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Network or graph theory has become a popular tool to represent and analyze large-scale interaction patterns in the brain. To derive a functional network representation from experimentally recorded neural time series one has to identify the structure of the interactions between these time series. In neuroscience, this is often done by pairwise bivariate analysis because a fully multivariate treatment is typically not possible due to limited data and excessive computational cost. Furthermore, a true multivariate analysis would consist of the analysis of the combined effects, including information theoretic synergies and redundancies, of all possible subsets of network components. Since the number of these subsets is the power set of the network components, this leads to a combinatorial explosion (i.e. a problem that is computationally intractable). In contrast, a pairwise bivariate analysis of interactions is typically feasible but introduces the possibility of false detection of spurious interactions between network components, especially due to cascade and common drive effects. These spurious connections in a network representation may introduce a bias to subsequently computed graph theoretical measures (e.g. clustering coefficient or centrality) as these measures depend on the reliability of the graph representation from which they are computed. Strictly speaking, graph theoretical measures are meaningful only if the underlying graph structure can be guaranteed to consist of one type of connections only, i.e. connections in the graph are guaranteed to be non-spurious. ...
When studying real world complex networks, one rarely has full access to all their components. As an example, the central nervous system of the human consists of 1011 neurons which are each connected to thousands of other neurons. Of these 100 billion neurons, at most a few hundred can be recorded in parallel. Thus observations are hampered by immense subsampling. While subsampling does not affect the observables of single neuron activity, it can heavily distort observables which characterize interactions between pairs or groups of neurons. Without a precise understanding how subsampling affects these observables, inference on neural network dynamics from subsampled neural data remains limited.
We systematically studied subsampling effects in three self-organized critical (SOC) models, since this class of models can reproduce the spatio-temporal activity of spontaneous activity observed in vivo. The models differed in their topology and in their precise interaction rules. The first model consisted of locally connected integrate- and fire units, thereby resembling cortical activity propagation mechanisms. The second model had the same interaction rules but random connectivity. The third model had local connectivity but different activity propagation rules. As a measure of network dynamics, we characterized the spatio-temporal waves of activity, called avalanches. Avalanches are characteristic for SOC models and neural tissue. Avalanche measures A (e.g. size, duration, shape) were calculated for the fully sampled and the subsampled models. To mimic subsampling in the models, we considered the activity of a subset of units only, discarding the activity of all the other units.
Under subsampling the avalanche measures A depended on three main factors: First, A depended on the interaction rules of the model and its topology, thus each model showed its own characteristic subsampling effects on A. Second, A depended on the number of sampled sites n. With small and intermediate n, the true A¬ could not be recovered in any of the models. Third, A depended on the distance d between sampled sites. With small d, A was overestimated, while with large d, A was underestimated.
Since under subsampling, the observables depended on the model's topology and interaction mechanisms, we propose that systematic subsampling can be exploited to compare models with neural data: When changing the number and the distance between electrodes in neural tissue and sampled units in a model analogously, the observables in a correct model should behave the same as in the neural tissue. Thereby, incorrect models can easily be discarded. Thus, systematic subsampling offers a promising and unique approach to model selection, even if brain activity was far from being fully sampled.
Two generic mechanisms for emergence of direction selectivity coexist in recurrent neural networks
(2013)
Poster presentation: Twenty Second Annual Computational Neuroscience Meeting: CNS*2013. Paris, France. 13-18 July 2013.
