Rapid detection of 2-hydroxyglutarate in frozen sections of IDH mutant tumors by MALDI-TOF mass spectrometry

All isocitrate dehydrogenase (IDH) mutant solid neoplasms exhibit highly elevated levels of D-2-hydroxyglutarate (D-2HG). Detection of 2HG in tumor tissues currently is performed by gas or liquid chromatography-mass spectrometry (GC- or LC-MS) or biochemical detection. While these methods are highly accurate, a considerable amount of time for tissue preparation and a relatively high amount of tissue is required for testing. We here present a rapid approach to detect 2HG in brain tumor tissue based on matrix-assisted laser desorption ionization - time of flight mass spectrometry (MALDI-TOF). We analyzed 26 brain tumor samples with known IDH1 or IDH2 mutation and compared readouts to those from 28 brain tumor samples of wildtype IDH status. IDH mutant samples exhibited a clear positive signal for 2HG which was not observed in any of the IDH wildtype tumors. Our analytical pipeline allowed for 2HG detection in less than 5 min. Data were validated by determining 2HG levels in all tissues with a biochemical assay. In conclusion, we developed a protocol for rapid detection of 2HG levels and illustrate the possibility to use MALDI-TOF for the detection of metabolites on frozen tissue sections in a diagnostic setting

DNA methylation-based classification of central nervous system tumours.

Accurate pathological diagnosis is crucial for optimal management of patients with cancer. For the approximately 100 known tumour types of the central nervous system, standardization of the diagnostic process has been shown to be particularly challenging-with substantial inter-observer variability in the histopathological diagnosis of many tumour types. Here we present a comprehensive approach for the DNA methylation-based classification of central nervous system tumours across all entities and age groups, and demonstrate its application in a routine diagnostic setting. We show that the availability of this method may have a substantial impact on diagnostic precision compared to standard methods, resulting in a change of diagnosis in up to 12% of prospective cases. For broader accessibility, we have designed a free online classifier tool, the use of which does not require any additional onsite data processing. Our results provide a blueprint for the generation of machine-learning-based tumour classifiers across other cancer entities, with the potential to fundamentally transform tumour pathology

Influence of Early and Late Fuel Injection on Air Flow Structure and Kinetic Energy in an Optical SIDI Engine

The turbulent in-cylinder air flow and the unsteady high-pressure fuel injection lead to a highly transient air fuel mixing process in spark-ignition direct-injection (SIDI) engines, which is the leading cause for combustion cycle-to-cycle variation (CCV) and requires further investigation. In this study, crank-angle resolution particle image velocimetry (PIV) was employed to simultaneously measure the air flow and fuel spray structure at 1300 rpm in an optically accessible single-cylinder SIDI engine. The measurement was conducted at the center tumble plane of the four-valve pent-roof engine, bisecting the spark plug and fuel injector. 84 consecutive cycles were recorded for three engine conditions, i.e. (1) none-fueled motored condition, (2) homogeneous-charge mode with start of injection (SOI) during intake (50 crank-angle degree (CAD) after top dead center exhaust, aTDCexh), and (3) stratified-charge mode with SOI during mid compression (270 aTDCexh). The air flow structure (quantified by the objective metric – relevance index) and kinetic energy were examined to study the effect of the fuel spray on the air flow. The air flow was nearly identical for three conditions before the fuel injection. During fuel injection, the entrainment of air into the spray was observed near the spray but the flow structure further away from the spray was not significantly affected for both homogeneous and stratified charge modes. Right after the fuel was atomized, the spray increased the kinetic energy of air flow by 48±25% and 45±40% (average ± standard variation, with CCV included in standard deviation) for spray at intake and compression stroke, respectively. Spray changed the flow structure and kinetic energy immediately after injection for both conditions. The changes caused by injection during intake did not affect the flow and CCV at spark timing. For injection during mid compression, both the flow-structure and kinetic-energy CCV were apparently affected at spark timing.This work is supported by the Engine Systems Division of the General Motors – University of Michigan Automotive Collaborative Research Laboratory.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/142812/1/2018-01-0205.pd

