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Understanding the dynamics of recurrent neural networks is crucial for explaining how the brain processes information. In the neocortex, a range of different plasticity mechanisms are shaping recurrent networks into effective information processing circuits that learn appropriate representations for time-varying sensory stimuli. However, it has been difficult to mimic these abilities in artificial neural network models. Here we introduce SORN, a self-organizing recurrent network. It combines three distinct forms of local plasticity to learn spatio-temporal patterns in its input while maintaining its dynamics in a healthy regime suitable for learning. The SORN learns to encode information in the form of trajectories through its high-dimensional state space reminiscent of recent biological findings on cortical coding. All three forms of plasticity are shown to be essential for the network's success. Keywords: synaptic plasticity, intrinsic plasticity, recurrent neural networks, reservoir computing, time series prediction
Diese Arbeit untersuchte die Epidemiologie und den Einfluss verschiedener Faktoren (Grunderkrankung, empirische Therapie, Schweregrad der Sepsis und Erreger mit Resistenz) auf das Überleben von Patienten mit Septikämien. Die häufigsten Grunderkrankungen dieses Kollektivs waren Leukämien (33%), solide Neoplasien (14%) sowie kardiale Vorerkrankungen (14%). Knapp die Hälfte der Patienten erwarb die Septikämie im Krankenhaus (47%). ...
The pictorial art of the Church, as a spiritual product of the Christian civilisation, has continually received great influences from its ecclesiastical tradition and it was defined by its formal aesthetical standards and its iconographic preferences. A more nuanced reading of the parallels can be attained by placing the images in their visual context, which would allow a better appreciation of the meanings within. The biblical story of Adam and Eve, which is the theme of the following thesis, reflects the differentiation between the Eastern and the Western understanding of the events of the history of the holy Oikonomia, a point, which is the major ground for the development of the relative pictorial motifs. The protoplasts are the protagonists from their creation and life in paradise, the fall and expulsion until their resurrection through Christ. Their story is visualised in a number of scenes and episodes, having thus their original sin and resurrection for specific reasons centralised. This doctoral thesis attempts to collect as many parallels of the scenes is possible, trying to collate the Eastern with the Western visual approach in a deductive way, in order to reach our constructive conclusions and make available the combination of the art, theology and liturgy in the scenes of Adam and Eve in Genesis and in Resurrection (Anastasis). The reading we tried to perform was based upon the specific iconographical elements, which were worth to be commented. Our aim was to detect the direct bond between the production of art and the relevant patristic and apocryphal writings or even the theological theories, by quoting texts from the ecclesiastical literature, as well as the liturgical praxis.
Background: Pathogenic bacteria infecting both animals as well as plants use various mechanisms to transport virulence factors across their cell membranes and channel these proteins into the infected host cell. The type III secretion system represents such a mechanism. Proteins transported via this pathway (‘‘effector proteins’’) have to be distinguished from all other proteins that are not exported from the bacterial cell. Although a special targeting signal at the N-terminal end of effector proteins has been proposed in literature its exact characteristics remain unknown. Methodology/Principal Findings: In this study, we demonstrate that the signals encoded in the sequences of type III secretion system effectors can be consistently recognized and predicted by machine learning techniques. Known protein effectors were compiled from the literature and sequence databases, and served as training data for artificial neural networks and support vector machine classifiers. Common sequence features were most pronounced in the first 30 amino acids of the effector sequences. Classification accuracy yielded a cross-validated Matthews correlation of 0.63 and allowed for genome-wide prediction of potential type III secretion system effectors in 705 proteobacterial genomes (12% predicted candidates protein), their chromosomes (11%) and plasmids (13%), as well as 213 Firmicute genomes (7%). Conclusions/Significance: We present a signal prediction method together with comprehensive survey of potential type III secretion system effectors extracted from 918 published bacterial genomes. Our study demonstrates that the analyzed signal features are common across a wide range of species, and provides a substantial basis for the identification of exported pathogenic proteins as targets for future therapeutic intervention. The prediction software is publicly accessible from our web server ( www.modlab.org ).
