Flow Cytometry Data Preparation Guidelines for Improved Automated Phenotypic Analysis.

Advances in flow cytometry (FCM) increasingly demand adoption of computational analysis tools to tackle the ever-growing data dimensionality. In this study, we tested different data input modes to evaluate how cytometry acquisition configuration and data compensation procedures affect the performance of unsupervised phenotyping tools. An analysis workflow was set up and tested for the detection of changes in reference bead subsets and in a rare subpopulation of murine lymph node CD103+ dendritic cells acquired by conventional or spectral cytometry. Raw spectral data or pseudospectral data acquired with the full set of available detectors by conventional cytometry consistently outperformed datasets acquired and compensated according to FCM standards. Our results thus challenge the paradigm of one-fluorochrome/one-parameter acquisition in FCM for unsupervised cluster-based analysis. Instead, we propose to configure instrument acquisition to use all available fluorescence detectors and to avoid integration and compensation procedures, thereby using raw spectral or pseudospectral data for improved automated phenotypic analysis.We thank Irene Palacios, Elena Prieto, Mariano Vito´n, and Raquel Nieto for excellent technical assistance and Dr. Salvador Iborra for helpful discussion of dendritic cell studies. Editorial assistance was provided by Simon Bartlett.S

Left ventricular apical diseases

There are many disorders that may involve the left ventricular (LV) apex; however, they are sometimes difficult to differentiate. In this setting cardiac imaging methods can provide the clue to obtaining the diagnosis. The purpose of this review is to illustrate the spectrum of diseases that most frequently affect the apex of the LV including Tako-Tsubo cardiomyopathy, LV aneurysms and pseudoaneurysms, apical diverticula, apical ventricular remodelling, apical hypertrophic cardiomyopathy, LV non-compaction, arrhythmogenic right ventricular dysplasia with LV involvement and LV false tendons, with an emphasis on the diagnostic criteria and imaging features

The IceCube Neutrino Observatory: Instrumentation and Online Systems

The IceCube Neutrino Observatory is a cubic-kilometer-scale high-energy neutrino detector built into the ice at the South Pole. Construction of IceCube, the largest neutrino detector built to date, was completed in 2011 and enabled the discovery of high-energy astrophysical neutrinos. We describe here the design, production, and calibration of the IceCube digital optical module (DOM), the cable systems, computing hardware, and our methodology for drilling and deployment. We also describe the online triggering and data filtering systems that select candidate neutrino and cosmic ray events for analysis. Due to a rigorous pre-deployment protocol, 98.4% of the DOMs in the deep ice are operating and collecting data. IceCube routinely achieves a detector uptime of 99% by emphasizing software stability and monitoring. Detector operations have been stable since construction was completed, and the detector is expected to operate at least until the end of the next decade.Comment: 83 pages, 50 figures; updated with minor changes from journal review and proofin

Detecting and quantifying stress granules in tissues of multicellular organisms with the Obj.MPP analysis tool

International audienceStress Granules (SGs) are macromolecular assemblies induced by stress and composed of proteins and mRNAs stalled in translation initiation. SGs play an important role in the response to stress and in the modulation of signaling pathways. Furthermore, these structures are related to the pathological ribonucleoprotein (RNP) aggregates found in neurodegenerative disease contexts, highlighting the need to understand how they are formed and recycled in normal and pathological contexts. Although genetically tractable multicellular organisms have been key in identifying modifiers of RNP aggregate toxicity, in vivo analysis of SG properties and regulation has lagged behind, largely due to the difficulty of detecting SG from images of intact tissues. Here, we describe the object detector software Obj.MPP and show how it overcomes the limits of classical object analyzers to extract the properties of SGs from wide-field and confocal images of respectively C. elegans and Drosophila tissues. We demonstrate that Obj.MPP enables the identification of genes modulating the assembly of endogenous and pathological SGs, and thus that it will be useful in the context of future genetic screens and in vivo studies. This article is protected by copyright. All rights reserved