In the mammalian visual cortex, the time-averaged response of many neurons is maximal for stimuli moving in a particular direction. Such a direction selective response is not found in LGN, upstream of the visual processing pathway, suggesting that cortical networks play a strong role in the generation of direction selectivity. Here we investigate the mechanisms for the emergence of direction selectivity in the recurrent networks of nonlinear firing rate neurons in layer 4 of V1 receiving the input from LGN. In the model the LGN inputs are characterized by different receptive field positions, and their relative temporal phase shifts are reversed for the stimuli moving in the opposite direction. We propose that two distinct mechanisms result in the neuronal direction selective response in these recurrent networks. The first one is a result of nonlinear feed-forward summation of several time-shifted inputs. The second mechanism is based on the competition between neurons for firing in a winner-take-all regime. Both mechanisms rely on inhibitory interactions in the connectivity matrix of lateral connections, but the second one involves inhibitory loops. Typically, the first mechanism results in lower selectivity values than the second, but the time-course of acquiring direction selective response is faster for the first mechanism. Importantly, the two mechanisms have different input frequency tuning. The first mechanism, based on the nonlinear summation, result in a relatively narrow tuning curve around the preferred frequency of the stimulus in the case of the moving grating. In contrast, the direction selectivity arising from the second mechanism depends only weakly on the input frequency, i.e. has a broader tuning curve. These differences allow us to provide the recipe for identifying in experiment which of the two mechanisms is used by a given direction selective neuron. We then analyze how the statistics of the connections in the random recurrent networks affect the relative contributions from these two mechanisms and determine the distributions of the direction selectivity values. We identify the motifs in the connectivity matrix, which are required for each mechanism and show that the minimal conditions for both mechanisms are met in a very broad set of random recurrent networks with sufficiently strong inhibitory connections. Thus, we propose that these mechanisms coexist in generic recurrent networks with inhibition. Our results may account for the recent experimental observations that direction selectivity is present in dark-reared mice and ferrets [1,2]. It can also explain the emergence of direction selectivity in species lacking a spatially organized direction selectivity map.
Neuronal dynamics differs between wakefulness and sleep stages, so does the cognitive state. In contrast, a single attractor state, called self-organized critical (SOC), has been proposed to govern human brain dynamics for its optimal information coding and processing capabilities. Here we address two open questions: First, does the human brain always operate in this computationally optimal state, even during deep sleep? Second, previous evidence for SOC was based on activity within single brain areas, however, the interaction between brain areas may be organized differently. Here we asked whether the interaction between brain areas is SOC. ...
Im Rahmen des Vortrags wird zunächst ein Überblick über die aktuell angewandten Linsensysteme in der (refraktiven) Kataraktchirurgie sowie im Rahmen des RLA gesprochen. Hierzu zählen die monofokalen sphärischen Standardlinsen, aber auch asphärische, torische und multifokale Implantate.
Speziell wird auf die Ergebnisse einer Studie zu einem neuen multifokalen-torischen Implantat eingegangen. Der Schwerpunkt des Vortrages liegt dann weiterhin auf den trifokalen Korrektionsmöglichkeiten. Zum einen wird die sog. binokulare Trifokalität, bei der zwei multifokale Intraokularlinsen unterschiedlicher Addition implantiert werden, besprochen. Durch die Anpassung jeweils eines Auges an den Intermediär- bzw. Nahbereich soll so bei verringerten optischen Phänomenen ein deutliches Sehen in drei Hauptdistanzen ermöglicht werden. Weiterhin befasst sich der Vortrag aber auch mit den neuen echten trifokalen Optiksystemen, welche ebenfalls deutliches Sehen in verschiedenen Entfernungen gewährleisten können.
Im dritten Teil des Vortrages werden aktuelle Langzeitergebnisse aus einer FDA Studie zur Evaluation einer kammerwinkelgestützten phaken Intraokularlinse, mit speziellem Augenmerk auf den cornealen Endothelzellverlust, sowie eine neuartige sulcusgestütze phake Intraokularlinse mit zentralem Loch zur Glaukomvermeidung vorgestellt.
Background: After induction of DNA double strand breaks (DSBs), the DNA damage response (DDR) is activated. One of the earliest events in DDR is the phosphorylation of serine 139 on the histone variant H2AX (gH2AX) catalyzed by phosphatidylinositol 3-kinases-related kinases. Despite being extensively studied, H2AX distribution[1] across the genome and gH2AX spreading around DSBs sites[2] in the context of different chromatin compaction states or transcription are yet to be fully elucidated.
Materials and methods: gH2AX was induced in human hepatocellular carcinoma cells (HepG2) by exposure to 10 Gy X-rays (250 kV, 16 mA). Samples were incubated 0.5, 3 or 24 hours post irradiation to investigate early, intermediate and late stages of DDR, respectively. Chromatin immunoprecipitation was performed to select H2AX, H3 and gH2AX-enriched chromatin fractions. Chromatin-associated DNA was then sequenced by Illumina ChIP-Seq platform. HepG2 gene expression and histone modification (H3K36me3, H3K9me3) ChIP-Seq profiles were retrieved from Gene Expression Omnibus (accession numbers GSE30240 and GSE26386, respectively).