Bacterial autotransporters represent a diverse family of proteins that autonomously translocate across the inner membrane of Gram-negative bacteria via the Sec complex and across the outer bacterial membrane. They often possess exceptionally long N-terminal signal sequences. We analyzed 90 long signal sequences of bacterial autotransporters and members of the two-partner secretion pathway in silico and describe common domain organization found in 79 of these sequences. The domains are in agreement with previously published experimental data. Our algorithmic approach allows for the systematic identification of functionally different domains in long signal sequences. Keywords: bacterial autotransporter, sequence analysis, pattern, protein targeting, signal peptide, protein trafficking
Streptomyces coelicolor ist der Modellorganismus der GC reichen, Gram+ Actinomyceten, die mehr als zwei Drittel aller bekannten Antibiotika produzieren. Phänotypisch zeichnet er sich durch die Bildung eines Substrat- und eines Luftmyzels aus, welches im Laufe der weiteren Differenzierung Sporen bildet. Streptomyceten produzieren neben Antibiotika noch eine Vielzahl biotechnologisch interessanter Metaboliten. Der komplexe Lebenszyklus und Stoffwechsel erfordern eine genaue Regulation der Genexpression. Die letzten Jahre haben gezeigt, dass neben Proteinen auch die RNA eine regulatorische Funktion hat. Verschiedene regulatorisch aktive RNA Elemente wie Riboswitche, RNA-Thermometer und kleine nicht kodierende RNAs (small noncoding RNAs – sRNAs) wurden identifiziert. sRNAs wirken meist als antisense Riboregulatoren, indem sie ihre Ziel-mRNA binden und dadurch die Translation hemmen oder fördern. In dieser Arbeit wurden verschiedene bioinformatische Methoden verwendet, um sRNAs im Genom von S. coelicolor vorherzusagen. Es wurden Terminatorstrukturen und konservierte Sekundärstrukturen in den intergenen Regionen vorhergesagt, die keinem Gen zuzuordnen waren. In einem weiteren Ansatz wurden Bindestellen des Regulatorproteins DasR vorhergesagt, um DasR kontrollierte sRNAs zu identifizieren. Zusätzlich wurde mittels 454 Sequenzierung erstmalig das Transkriptom von S. coeliocolor analysiert. Auf diese Weise konnten etwa 500 sRNAs vorhergesagt werden. Eine der beiden charakterisierten sRNAs, sc32, ist 139 nt lang. Ihr Promoter liegt im kodierenden Bereich des Gens bldC und sie wird spezifisch durch Kälteschock induziert. Die zweite charakterisierte sRNA, sc1, ist 159 nt lang und in allen sequenzierten Streptomyceten konserviert. Ihre Expression wird nur bei Stickstoffmangel in der Stationärphase reprimiert. Durch molekularbiologische Analysen konnte ein Zielgen von sc1 identifiziert werden, die extrazelluläre Agarase DagA. Es konnte gezeigt werden, dass sc1 an die dagA-mRNA bindet und dadurch die Translation inhibiert. Als zweites mögliches Ziel von sc1 konnte die Histidinkinase SCO5239 identifiziert werden. Hier wurde gezeigt, dass Koexpression von sc1 die Expression einer SCO5239 Reportergenfusion um den Faktor acht steigert. Durch Analyse des Proteoms von sc1 Mutanten, konnte die differenzierte Expression von elf weiteren Proteinen gezeigt werden. Sc1 scheint als Regulator zu agieren, indem es auf die Stickstoffversorgung der Zelle reagiert und den Sekundärmetabolismus deaktiviert.
Atmospheric observation-based global SF6 emissions - comparison of top-down and bottom-up estimates
(2009)
Emissions of sulphur hexafluoride (SF6), one of the strongest greenhouse gases on a per molecule basis, are targeted to be collectively reduced under the Kyoto Protocol. Because of its long atmospheric lifetime (≈3000 years), the accumulation of SF6 in the atmosphere is a direct measure of its global emissions. Examination of our extended data set of globally distributed high-precision SF6 observations shows an increase in SF6 abundance from near zero in the 1970s to a global mean of 6.7 ppt by the end of 2008. In-depth evaluation of our long-term data records shows that the global source of SF6 decreased after 1995, most likely due to SF6 emission reductions in industrialised countries, but increased again after 1998. By subtracting those emissions reported by Annex I countries to the United Nations Framework Convention of Climatic Change (UNFCCC) from our observation-inferred SF6 source leaves a surprisingly large gap of more than 70–80% of non-reported SF6 emissions in the last decade.
