FACT - Threshold prediction for higher duty cycle and improved scheduling

The First G-APD Cherenkov telescope (FACT) is the first telescope using silicon photon detectors (G-APD aka. SiPM). The use of Silicon devices promise a higher photon detection efficiency, more robustness and higher precision than photo-multiplier tubes. Being operated during different light-conditions, the threshold settings of a Cherenkov telescope have to be adapted to feature the lowest possible threshold but also an efficient suppression of triggers from night-sky background photons. Usually this threshold is set either by experience or a mini-ratescan. Since the measured current through the sensors is directly correlated with the noise level, the current can be used to set the best threshold at any time. Due to the correlation between the physical threshold and the final energy threshold, the current can also be used as a measure for the energy threshold of any observation. This presentation introduces a method which uses the properties of the moon and the source position to predict the currents and the corresponding energy threshold for every upcoming observation allowing to adapt the observation schedule accordingly

FACT - Long-term stability and observations during strong Moon light

The First G-APD Cherenkov Telescope (FACT) is the first Cherenkov telescope equipped with a camera made of silicon photon detectors (G-APD aka. SiPM). Since October 2011, it is regularly taking data on the Canary Island of La Palma. G-APDs are ideal detectors for Cherenkov telescopes as they are robust and stable. Furthermore, the insensitivity of G-APDs towards strong ambient light allows to conduct observations during bright Moon and twilight. This gain in observation time is essential for the long-term monitoring of bright TeV blazars. During the commissioning phase, hundreds of hours of data (including data from the the Crab Nebula) were taken in order to understand the performance and sensitivity of the instrument. The data cover a wide range of observation conditions including different weather conditions, different zenith angles and different light conditions (ranging from dark night to direct full Moon). We use a new parmetrisation of the Moon light background to enhance our scheduling and to monitor the atmosphere. With the data from 1.5 years, the long-term stability and the performance of the camera during Moon light is studied and compared to that achieved with photomultiplier tubes so far.Comment: 3 pages, 3 figures, FACT Contribution to the 33rd International Cosmic Ray Conference (ICRC), Rio de Janeir

FACT - Long-term Monitoring of Bright TeV-Blazars

Since October 2011, the First G-APD Cherenkov Telescope (FACT) is operated successfully on the Canary Island of La Palma. Apart from the proof of principle for the use of G-APDs in Cherenkov telescopes, the major goal of the project is the dedicated long-term monitoring of a small sample of bright TeV blazars. The unique properties of G-APDs permit stable observations also during strong moon light. Thus a superior sampling density is provided on time scales at which the blazar variability amplitudes are expected to be largest, as exemplified by the spectacular variations of Mrk 501 observed in June 2012. While still in commissioning, FACT monitored bright blazars like Mrk 421 and Mrk 501 during the past 1.5 years so far. Preliminary results including the Mrk 501 flare from June 2012 will be presented.Comment: 4 pages, 4 figures, presented at the 33rd ICRC (2013

FACT - How stable are the silicon photon detectors?

The First G-APD Cherenkov telescope (FACT) is the first telescope using silicon photon detectors (G-APD aka. SiPM). The use of Silicon devices promise a higher photon detection efficiency, more robustness and higher precision than photo-multiplier tubes. Since the properties of G-APDs depend on auxiliary parameters like temperature, a feedback system adapting the applied voltage accordingly is mandatory. In this presentation, the feedback system, developed and in operation for FACT, is presented. Using the extraction of a single photon-equivalent (pe) spectrum as a reference, it can be proven that the sensors can be operated with very high precision. The extraction of the single-pe, its spectrum up to 10\,pe, its properties and their precision, as well as their long-term behavior during operation are discussed. As a by product a single pulse template is obtained. It is shown that with the presented method, an additional external calibration device can be omitted. The presented method is essential for the application of G-APDs in future projects in Cherenkov astronomy and is supposed to result in a more stable and precise operation than possible with photo-multiplier tubes

Individual Profiling of Circulating Tumor Cell Composition and Therapeutic Outcome in Patients with Hepatocellular Carcinoma

