in UniPROBE provides the quantitative preferences for all possible nucleotide sequence variants (‘words’) of length k (‘k-mers’), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. In this update, we describe >130% expansion of the database content, incorporation of a protein BLAST (blastp) tool for finding protein sequence matches in UniPROBE, the introduction of UniPROBE accession numbers and additional database enhancements. The UniPROBE database is available at http://uniprobe.org.National Institutes of Health (U.S.) (grant number R01 HG003985

Targetfinder.org: a resource for systematic discovery of transcription factor target genes

Targetfinder.org (http://targetfinder.org/) provides a web-based resource for finding genes that show a similar expression pattern to a group of user-selected genes. It is based on a large-scale gene expression compendium (>1200 experiments, >13 000 genes). The primary application of Targetfinder.org is to expand a list of known transcription factor targets by new candidate target genes. The user submits a group of genes (the ‘seed’), and as a result the web site provides a list of other genes ranked by similarity of their expression to the expression of the seed genes. Additionally, the web site provides information on a recovery/cross-validation test to check for consistency of the provided seed and the quality of the ranking. Furthermore, the web site allows to analyse affinities of a selected transcription factor to the promoter regions of the top-ranked genes in order to select the best new candidate target genes for further experimental analysis

Salvage brachytherapy in combination with interstitial hyperthermia for locally recurrent prostate carcinoma following external beam radiation therapy: a prospective phase II study.

Optimal treatment for patients with only local prostate cancer recurrence after external beam radiation therapy (EBRT) failure remains unclear. Possible curative treatments are radical prostatectomy, cryosurgery, and brachytherapy. Several single institution series proved that high-dose-rate brachytherapy (HDRBT) and pulsed-dose-rate brachytherapy (PDRBT) are reasonable options for this group of patients with acceptable levels of genitourinary and gastrointestinal toxicity. A standard dose prescription and scheme have not been established yet, and the literature presents a wide range of fractionation protocols. Furthermore, hyperthermia has shown the potential to enhance the efficacy of re-irradiation. Consequently, a prospective trial is urgently needed to attain clear structured prospective data regarding the efficacy of salvage brachytherapy with adjuvant hyperthermia for locally recurrent prostate cancer. The purpose of this report is to introduce a new prospective phase II trial that would meet this need. The primary aim of this prospective phase II study combining Iridium-192 brachytherapy with interstitial hyperthermia (IHT) is to analyze toxicity of the combined treatment; a secondary aim is to define the efficacy (bNED, DFS, OS) of salvage brachytherapy. The dose prescribed to PTV will be 30 Gy in 3 fractions for HDRBT, and 60 Gy in 2 fractions for PDRBT. During IHT, the prostate will be heated to the range of 40-47°C for 60 minutes prior to brachytherapy dose delivery. The protocol plans for treatment of 77 patients

Statistical detection of cooperative transcription factors with similarity adjustment

Motivation: Statistical assessment of cis-regulatory modules (CRMs) is a crucial task in computational biology. Usually, one concludes from exceptional co-occurrences of DNA motifs that the corresponding transcription factors (TFs) are cooperative. However, similar DNA motifs tend to co-occur in random sequences due to high probability of overlapping occurrences. Therefore, it is important to consider similarity of DNA motifs in the statistical assessment

TransFind—predicting transcriptional regulators for gene sets

The analysis of putative transcription factor binding sites in promoter regions of coregulated genes allows to infer the transcription factors that underlie observed changes in gene expression. While such analyses constitute a central component of the in-silico characterization of transcriptional regulatory networks, there is still a lack of simple-to-use web servers able to combine state-of-the-art prediction methods with phylogenetic analysis and appropriate multiple testing corrected statistics, which returns the results within a short time. Having these aims in mind we developed TransFind, which is freely available at http://transfind.sys-bio.net/