A new artificial regulatory system for essential genes in yeast is described. It prevents translation of target mRNAs upon tetracycline (tc) binding to aptamers introduced into their 5'UTRs. Exploiting direct RNA–ligand interaction renders auxiliary protein factors unnecessary. Therefore, our approach is strain independent and not susceptible to interferences by heterologous expressed regulatory proteins. We use a simple PCR-based strategy, which allows easy tagging of any target gene and the level of gene expression can be adjusted due to various tc aptamer-regulated promoters. As proof of concept, five differently expressed genes were targeted, two of which could not be regulated previously. In all cases, adding tc completely prevented growth and, as shown for Nop14p, rapidly abolished de novo protein synthesis providing a powerful tool for conditional regulation of yeast gene expression.
Alternative education or teaching radicalism? New literature on Islamic education in Southeast Asia
(2009)
This review article focuses on three recent publications on Islamic education in Southeast Asia. While two are monographs on South Thailand and Myanmar/ Burma, one is a collection of essays on Indonesia, Malaysia, South Thailand, Cambodia, and the Southern Philippines. All works highlight local, regional and international educational networks, as well as their connections to the Indian subcontinent and the Middle East. Based chiefly on first-hand fieldwork, the works deliver an up-to-date and detailed picture of current discussions and developments regarding Islamic education in Southeast Asia. Key words Education ; Islam ; Southeast Asia ; Indonesia ; Malaysia ; Thailand ; Myanmar
Samples of freshly fallen snow were collected at the high alpine research station Jungfraujoch, Switzerland, during the Cloud and Aerosol Characterization Experiments (CLACE) 5 in February and March 2006. Sampling was carried out on the Sphinx platform. Headspace-solid-phase-dynamic extraction (HS-SPDE) combined with gas chromatography/mass spectrometry (GC/MS) was used to quantify C6–C10 n-aldehydes in the snow samples. The most abundant n-aldehyde was n-hexanal (median concentration 1.324 micro g L -1) followed by n-nonanal, n-decanal, n-octanal and n-heptanal (median concentrations 1.239, 0.863, 0.460, and 0.304 micro g L -1, respectively). A wide range of concentrations was found among individual snow samples, even for samples taken at the same time. Higher median concentrations of all n-aldehydes were observed when air masses reached Jungfraujoch from the north-northwest in comparison to air masses arriving from the southeast-southwest. Results suggest that the n-aldehydes detected most likely are of direct and indirect biogenic origin, and that they entered the snow through the particle phase.
Responding to inadequate awareness of the outstanding importance of biodiversity, the BioFrankfurt network was founded in 2004 in the State of Hesse, Germany. It is presented here as a case study and may serve as a model for other parts of the world, such as the Middle East. In 2007, only about 26% of the German population were familiar with the term “Biodiversity”, and most of them only had a vague idea about its meaning. The BioFrankfurt network of institutions addressed this problem, raising public awareness and supporting research, education and conservation. A regional biodiversity education program has been developed and delivered to more than 500 schools. Since 2007, an innovative public relations campaign combines raising awareness on regional biodiversity issues with activities to improve the public image of the Frankfurt area. Because of its geographical focus, the network’s activities gained the attention of local and regional politicians and other decision makers, culminating in the joint establishment of a new Biodiversity and Climate Research Centre by BioFrankfurt member institutions. The success of current activities attracts interesting partners, resulting in challenging cooperation initiatives. The authors are convinced that the network’s concepts and activities have a great potential to profoundly enhance the notion and acceptance of biodiversity issues elsewhere. Keywords: BioFrankfurt, biodiversity network, education, public awareness, scientifi c communication