AbstractBACKGROUND AND AIMS: Circulating tumor cells (CTCs) have been proposed as a monitoring tool in patients with solid tumors. So far, automated approaches are challenged by the cellular heterogeneity of CTC, especially the epithelial-mesenchymal transition. Recently, Yu and colleagues showed that shifts in these cell populations correlated with response and progression, respectively, to chemotherapy in patients with breast cancer. In this study, we assessed which non-hematopoietic cell types were identifiable in the peripheral blood of hepatocellular carcinoma (HCC) patients and whether their distribution during treatment courses is associated with clinical characteristics. METHODS: Subsequent to few enrichment steps, cell suspensions were spun onto glass slides and further characterized using multi-immunofluorescence staining. All non-hematopoietic cells were counted and individual cell profiles were analyzed per patient and treatment. RESULTS:We detected a remarkable variation of cells with epithelial, mesenchymal, liver-specific, and mixed characteristics and different size ranges. The distribution of these subgroups varied significantly between different patient groups and was associated with therapeutic outcome. Kaplan-Meier logrank test showed that a change in the ratio of epithelial to mesenchymal cells was associated with longer median time to progression (1 vs 15 months; P = .03; hazard ratio = 0.18; 95%confidence interval = 0.01-2.75). CONCLUSIONS: Our data suggest that different CTC populations are identifiable in peripheral blood of HCC patients and, for the first time in HCC, that these individual cell type profiles may have distinct clinical implications. The further characterization and analysis of patients in this ongoing study seems to be warranted

A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects

Sustainable noncommercial bioinformatics infrastructures are a prerequisite to use and take advantage of the potential of big data analysis for research and economy. Consequently, funders, universities and institutes as well as users ask for a transparent value model for the tools and services offered. In this article, a generally applicable lightweight method is described by which bioinformatics infrastructure projects can estimate the value of tools and services offered without determining exactly the total costs of ownership. Five representative scenarios for value estimation from a rough estimation to a detailed breakdown of costs are presented. To account for the diversity in bioinformatics applications and services, the notion of service-specific ‘service provision units’ is introduced together with the factors influencing them and the main underlying assumptions for these ‘value influencing factors’. Special attention is given on how to handle personnel costs and indirect costs such as electricity. Four examples are presented for the calculation of the value of tools and services provided by the German Network for Bioinformatics Infrastructure (de.NBI): one for tool usage, one for (Web-based) database analyses, one for consulting services and one for bioinformatics training events. Finally, from the discussed values, the costs of direct funding and the costs of payment of services by funded projects are calculated and compared

Calibration and performance of the photon sensor response of FACT -- The First G-APD Cherenkov telescope

The First G-APD Cherenkov Telescope (FACT) is the first in-operation test of the performance of silicon photo detectors in Cherenkov Astronomy. For more than two years it is operated on La Palma, Canary Islands (Spain), for the purpose of long-term monitoring of astrophysical sources. For this, the performance of the photo detectors is crucial and therefore has been studied in great detail. Special care has been taken for their temperature and voltage dependence implementing a correction method to keep their properties stable. Several measurements have been carried out to monitor the performance. The measurements and their results are shown, demonstrating the stability of the gain below the percent level. The resulting stability of the whole system is discussed, nicely demonstrating that silicon photo detectors are perfectly suited for the usage in Cherenkov telescopes, especially for long-term monitoring purpose

FACT -- Operation of the First G-APD Cherenkov Telescope

Since more than two years, the First G-APD Cherenkov Telescope (FACT) is operating successfully at the Canary Island of La Palma. Apart from its purpose to serve as a monitoring facility for the brightest TeV blazars, it was built as a major step to establish solid state photon counters as detectors in Cherenkov astronomy. The camera of the First G-APD Cherenkov Telesope comprises 1440 Geiger-mode avalanche photo diodes (G-APD aka. MPPC or SiPM) for photon detection. Since properties as the gain of G-APDs depend on temperature and the applied voltage, a real-time feedback system has been developed and implemented. To correct for the change introduced by temperature, several sensors have been placed close to the photon detectors. Their read out is used to calculate a corresponding voltage offset. In addition to temperature changes, changing current introduces a voltage drop in the supporting resistor network. To correct changes in the voltage drop introduced by varying photon flux from the night-sky background, the current is measured and the voltage drop calculated. To check the stability of the G-APD properties, dark count spectra with high statistics have been taken under different environmental conditions and been evaluated. The maximum data rate delivered by the camera is about 240 MB/s. The recorded data, which can exceed 1 TB in a moonless night, is compressed in real-time with a proprietary loss-less algorithm. The performance is better than gzip by almost a factor of two in compression ratio and speed. In total, two to three CPU cores are needed for data taking. In parallel, a quick-look analysis of the recently recorded data is executed on a second machine. Its result is publicly available within a few minutes after the data were taken. [...]Comment: 19th IEEE Real-Time Conference, Nara, Japan (2014

PRIDE: Quality control in a proteomics data repository

The PRoteomics IDEntifications (PRIDE) database is a large public proteomics data repository, containing over 270 million mass spectra (by November 2011). PRIDE is an archival database, providing the proteomics data supporting specific scientific publications in a computationally accessible manner. While PRIDE faces rapid increases in data deposition size as well as number of depositions, the major challenge is to ensure a high quality of data depositions in the context of highly diverse proteomics work flows and data representations. Here, we describe the PRIDE curation pipeline and its practical application in quality control of complex data depositions