The atmospheric effects of stratospheric aircraft

This document presents a second report from the Atmospheric Effects of Stratospheric Aircraft (AESA) component of NASA's High-Speed Research Program (HSRP). This document presents a second report from the Atmospheric Effects of Stratospheric Aircraft (AESA) component of NASA's High Speed Research Program (HSRP). Market and technology considerations continue to provide an impetus for high-speed civil transport research. A recent United Nations Environment Program scientific assessment has shown that considerable uncertainty still exists about the possible impact of aircraft on the atmosphere. The AESA was designed to develop the body of scientific knowledge necessary for the evaluation of the impact of stratospheric aircraft on the atmosphere. The first Program report presented the basic objectives and plans for AESA. This second report presents the status of the ongoing research as reported by the principal investigators at the second annual AESA Program meeting in May 1992: Laboratory studies are probing the mechanism responsible for many of the heterogeneous reactions that occur on stratospheric particles. Understanding how the atmosphere redistributes aircraft exhaust is critical to our knowing where the perturbed air will go and for how long it will remain in the stratosphere. The assessment of fleet effects is dependent on the ability to develop scenarios which correctly simulate fleet operations

Rapakivi-related In-rich mineralisations in southeastern Fennoscandia

Indium is a critical metal for the world’s electronic industry due to its use in flat panel devices such as liquid crystal displays, plasma display panels and OLED displays. Thus, indium is used in televisions, mobile phones, laptops and notebooks. The current supply and demand has led to an increased interest for indium exploration globally. This thesis describes features of two different rapakivi-related In-rich mineralisations in southeastern Fennoscandia; polymetallic veins in Sarvlaxviken, Lovisa, southeastern Finland and skarn ore in Pitkäranta, Ladoga-Karelia, westernmost Russia. The polymetallic veins in Sarvlaxviken occur in two rapakivi granite varieties and can be divided into five metal associations: Li-As-W-Zn-Mn, Pb-Zn and Cu-As-In in wiborgite bedrock and As-Sn-Cu and Mo-Bi-Be in even-grained granite. These veins form complex systems, with multiple vein generations. The first three associations are strongly controlled by NNW-trending structures and evolved in two main stages (generation 1 and 2). The two latter associations exist in alteration zones of the Marviken granite but have only been observed in glacier transported boulders and thus, the timing of these are uncertain (generation x). The fluid inclusion data indicate that the depositional conditions of the wiborgite hosted veins were almost identical in all generations. The chlorine and sulphur contents in the fluids affected the formation of metals. The F-rich ore forming fluids emanated most likely from the Marviken granite. The skarn ore in the historic mining district of Pitkäranta is composed of four end member ore types, dominated by the metals Fe, Cu, Sn and Zn. However, several ore types exist in one and the same mine with gradational borders between each ore type, most likely reflecting variations in the depositional conditions. Some metals are, however, more common in certain areas and associated with certain trace elements, e.g. Ag, Bi, In and Li. Indium is in both study areas commonly associated with Zn –rich ores with sphalerite as the main carrier. Yet, the indium mineral roquesite has been observed in both study areas. The presence of indium minerals can be predicted by calculating the ppm In / % Zn ratios. If the ppm In / % Zn ratio exceeds 50, it is likely that the sample contains indium minerals. Over 2000 till samples were collected at 100-m or 20-m intervals for geochemical investigations in the Sarvlaxviken area. Numerous anomalous samples indicate several metal sources. The clear connection between anomalies and the already discovered polymetallic veins were not detected. These anomalies strongly suggest undiscovered veins under the soil cover. This thesis provides important information about rapakivi-related In-rich mineralisations in the Fennoscandian Shield. It includes mineralogical, geochemical and fluid inclusion studies, as well as detailed mapping of the bedrock and the till anomaly patterns, and thus provides a tool for exploration of metals in the rapakivi areas