The huntsman spider genera Sparianthina Banks, 1929 and Anaptomecus Simon, 1903 are reviewed. The type species of Sparianthina, Sparianthina selenopoides Banks, 1929, is redescribed, illustrated, and recorded from Costa Rica for the first time; a lectotype and paralectotype are designated. Three species are transferred to the genus: Sparianthina pumilla (Keyserling, 1880) comb. n. from Heteropoda Latreille, 1804 (lectotype and paralectotype are designated), Sparianthina rufescens (Mello-Leitão, 1940) comb. n. from Anaptomecus and Sparianthina milleri (Caporiacco, 1955) comb. n. from Macrinus Simon, 1887. The ♂ of S. rufescens (Mello-Leitão, 1940) comb. n. and the ♀ of S. milleri comb. n. are described for the first time. Three new species are described: Sparianthina adisi sp. n., S. deltshevi sp. n., and S. saaristoi sp. n. The male and female of Anaptomecus longiventris Simon, 1903 are described for the first time and the species is recorded from Panama for the first time. Two new species are described: Anaptomecus temii sp. n. and A. levyi sp. n. Keywords: Taxonomy, re-description, transfer, review
A new species of the basal araneomorph spider genus Ectatosticta (Araneae, Hypochilidae) from China
(2009)
The hypochilid spider Ectatosticta davidi (Simon) is redescribed on the basis of adults from Mt. Taibaishan in Shaanxi Province, China; the specimens from Qinghai Province previously identified as E. davidi by most modern authors belong to a new species described as E. deltshevi. Keywords: Araneae, Araneomorphae, Hypochilidae, Ectatosticta, China
Despite prevailing arid conditions, the diversity of terrestrial and freshwater biota in the Middle East is amazingly high and marine biodiversity is among the highest on Earth. Th roughout the Region, threats to the environment are moderate to severe. Despite the outstanding economic and ecological importance of biological diversity, the capacity in biodiversity-related research and academic education is inadequate. The "Middle Eastern Biodiversity Network" (MEBN), founded in 2006 by six universities and research institutes in Iran, Jordan, Germany, Lebanon and Yemen was designed to fi ll this gap. An integrated approach is taken to upgrade biodiversity research and education in order to improve regional ecosystem conservation and management capacities. A wide range of activities are carried out in the framework of the Network, including capacity building in biological collection management and professional natural history curatorship, developing university curricula in biodiversity, conducting scientifi c research, organising workshops and conferences on Middle Eastern biodiversity, and translating the results of biodiversity research into conservation and sustainable development. Keywords: Middle Eastern biodiversity, nature museums, biodiversity research, biodiversity education, biodiversity conservation, biodiversity networks
Das Ziel dieser Studie war die Etablierung von Grenzwerten für die bronchiale Methacholinprovokation durch Vergleich des Aerosol Provokation Systems (APS-SC) mit einem ATS Standard (five-breath dosimeter method, SDM). Unsere Ergebnisse zeigen, dass die APS-SC Methode unter Verwendung eines Kurzprotokolls und des Systems der Firma Cardinal Health eine sichere, schnelle und verlässliche Methode der bronchialen MCP darstellt. Im Schnitt erspart dieses Verfahren acht Minuten gegenüber der klassischen SDM gemäß dem von der ATS empfohlenen „short five breath dosimeter protocol“. Zudem entfallen in der Vorbereitung das Herstellen und die Lagerung mehrerer unterschiedlich konzentrierter Methacholinlösungen; während der Untersuchung existiert daher auch kein Verwechslungsrisiko. Der Test selbst ist für Untersucher und Patient weniger belastend. Die Verwendung einer Konzentration von 16,00 mg/ml für die Methacholin-Testlösung stellt einen guten Mittelweg zwischen akzeptablen Inhalationszeiten innerhalb der Stufen und einer nicht zu aggressiven Konzentration dar, mit der vom Anfang eines Tests bis zu seinem Ende gearbeitet werden kann. Zwischen den Kategorien der BHR für die SDM- und die APS-SC Methode besteht ein enger Zusammenhang. Als Grenzwert für die Annahme einer BHR – definiert als diejenige Methacholindosis bzw. -konzentration, die zu einem Abfall der FEV1 um 20 % vom Ausgangswert führt – stimmt der bestehende und von der ATS publizierte Grenzwert von 8,00 mg/ml am besten mit einer Dosis von 1,00 mg Methacholin in der APS-SC Methode überein.
