Niederenergetische Anregungen in eindimensionalen Quanten-Antiferromagneten

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Comparative anatomy of nitrergic intrinsic choroidal neurons (ICN) in various avian species

Intrinsic choroidal neurons (ICN) represent a peculiar feature of eyes in higher primates and birds. They account for up to 2000 in human and duck eyes but are virtually absent or rare in all other mammalian species investigated so far. It has been suggested that ICN are involved in regulation of ocular blood supply, hence influencing intraocular pressure, and changes in choroidal thickness, thus influencing accommodation. The present study was undertaken in order to compare differences in various avian species with respect to ICN as well as to provide data on some avian species relevant for experimental ophthalmic research, i.e. chicken and quail. Choroids from 12 avian species were processed for NADPH-diaphorase histochemistry or, in some cases, neuronal nitric oxide synthase immunocytochemistry. ICN were quantified and normalized to mean choroidal area. Three choroids of each galliformes (i.e. chicken, quail, turkey) and anseriformes (i.e. Muscovy duck, Mallard duck, goose) were rastered in squares of 1 mm(2) and x/y coordinates were transferred into a 3D-diagram with the amount of ICN represented in the z-axis. ICN were detected in all species investigated. They were predominantly small cells with soma diameters of 20-30 mum. In turkey, and to a lesser amount in chicken, a subpopulation of ICN with somal diameters of up to 70 mum was observed. Highest mean cell counts were found in goose (6195(.)4; turkey 3558(.)4; chicken 1681(.)4; Muscovy duck 785(.)4; Mallard duck 640(.)8; quail 440(.)2). Normalized to choroidal area, highest mean cell counts were (per mm(2)): 12(.)62 in goose, 4(.)42 in both chicken and turkey, 2(.)86 in quail, 2(.)66 in Mallard duck and 1(.)89 in Muscovy duck. In galliformes, ICN were found to be accumulated temporo-cranial, while in anseriformes they were arranged in a more belt-like fashion, passing from cranio-nasal to temporo-caudal. Our results show that besides Muscovy duck, other avian species appear as suitable models for further functional experiments on ICN. The temporo-cranial accumulation of ICN in galliformes and the belt-like arrangement in anseriformes may reflect special functional requirements in regions of high visual acuity. (C) 2003 Elsevier Ltd. All rights reserved

INTRAGO: intraoperative radiotherapy in glioblastoma multiforme – a Phase I/II dose escalation study

Background: Glioblastoma multiforme (GBM) is the most frequent primary malignant brain tumor in adults. Despite multimodal therapies, almost all GBM recur within a narrow margin around the initial resected lesion. Thus, novel therapeutic intensification strategies must target both, the population of dispersed tumor cells around the cavity and the postoperative microenvironment. Intraoperative radiotherapy (IORT) is a pragmatic and effective approach to sterilize the margins from persistent tumor cells, abrogate post-injury proliferative stimuli and to bridge the therapeutic gap between surgery and radiochemotherapy. Therefore, we have set up INTRAGO, a phase I/II dose-escalation study to evaluate the safety and tolerability of IORT added to standard therapy in newly diagnosed GBM. In contrast to previous approaches, the study involves the application of isotropic low-energy (kV) x-rays delivered by spherical applicators, providing optimal irradiation properties to the resection cavity. Methods/Design: INTRAGO includes patients aged 50 years or older with a Karnofsky performance status of at least 50% and a histologically confirmed (frozen sections) supratentorial GBM. Safety and tolerability (i.e., the maximum tolerated dose, MTD) will be assessed using a classical 3 + 3 dose-escalation design. Dose-limiting toxicities (DLT) are wound healing deficits or infections requiring surgical intervention, IORT-related cerebral bleeding or ischemia, symptomatic brain necrosis requiring surgical intervention and early termination of external beam radiotherapy (before the envisaged dose of 60 Gy) due to radiotoxicity. Secondary end points are progression-free and overall survival. Trial registration: The study is registered with clinicaltrials.gov, number: NCT02104882 (Registration Date: 03/26/2014)

SOFTWARE STANDARDS FOR THE MULTICORE ERA

Systems architects commonly use multiple cores to improve system performance. Unfortunately, multicore hardware is evolving faster than software technologies. New multicore software standards are necessary in light of the new challenges and capabilities that embedded multicore systems provide. The newly released multicore communications API standard targets small-footprint, highly efficient intercore and interchip communications