Results: First, we combined G/C usage, gene content, gene expression or histone modification profiles (H3K36me3, H3K9me3) to define genomic compartments characterized by different chromatin compaction states or transcriptional activity. Next, we investigated H3, H2AX and gH2AX distributions in such defined compartments before and after exposure to ionizing radiation (IR) to study DNA repair kinetics during DDR. Our sequencing results indicate that H2AX distribution followed H3 occupancy and, thus, the nucleosome pattern. The highest H2AX and H3 enrichment was observed in transcriptionally active compartments (euchromatin) while the lowest was found in low G/C and gene-poor compartments (heterochromatin). Under physiological conditions, the body of highly and moderately transcribed genes was devoid of gH2AX, despite presenting high H2AX levels. gH2AX accumulation was observed in 5’ or 3’ flanking regions, instead. The same genes showed a prompt gH2AX accumulation during the early stage of DDR which then decreased over time as DDR proceeded.
Finally, during the late stage of DDR the residual gH2AX signal was entirely retained in heterochromatic compartments. At this stage, euchromatic compartments were completely devoid of gH2AX despite presenting high levels of non-phosphorylated H2AX.
Conclusions: We show that gH2AX distribution ultimately depends on H2AX occupancy, the latter following H3 occupancy and, thus, nucleosome pattern. Both H2AX and H3 levels were higher in actively transcribed compartments. However, gH2AX levels were remarkably low over the body of actively transcribed genes suggesting that transcription levels antagonize gH2AX spreading. Moreover, repair processes did not take place uniformly across the genome; rather, DNA repair was affected by genomic location and transcriptional activity. We propose that higher H2AX density in euchromaticcompartments results in high relative gH2AXconcentration soon after the activation of DDR, thus favoring the recruitment of the DNA repair machinery to those compartments. When the damage is repaired and gH2AX is removed, its residual fraction is retained in the heterochromatic compartments which are then targeted and repaired at later times.
Bibliotheken sind im Erwerbungsalltag mit einer Vielzahl unterschiedlichster Lizenzverträge für die Beschaffung von elektronischen Medien konfrontiert. Dabei nimmt die Komplexität durch das Anwachsen der Zahl der Marktteilnehmer aus Buchhandel und Agenturen, Verlagen und auch der verschiedenen Konsortien sowohl auf nationaler als auch auf internationaler Ebene wie durch die immer größer werdende Vielzahl der Produkte und Lizenzmodelle ständig zu. Die Transaktionskosten bei der Lizenzierung neuer Produkte, aber auch die Aktivitäten zur Verlängerung bestehender Lizenzverträge, steigen proportional mit der Zunahme der Bedeutung und Gewichtung, die elektronische Medienangebote einnehmen. Geschäftsgangmodelle, die ein Verfahren ohne Reibungsverluste garantieren, sind nicht vorhanden - wenn denn ein entsprechendes Problembewusstsein für die Bedeutung und den Wirkungsgrad bestimmter Lizenzvertragsklauseln existiert. Aufgrund der prinzipiell vorhandenen Vertragsfreiheit steht es den Partnern im Grunde frei, einen Vertrag entsprechend den Wünschen und Vorstellungen auszuhandeln. Dies wird in bestimmten Fällen von Vorteil sein, wenn es sich z.B. um Verträge von Konsortien mit Produkteanbietern handelt. Wie aber verhält es sich mit individuell abzuschließenden Lizenzverträgen einzelner Institutionen, z.B. beim Nachkauf von E-Books oder Ergänzungen von weiteren Datenbankprodukten des gleichen Anbieters. In vielen Fällen ist jedesmal ein Lizenzvertrag neu abzuschließen, wobei die minutiöse Lektüre aller Klauseln dringend angeraten sei. Hier würde sich anbieten, den Geschäftsverkehr der Vertragspartner zu vereinfachen, wenn nur schon die Vertragstexte soweit standardisiert wären, dass einheitliche Definitionen und Formulierungen für die einzelnen Regelungspunkte Verwendung fänden und lediglich Sonderabsprachen oder -vereinbarungen als Addenda beizufügen wären.
