From Big Data to Big Displays: High-Performance Visualization at Blue Brain

Blue Brain has pushed high-performance visualization (HPV) to complement its HPC strategy since its inception in 2007. In 2011, this strategy has been accelerated to develop innovative visualization solutions through increased funding and strategic partnerships with other research institutions. We present the key elements of this HPV ecosystem, which integrates C++ visualization applications with novel collaborative display systems. We motivate how our strategy of transforming visualization engines into services enables a variety of use cases, not only for the integration with high-fidelity displays, but also to build service oriented architectures, to link into web applications and to provide remote services to Python applications.Comment: ISC 2017 Visualization at Scale worksho

Reconstruction and simulation of neocortical microcircuitry

We present a first-draft digital reconstruction of the microcircuitry of somatosensory cortex of juvenile rat. The reconstruction uses cellular and synaptic organizing principles to algorithmically reconstruct detailed anatomy and physiology from sparse experimental data. An objective anatomical method defines a neocortical volume of 0.29 ± 0.01 mm3 containing ∼31,000 neurons, and patch-clamp studies identify 55 layer-specific morphological and 207 morpho-electrical neuron subtypes. When digitally reconstructed neurons are positioned in the volume and synapse formation is restricted to biological bouton densities and numbers of synapses per connection, their overlapping arbors form ∼8 million connections with ∼37 million synapses. Simulations reproduce an array of in vitro and in vivo experiments without parameter tuning. Additionally, we find a spectrum of network states with a sharp transition from synchronous to asynchronous activity, modulated by physiological mechanisms. The spectrum of network states, dynamically reconfigured around this transition, supports diverse information processing strategies

Die Poesiemaschine : Roland Barthes, Walter Benjamin und die Deutsche Frühromantik

Die Analogien zwischen der Barthes'schen Theorie und den Konzepten der deutschen Romantik sind von der Forschung durchaus registriert worden, Beobachtungen in diese Richtung haben aber bislang kaum über die Nominierung des Desiderats hinausgeführt. Das ist sicher überraschend, da in den letzten Jahrzehnten bekanntermaßen eine Vielzahl aktualisierender Romantik-Lektüren vor der Folie postmoderner Ästhetik und Erkenntnistheorie veröffentlicht wurden. Zur Behebung dieses Defizits beizutragen, ist dementsprechend das Anliegen dieses Beitrags. Im Folgenden sind Ansätze zur systematischen Aufarbeitung der vielfachen Bezüge zu konzipieren, die sich zwischen dem Text der Deutschen Romantik und den Arbeiten Barthes' aufzeigen lassen. In methodologischer Hinsicht bewegt sich ein solcher Vergleich allerdings auf nicht eben einfachem Terrain. Das resultiert zunächst aus dem beträchtlichen Volumen der theoretischen Erträge Roland Barthes' sowie der romantischen Autoren, infolgedessen eine strenge Reduktion der Textbasis notwendig wird. Hinzu kommt, dass diese Erträge jeweils in rigoros fragmentierten und hermetischen Schreibweisen codiert sind, die das Paradox und die begriffliche Unklarheit bewusst suchen. Das multipliziert die Zahl der Blickwinkel und wirft die Frage nach der Wahl der interpretativen Zugänge auf. Um diesem Dilemma zu entgehen, rekurriert das Folgende bewusst auf eine einzelne Darstellung romantischer Theorie, die sich durch ihre besondere Prägnanz und ein überdurchschnittliches analytisches Niveau auszeichnet: Walter Benjamins Dissertation zum Begriff der Kunstkritik in der deutschen Romantik

An integrative approach sheds new light onto the systematics and ecology of the widespread ciliate genus Coleps (Ciliophora, Prostomatea)

Species of the genus Coleps are one of the most common planktonic ciliates in lake ecosystems. The study aimed to identify the phenotypic plasticity and genetic variability of different Coleps isolates from various water bodies and from culture collections. We used an integrative approach to study the strains by (i) cultivation in a suitable culture medium, (ii) screening of the morphological variability including the presence/absence of algal endosymbionts of living cells by light microscopy, (iii) sequencing of the SSU and ITS rDNA including secondary structures, (iv) assessment of their seasonal and spatial occurrence in two lakes over a one-year cycle both from morphospecies counts and high-throughput sequencing (HTS), and, (v) proof of the co-occurrence of Coleps and their endosymbiotic algae from HTS-based network analyses in the two lakes. The Coleps strains showed a high phenotypic plasticity and low genetic variability. The algal endosymbiont in all studied strains was Micractinium conductrix and the mutualistic relationship turned out as facultative. Coleps is common in both lakes over the whole year in different depths and HTS has revealed that only one genotype respectively one species, C. viridis, was present in both lakes despite the different lifestyles (mixotrophic with green algal endosymbionts or heterotrophic without algae). Our results suggest a future revision of the species concept of the genus Coleps

BlueBrain/Brayns: 3.2.2 Release

Visualizer for large-scale and interactive ray-tracing of neuron

BlueBrain/MorphIO: Allow to throw warnings instead of writing them to stderr/stdout

remove -j2 from cpp_test.sh - not an option for cmake (#269) Adding C++ tests (#263) Fix for compat with recent HighFive (#268) Minimal solution to raising of warning instead of writing them (#266) apply ignoring logic to raised warnings as well (#271) Consider custom section types from 5 up to 10 (#274) fix broken links and include README to readthedocs (#276) narrow conditions when WARNING_NEUROMORPHO_SOMA_NON_CONFORM is thrown (#275

Impact of renal impairment on outcomes after autologous stem cell transplantation in multiple myeloma: a multi-center, retrospective cohort study

Abstract Background Renal impairment (RI) is a negative prognostic factor in Multiple Myeloma (MM) and affected patients are often excluded from autologous stem cell transplantation (ASCT). However, it remains unclear whether historically inferior outcome data still hold true. Methods From a total of 475 eligible MM patients who had undergone ASCT between 1998 and 2016, 374 were included in this multi-centric retrospective cohort study. Renal function was determined both at the time of MM diagnosis and ASCT by estimated glomerular filtration rate (eGFR according to the MDRD formula, RI defined as eGFR < 60 ml/min/1.73m2). Patients were categorized into 3 groups: A) no RI diagnosis and ASCT, B) RI at diagnosis with normalization before ASCT and C) RI both at the time of diagnosis and ASCT. Log-rank testing was used for overall and progression-free survival (OS, PFS) analysis. Conclusion While severe RI at MM diagnosis confers a risk of shorter OS, MM progression after ASCT is not affected by any stage of renal failure. It can be concluded that ASCT can be safely carried out in MM patients with mild to moderate RI and should be pro-actively considered in those with severe RI. Results When comparing all groups, no difference in OS and PFS was found (p = 0.319 and p = 0.904). After further stratification according to the degree of RI at the time of diagnosis, an OS disadvantage was detected for patients with an eGFR < 45 ml/min/m2. PFS was not affected by any RI stage