Using the Mass Storage System at ZIB within I3HP

In the framework of I3HP there are two Transnational Access Activities related to Computational Hadron Physics. One of these activities is access to the mass storage system at Konrad-Zuse-Zentrum fuer Informationstechnik Berlin (ZIB). European lattice physics collaborations can apply for mass storage capacity in order to store and share their configurations or other data (see http://www.zib.de/i3hp/). In this paper formal and technical aspects of usage as well as the conformance to the International Lattice DataGrid (ILDG) are explained.Comment: Talk given at the Workshop on Computational Hadron Physics, Nicosia, Cyprus, 14--17 September 200

Grid simulation services for the medical community

The first part of this paper presents a selection of medical simulation applications, including image reconstruction, near real-time registration for neuro-surgery, enhanced dose distribution calculation for radio-therapy, inhaled drug delivery prediction, plastic surgery planning and cardio-vascular system simulation. The latter two topics are discussed in some detail. In the second part, we show how such services can be made available to the clinical practitioner using Grid technology. We discuss the developments and experience made during the EU project GEMSS, which provides reliable, efficient, secure and lawful medical Grid services

Development of a 1 GS/s high-resolution transient recorder

With present-day detectors in high energy physics one is often faced with short analog pulses of a few nanoseconds length which may cover large dynamic ranges. In many experiments both amplitude and timing information have to be measured with high accuracy. Additionally, the data rate per readout channel can reach several MHz, which makes high demands on the separation of pile-up pulses. For such applications we have built the GANDALF transient recorder with a resolution of 12bit@1GS/s and an analog bandwidth of 500 MHz. Signals are digitized and processed by fast algorithms to extract pulse arrival times and amplitudes in real-time and to generate experiment trigger signals. With up to 16 analog channels, deep memories and a high data rate interface, this 6U-VME64x/VXS module is not only a dead-time free digitization unit but also has huge numerical capabilities provided by the implementation of a Virtex5-SXT FPGA. Fast algorithms implemented in the FPGA may be used to disentangle possible pile-up pulses and determine timing information from sampled pulse shapes with a time resolution in the picosecond range. Recently the application spectrum has been extended by implementing a 128-channel time-to-digital converter inside the FPGA and an appropriate input mezzanine card

Neurocognitive subgroups in major depressive disorder

Background: Major depressive disorder (MDD) is commonly associated with neurocognitive dysfunction. However, there remains substantial heterogeneity between patients and inconsistent findings regarding the magnitude and prevalence of specific neurocognitive deficits. This study aimed to investigate the potential for different neurocognitive subgroups in patients diagnosed with MDD. Method: Data were pooled from 4 different clinical trials that involved adults diagnosed with MDD. Neurocognitive outcomes included measures of verbal learning and memory, executive function, attention, and processing speed. Latent class analysis was conducted to examine for different subgroups based on neurocognitive profiles of performance across outcome measures. Subgroups were compared to a separate sample of age-matched adult healthy controls, across illness factors, and individual mood items on the Montgomery-Asberg Depression Rating Scale (MADRS). Results: Within the MDD cohort (N = 149), 45% of participants were considered relatively "cognitively preserved, " with the remainder "cognitively reduced" (39%) or "cognitively impaired" (16%). Verbal memory performance was significantly poorer compared to attention and processing speed only in the "cognitively impaired" subgroup. There was no association between subgroup membership and relevant illness factors, including ratings on individual MADRS items. Limitations: Data were pooled from several studies that included different neurocognitive measures and cohorts. Conclusions: Approximately half of MDD participants had no or minimal objective cognitive difficulties, and neurocognitive functioning was found generally unrelated to illness factors. Future longitudinal research is warranted to determine whether the people who are relatively cognitively impaired are at increased risk for further cognitive decline

Spatially resolved simulation of a radio frequency driven micro atmospheric pressure plasma jet and its effluent

Radio frequency driven plasma jets are frequently employed as efficient plasma sources for surface modification and other processes at atmospheric pressure. The radio-frequency driven micro atmospheric pressure plasma jet ($\mu$APPJ) is a particular variant of that concept whose geometry allows direct optical access. In this work, the characteristics of the $\mu$APPJ operated with a helium-oxygen mixture and its interaction with a helium environment are studied by numerical simulation. The density and temperature of the electrons, as well as the concentration of all reactive species are studied both in the jet itself and in its effluent. It is found that the effluent is essentially free of charge carriers but contains a substantial amount of activated oxygen (O, O$_3$ and O$_2(^1\Delta)$). The simulation results are verified by comparison with experimental data

Inferring and perturbing cell fate regulomes in human brain organoids

Self-organizing neural organoids grown from pluripotent stem cells(1-3) combined with single-cell genomic technologies provide opportunities to examine gene regulatory networks underlying human brain development. Here we acquire single-cell transcriptome and accessible chromatin data over a dense time course in human organoids covering neuroepithelial formation, patterning, brain regionalization and neurogenesis, and identify temporally dynamic and brain-region-specific regulatory regions. We developed Pando-a flexible framework that incorporates multi-omic data and predictions of transcription-factor-binding sites to infer a global gene regulatory network describing organoid development. We use pooled genetic perturbation with single-cell transcriptome readout to assess transcription factor requirement for cell fate and state regulation in organoids. We find that certain factors regulate the abundance of cell fates, whereas other factors affect neuronal cell states after differentiation. We show that the transcription factor GLI3 is required for cortical fate establishment in humans, recapitulating previous research performed in mammalian model systems. We measure transcriptome and chromatin accessibility in normal or GLI3-perturbed cells and identify two distinct GLI3 regulomes that are central to telencephalic fate decisions: one regulating dorsoventral patterning with HES4/5 as direct GLI3 targets, and one controlling ganglionic eminence diversification later in development. Together, we provide a framework for how human model systems and single-cell technologies can be leveraged to reconstruct human developmental biology

Volatile organic compounds composition of merged and aged forest fire plumes from Alaska and western Canada

The NOAA WP-3 aircraft intercepted aged forest fire plumes from Alaska and western Canada during several flights of the NEAQS-ITCT 2k4 mission in 2004. Measurements of acetonitrile (CH3CN) indicated that the air masses had been influenced by biomass burning. The locations of the plume intercepts were well described using emissions estimates and calculations with the transport model FLEXPART. The best description of the data was generally obtained when FLEXPART injected the forest fire emissions to high altitudes in the model. The observed plumes were generally drier than the surrounding air masses at the same altitude, suggesting that the fire plumes had been processed by clouds and that moisture had been removed by precipitation. Different degrees of photochemical processing of the plumes were determined from the measurements of aromatic VOCs. The removal of aromatic VOCs was slow considering the transport times estimated from the FLEXPART model. This suggests that the average OH levels were low during the transport, which may be explained by the low humidity and high concentrations of carbon monoxide and other pollutants. In contrast with previous work, no strong secondary production of acetone, methanol and acetic acid is inferred from the measurements. A clear case of removal of submicron particle volume and acetic acid due to precipitation scavenging was observed. Copyright 2006 by the American Geophysical Union