Zürich, 22. März 1937 - im ersten Stock des renommierten Herrenausstatters "London House" probiert Thomas Mann gerade einen neuen Anzug an, als ihn ein Verkäufer informiert, dass im Erdgeschoss Gerhart Hauptmann eingetroffen sei. "Möchten Sie ihn sehen?" Nach kurzem Zögern lehnt Thomas Mann ab - mit den Worten: "Ach, da wollen wir vielleicht doch andere Zeiten abwarten." Replik des Verkäufers: "Genau das hat Herr Hauptmann auch gesagt." Die Zürcher Nicht-Begegnung der beiden Nobelpreisträger ist in verschiedener Hinsicht bemerkenswert. Schließlich handelte es sich nicht nur um die international bekanntesten deutschen Schriftsteller, sondern auch um alte Bekannte. Und jeder von beiden hatte dem anderen manches zu verdanken. Warum also wollten die beiden einander nicht begegnen?
Um die literaturgeschichtliche Bedeutung der Situation im Zürcher Herrengeschäft einschätzen zu können, muss man die gesamte Beziehung zwischen beiden in den Blick fassen. Sie könnte wechselvoller kaum sein. Nach dreißig Jahren kollegialer, phasenweise nahezu freundschaftlicher Verbundenheit brach der Kontakt abrupt ab und wurde bis zu Hauptmanns Tod 1946 nicht mehr aufgenommen. Nach dem Ableben des älteren Kollegen ändert sich Thomas Manns Sicht auf Gerhart Hauptmann jedoch wieder. Und – soviel vorweg – dabei spielten Jubiläumsgeburtstage stets eine wichtige Rolle. Ich gehe zunächst auf die Phase der engen Bekanntschaft ein; im zweiten Teil dann auf die Umstände des Abbruchs der Beziehungen. Dabei soll vor allem der letzte Kontaktversuch genauer analysiert werden. Ein resümierender Blick auf die dritte Phase steht am Ende dieser Überlegungen. ...
Background: The rationale for gathering information from plants procuring nitrogen through symbiotic interactions controlled by a common genetic program for a sustainable biofuel production is the high energy demanding application of synthetic nitrogen fertilizers. We curated sequence information publicly available for the biofuel plant sugarcane, performed an analysis of the common SYM pathway known to control symbiosis in other plants, and provide results, sequences and literature links as an online database.
Methods: Sugarcane sequences and informations were downloaded from the nucEST database, cleaned and trimmed with seqclean, assembled with TGICL plus translating mapping method, and annotated. The annotation is based on BLAST searches against a local formatted plant Uniprot90 generated with CD-HIT for functional assignment, rpsBLAST to CDD database for conserved domain analysis, and BLAST search to sorghum's for Gene Ontology (GO) assignment. Gene expression was normalized according the Unigene standard, presented as ESTs/100 kb. Protein sequences known in the SYM pathway were used as queries to search the SymGRASS sequence database. Additionally, antimicrobial peptides described in the PhytAMP database served as queries to retrieve and generate expression profiles of these defense genes in the libraries compared to the libraries obtained under symbiotic interactions.
Results: We describe the SymGRASS, a database of sugarcane orthologous genes involved in arbuscular mycorrhiza (AM) and root nodule (RN) symbiosis. The database aggregates knowledge about sequences, tissues, organ, developmental stages and experimental conditions, and provides annotation and level of gene expression for sugarcane transcripts and SYM orthologous genes in sugarcane through a web interface. Several candidate genes were found for all nodes in the pathway, and interestingly a set of symbiosis specific genes was found.
Conclusions: The knowledge integrated in SymGRASS may guide studies on molecular, cellular and physiological mechanisms by which sugarcane controls the establishment and efficiency of endophytic associations. We believe that the candidate sequences for the SYM pathway together with the pool of exclusively expressed tentative consensus (TC) sequences are crucial for the design of molecular studies to unravel the mechanisms controlling the establishment of symbioses in sugarcane, ultimately serving as a basis for the improvement of grass crops.