Highly Multiplexed Targeted Proteomics Acquisition on a TIMS-QTOF

peer reviewedTargeted proteomics allows the highly sensitive detection of specific peptides and proteins in complex biological samples. Here, we describe a methodology for targeted peptide quantification using a trapped ion mobility quadrupole time-of-flight mass spectrometer (timsTOF Pro). The prm-PASEF method exploits the multiplexing capability provided by the trapped ion mobility separation, allowing more than 200 peptides to be monitored over a 30 min liquid chromatography separation. Compared to conventional parallel reaction monitoring (PRM), precursor ions are accumulated in the trapped ion mobility spectrometry (TIMS) cells and separated according to their shape and charge before eluting into the quadrupole time-of-flight (QTOF) part of the mass spectrometer. The ion mobility trap allows measuring up to six peptides from a single 100 ms ion mobility separation with the current setup. Using these improved mass spectrometric capabilities, we detected and quantified 216 isotope-labeled synthetic peptides (AQUA peptides) spiked in HeLa human cell extract with limits of quantification of 17.2 amol for some peptides. The acquisition method is highly reproducible between injections and enables accurate quantification in biological samples, as demonstrated by quantifying KRas, NRas, and HRas as well as several Ras mutations in lung and colon cancer cell lines on fast 10 min gradient separations

Maxquant software for ion mobility enhanced shotgun proteomics

Ion mobility can add a dimension to LC-MS based shotgun proteomics which has the potential to boost proteome coverage, quantification accuracy and dynamic range. Required for this is suitable software that extracts the information contained in the four-dimensional (4D) data space spanned by m/z, retention time, ion mobility and signal intensity. Here we describe the ion mobility enhanced MaxQuant software, which utilizes the added data dimension. It offers an end to end computational workflow for the identification and quantification of peptides and proteins in LC-IMS-MS/MS shotgun proteomics data. We apply it to trapped ion mobility spectrometry (TIMS) coupled to a quadrupole time-of-flight (QTOF) analyzer. A highly parallelizable 4D feature detection algorithm extracts peaks which are assembled to isotope patterns. Masses are recalibrated with a non-linear m/z, retention time, ion mobility and signal intensity dependent model, based on peptides from the sample. A new matching between runs (MBR) algorithm that utilizes collisional cross section (CCS) values of MS1 features in the matching process significantly gains specificity from the extra dimension. Prerequisite for using CCS values in MBR is a relative alignment of the ion mobility values between the runs. The missing value problem in protein quantification over many samples is greatly reduced by CCS aware MBR.MS1 level label-free quantification is also implemented which proves to be highly precise and accurate on a benchmark dataset with known ground truth. MaxQuant for LC-IMS-MS/MS is part of the basic MaxQuant release and can be downloaded from http://maxquant.org

The GlycoPaSER Prototype as a Real-Time N-Glycopeptide Identification Tool Based on the PaSER Parallel Computing Platform

Real-time database searching allows for simpler and automated proteomics workflows as it eliminates technical bottlenecks in high-throughput experiments. Most importantly, it enables results-dependent acquisition (RDA), where search results can be used to guide data acquisition during acquisition. This is especially beneficial for glycoproteomics since the wide range of physicochemical properties of glycopeptides lead to a wide range of optimal acquisition parameters. We established here the GlycoPaSER prototype by extending the Parallel Search Engine in Real-time (PaSER) functionality for real-time glycopeptide identification from fragmentation spectra. Glycopeptide fragmentation spectra were decomposed into peptide and glycan moiety spectra using common N-glycan fragments. Each moiety was subsequently identified by a specialized algorithm running in real-time. GlycoPaSER can keep up with the rate of data acquisition for real-time analysis with similar performance to other glycoproteomics software and produces results that are in line with the literature reference data. The GlycoPaSER prototype presented here provides the first proof-of-concept for real-time glycopeptide identification that unlocks the future development of RDA technology to transcend data acquisition

CD74-NRG1 Fusions in Lung Adenocarcinoma

We discovered a novel somatic gene fusion, CD74-NRG1, by transcriptome sequencing of 25 lung adenocarcinomas of never smokers. By screening 102 lung adenocarcinomas negative for known oncogenic alterations, we found four additional fusion-positive tumors, all of which were of the invasive mucinous subtype. Mechanistically, CD74-NRG1 leads to extracellular expression of the EGF-like domain of NRG1 III- ss 3, thereby providing the ligand for ERBB2-ERBB3 receptor complexes. Accordingly, ERBB2 and ERBB3 expression was high in the index case, and expression of phospho-ERBB3 was specifically found in tumors bearing the fusion ( P < 0.0001). Ectopic expression of CD74-NRG1 in lung cancer cell lines expressing ERBB2 and ERBB3 activated ERBB3 and the PI3K-AKT pathway, and led to increased colony formation in soft agar. Thus, CD74-NRG1 gene fusions are activating genomic alterations in invasive mucinous adenocarcinomas and may offer a therapeutic opportunity for a lung tumor subtype with, so far, no effective treatment. SIGNIFICANCE: CD74-NRG1 fusions may represent a therapeutic opportunity for invasive mucinous lung adenocarcinomas, a tumor with no effective treatment that frequently presents with multifocal unresectable disease. Cancer Discov; 4(4); 415- 22. (c) 2014 AACR