Code for Proper Orthogonal Decomposition

This is a free Matlab (R) code that can be used to perform Proper Orthogonal Decomposition of vector fields. Scalar fields can be handled after minor editing.Proper orthogonal decomposition (POD) has been utilized for well over a decade to study turbulence and cyclic variation of flow and combustion properties in internal combustion engines. In addition, POD is useful to quantitatively compare multi-cycle in-cylinder measurements with numerical simulations (Large-eddy simulation, LES). However, the application can be daunting and physical interpretation of POD can be ambiguous. In this paper, the mathematical procedure of POD is described conceptually and a compact MATLAB® code is provided. (Details are provided in a forthcoming paper (accepted) in the International Journal of Engine Research.This work was supported by General Motors R&D within the GM-UM Collaborative Research Laboratory on Engine Systems Research at The University of Michigan. Hao Chen is grateful for financial support from Shanghai Jiao Tong University to enable a ten-month visit to the University of Michigan. The authors would also like to acknowledge discussions with Professor Min Xu from Shanghai Jiao Tong University.http://deepblue.lib.umich.edu/bitstream/2027.42/92348/1/POD_Code_Chen_et_al.pd

Fabrication of bipolar transistors by maskless ion implantation

The first focused ion beam (FIB) arsenic ion implants are reported. A shallow junction, vertical npn bipolar transistor fabricated by maskless implantation of B and As is described. For comparison, devices on the same wafer were also processed with conventional, broad‐beam B and/or As implants. Good transistor performance is obtained for each type of implanted transistor. Device characteristics for FIB and conventional implants are generally the same. However, initial results indicate that diode quality and junction leakage appear somewhat degraded (excess generation–recombination) for FIB arsenic implanted devices. Characteristics of FIB boron implanted devices obtained over an extended period have been measured. These data indicate that wafer‐to‐wafer dose uniformity and quality (diode ideality and leakage currents) is equal to that for conventional implants (standard deviation

Particle-image velocimetry measurement errors when imaging through a transparent engine cylinder

When making particle-image velocimetry measurements through the quartz cylinder of a reciprocating engine, the particle images are aberrated. This work quantifies the practical field-of-view and the errors in the velocity measurements caused by those aberrations. Electro-optical image shifting was used to create a repeatable particle-image displacement distribution for 60 images. Ensemble averaging of these images is used to quantify the rms errors due to the shot-to-shot variation in (1) the particle-image fields, (2) the camera noise, (3) the variance in the correlation-peak detection and (4) the particle-image aberrations. These results demonstrate that the field-of-view is restricted to the centre 66 mm of the 86 mm inside-diameter cylinder due to decreased accuracy, decreased image-to-image precision and decreased displacement-peak detectability of the image-displacement correlation. The correlation-peak detectability was degraded by both particle-image aberrations and decreased transmission of the scattered light.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/49062/2/e20709.pd

Measurement of digital particle image velocimetry precision using electro-optically created particle-image displacements

The displacement (velocity) precision achieved with digital particle image velocimetry (PIV) was measured. The purpose of this work was to determine the precision and sensitivity of digital PIV using real rather than theoretical images at 1 and 2 mm spatial resolution. The displacement measurement precision was determined by measuring the RMS noise from 60 identical displacement distributions. This work is unique in that it uses electro-optical image shifting to create a repeatable image displacement distribution of random particle fields. The displacement variance between images is caused by the shot-to-shot variation in: (1) the particle-image fields, (2) the camera noise and (3) the variance in the correlation peak detection. In addition to magnification variations, the particle-number density, imaging-lens f-stop and image-plane position errors were varied to determine the best configuration. The results indicate that both the ensemble-mean and the RMS fluctuations of the image displacements are affected by these parameters and comparisons with results found in the literature are presented. The extents of these variations are quantified. This variance does not, of course, include errors due to random gradients and out-of-plane pairing losses, which exist in real turbulent flows.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/49061/2/e20705.pd

Glioma Through the Looking GLASS: Molecular Evolution of Diffuse Gliomas and the Glioma Longitudinal AnalySiS Consortium

Adult diffuse gliomas are a diverse group of brain neoplasms that inflict a high emotional toll on patients and their families. The Cancer Genome Atlas (TCGA) and similar projects have provided a comprehensive understanding of the somatic alterations and molecular subtypes of glioma at diagnosis. However, gliomas undergo significant cellular and molecular evolution during disease progression. We review the current knowledge on the genomic and epigenetic abnormalities in primary tumors and after disease recurrence, highlight the gaps in the literature, and elaborate on the need for a new multi-institutional effort to bridge these knowledge gaps and how the Glioma Longitudinal AnalySiS Consortium (GLASS) aims to systemically catalog the longitudinal changes in gliomas. The GLASS initiative will provide essential insights into the evolution of glioma toward a lethal phenotype, with the potential to reveal targetable vulnerabilities, and ultimately, improved outcomes for a patient population in need