Akute Hochrisiko-Leukämien oder deren Rezidive, chronische Leukämien, Myelodysplastische Syndrome und Hodgkin- und Non-Hodgkin-Lymphome sind Indikationen für hämatopoetische Stammzelltransplantationen. Das Verfahren ist mit einer hohen Therapie-assoziierten Morbidität und Mortalität (TRM), die bei 5-40% liegt, assoziiert. Hauptprobleme sind dabei neben Infektionen die akute und chronische Transplantatreaktion (Graft-versus-Host-Erkrankung, GvHD). Die TRM variiert je nach Grunderkrankung, Spender und Allgemeinzustand des Patienten. Um Risikofaktoren für die TRM zu identifizieren, analysierten wir in einer retrospektiven Studie 205 allogene pädiatrische SZT in 4 Kliniken, von denen jeweils 2 Kliniken ein hohes bzw. niedriges Risikoprofil hinsichtlich der TRM hatten. Wir überprüften die Anwendbarkeit und Validität des von Matthes-Martin et al. entwickelten Risikoscores (TRMScore), der aus drei Risiko-Punkten Patienten-spezifische (Alter, Grunderkrankung) und Therapie-spezifische (Spender) Charakteristika miteinander kombiniert. Dieser Score teilt die Patienten in 4 TRM–Risikogruppen ein mit einem Score von 0 Punkten (Patient unter 10 Jahren mit HLA-identischen Geschwister als Donor) bis zu 3 Punkten (Patient über 10 Jahren, CR3 und HLA-nicht passenden Spender). Wir modifizierten den TRM-Score von Matthes-Martin et al., indem wir die Patienten mit einem TRM-Score von 0 und 1 in eine erste Gruppe (TRM-Score I) und die Patienten mit dem TRM-Score von 2 und 3 in eine zweite Gruppe zusammen (TRM-Score II) zusammenfassten, und entwickelten den mTRM-Score (modifizierter TRM-Score). Die Indikationen zur SZT waren ALL, AML, CML, Non-Hodgkin-Lymphome, Hodgkin-Lymphome und MDS. Es gab 88 KMT und 115 PBSZT und in 2 Fällen war die Stammzellquelle eine Kombination aus Knochenmark und peripherem Blut. Das Patientenalter lag zwischen 0 und 23 Jahren. Spender waren MSD (26,8%), MRD (1%), MUD (53,2), MMUD (10,2%) und MMRD (8,8). Am LFU lebten 61% der Patienten. Von den 39% der verstorbenen Patienten sind 40% aufgrund eines Rezidivs verstorben und 60% transplantationsassoziiert. Die Gesamt-TRM lag bei 22,4%. Wir teilten transplantationsassoziierte Faktoren in folgende Gruppen ein: Patienten-assoziierte Variablen, Spender-assoziierte, Krankheits-assoziierte, Therapie-assoziierte Variablen und sonstige Variablen. Die logistische Regression zeigte signifikant prognostische Faktoren, die die TRM beeinflussen. Das waren die Klinik (P=0,0045), in der die SZT durchgeführt wurde, das Jahr der SZT (P=0,0457, ab 2001) und der Spendertyp (P=0,0083, kein MSD). Die Diagnose, der Remissionsstatus bei SZT und der TRM-Score waren keine prognostischen Risikofaktoren für die TRM. Bei Anwendung des mTRM-Scores kristallisierte sich dieser als ein Prädiktor für die TRM (P=0,0447) heraus. Ein TRM-Score von I ging mit einer niedrigen TRM-Rate einher. Der mTRM-Score kann aufgrund der Ergebnisse zur Therapieentscheidung herangezogen werden, da er eine Einschätzung der tatsächlichen Überlebenswahrscheinlichkeit für die Patienten möglich macht. Die Klinik als Risikofaktor für die TRM ist nicht alleine durch das Patientenkollektiv und durch die Auswahl des Spendertyps zu erklären. Anhand der 1-Jahres-TRM (23%) von Matthes-Martin et al. errechneten wir die zu erwartende TRM-Rate für unsere Kliniken. Die erwartete TRM wich in Klinik C und Klinik D stark von der beobachteten TRM ab, in Klinik A und Klinik B waren sie annähernd gleich. Ein signifikanter Unterschied bestand nur bei Klinik C mit einem p-Wert von 0,05 bei dem TRM-Score und 0,02 bei dem mTRM-Score. Die Ergebnisse lassen darauf schließen, dass das Outcome der SZT von den Kliniken an sich bzw. deren Therapiemodalitäten beeinflusst wurde.
Short-term memory requires the coordination of sub-processes like encoding, retention, retrieval and comparison of stored material to subsequent input. Neuronal oscillations have an inherent time structure, can effectively coordinate synaptic integration of large neuron populations and could therefore organize and integrate distributed sub-processes in time and space. We observed field potential oscillations (14–95 Hz) in ventral prefrontal cortex of monkeys performing a visual memory task. Stimulus-selective and performance-dependent oscillations occurred simultaneously at 65–95 Hz and 14–50 Hz, the latter being phase-locked throughout memory maintenance. We propose that prefrontal oscillatory activity may be instrumental for the dynamical integration of local and global neuronal processes underlying short-term memory.