@article{NickersonAtalagdeBonoetal.2016, author = {Nickerson, David and Atalag, Koray and de Bono, Bernard and Geiger, J{\"o}rg and Goble, Carole and Hollmann, Susanne and Lonien, Joachim and M{\"u}ller, Wolfgang and Regierer, Babette and Stanford, Natalie J. and Golebiewski, Martin and Hunter, Peter}, title = {The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable}, series = {Interface Focus}, volume = {6}, journal = {Interface Focus}, number = {2}, doi = {10.1098/rsfs.2015.0103}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-189584}, pages = {13 Seiten}, year = {2016}, abstract = {Reconstructing and understanding the Human Physiome virtually is a complex mathematical problem, and a highly demanding computational challenge. Mathematical models spanning from the molecular level through to whole populations of individuals must be integrated, then personalized. This requires interoperability with multiple disparate and geographically separated data sources, and myriad computational software tools. Extracting and producing knowledge from such sources, even when the databases and software are readily available, is a challenging task. Despite the difficulties, researchers must frequently perform these tasks so that available knowledge can be continually integrated into the common framework required to realize the Human Physiome. Software and infrastructures that support the communities that generate these, together with their underlying standards to format, describe and interlink the corresponding data and computer models, are pivotal to the Human Physiome being realized. They provide the foundations for integrating, exchanging and re-using data and models efficiently, and correctly, while also supporting the dissemination of growing knowledge in these forms. In this paper, we explore the standards, software tooling, repositories and infrastructures that support this work, and detail what makes them vital to realizing the Human Physiome.}, language = {en} } @article{Kuemmel2016, author = {K{\"u}mmel, Reiner}, title = {The Impact of Entropy Production and Emission Mitigation on Economic Growth}, series = {Entropy}, volume = {18}, journal = {Entropy}, number = {3}, doi = {10.3390/e18030075}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-163185}, pages = {75}, year = {2016}, abstract = {Entropy production in industrial economies involves heat currents, driven by gradients of temperature, and particle currents, driven by specific external forces and gradients of temperature and chemical potentials. Pollution functions are constructed for the associated emissions. They reduce the output elasticities of the production factors capital, labor, and energy in the growth equation of the capital-labor-energy-creativity model, when the emissions approach their critical limits. These are drawn by, e.g., health hazards or threats to ecological and climate stability. By definition, the limits oblige the economic actors to dedicate shares of the available production factors to emission mitigation, or to adjustments to the emission-induced changes in the biosphere. Since these shares are missing for the production of the quantity of goods and services that would be available to consumers and investors without emission mitigation, the "conventional" output of the economy shrinks. The resulting losses of conventional output are estimated for two classes of scenarios: (1) energy conservation; and (2) nuclear exit and subsidies to photovoltaics. The data of the scenarios refer to Germany in the 1980s and after 11 March 2011. For the energy-conservation scenarios, a method of computing the reduction of output elasticities by emission abatement is proposed.}, language = {en} } @article{KurabiPakBernhardtetal.2016, author = {Kurabi, Arwa and Pak, Kwang K. and Bernhardt, Marlen and Baird, Andrew and Ryan, Allen F.}, title = {Discovery of a Biological Mechanism of Active Transport through the Tympanic Membrane to the Middle Ear}, series = {Scientific Reports}, volume = {6}, journal = {Scientific Reports}, number = {22663}, doi = {10.1038/srep22663}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-167741}, year = {2016}, abstract = {Otitis media (OM) is a common pediatric disease for which systemic antibiotics are often prescribed. While local treatment would avoid the systemic treatment side-effects, the tympanic membrane (TM) represents an impenetrable barrier unless surgically breached. We hypothesized that the TM might harbor innate biological mechanisms that could mediate trans-TM transport. We used two M13-bacteriophage display biopanning strategies to search for mediators of trans-TM transport. First, aliquots of linear phage library displaying 10\(^{10th}\) 12mer peptides were applied on the TM of rats with active bacterial OM. The middle ear (ME) contents were then harvested, amplified and the preparation re-applied for additional rounds. Second, the same na{\"i}ve library was sequentially screened for phage exhibiting TM binding, internalization and then transit. Results revealed a novel set of peptides that transit across the TM to the ME in a time and temperature dependent manner. The peptides with highest transport capacities shared sequence similarities. Historically, the TM was viewed as an impermeable barrier. However, our studies reveal that it is possible to translocate peptide-linked small particles across the TM. This is the first comprehensive biopanning for the isolation of TM transiting peptidic ligands. The identified mechanism offers a new drug delivery platform into the ME.}, language = {en} } @article{KuntzenKuhnKuntzenetal.2016, author = {Kuntzen, Thomas and Kuhn, Sereina and Kuntzen, Daniela and Seifert, Burkhardt and M{\"u}llhaupt, Beat and Geier, Andreas}, title = {Influence of Ribavirin Serum Levels on Outcome of Antiviral Treatment and Anemia in Hepatitis C Virus Infection}, series = {PLoS ONE}, volume = {11}, journal = {PLoS ONE}, number = {7}, doi = {10.1371/journal.pone.0158512}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166888}, pages = {e0158512}, year = {2016}, abstract = {Background Ribavirin blood levels vary considerably between patients with standard weight-based dosing. Their impact on sustained virological response (SVR) with pegylated interferon and ribavirin is controversial, but has mostly been studied before the IL28b gene polymorphism as a possible confounder was discovered. Methods The impact of serum ribavirin trough levels at week 4, at the end of treatment and of mean levels across the entire antiviral treatment with pegylated interferon and ribavirin on relapse, SVR rates and anemia was retrospectively studied by univariate and multivariable logistic regression analyses in 214 patients with HCV genotype 1-4 infection, including 88 patients with available IL28b genotyping. Results Mean ribavirin levels varied between 0.68-5.65 mg/l and significantly differed between patients with or without SVR. By multivariable regression including age, sex, HCV viral load, HCV genotype, liver fibrosis stage, prior treatments, immunosuppression and IL28b genotype, ribavirin levels consistently displayed significant influence on SVR and relapse without indication for a specific importance of higher concentrations early or late in the treatment course. Although hemoglobin decline was on average more pronounced in patients with higher ribavirin levels, hemoglobin remained relatively stable in a significant proportion of these, indicating that ribavirin levels alone are insufficient to predict anemia. Conclusion While data are scarce to draw conclusions applicable for modern DAA therapies, these results support ribavirin treatment based on serum levels instead of purely weight-based dosing in combination with pegylated interferon.}, language = {en} } @article{LousadaSorokaYagodzinskyyetal.2016, author = {Lousada, Cl{\´a}udio M. and Soroka, Inna L. and Yagodzinskyy, Yuriy and Tarakina, Nadezda V. and Todoshchenko, Olga and H{\"a}nninen, Hannu and Korzhavyi, Pavel A. and Jonsson, Mats}, title = {Gamma radiation induces hydrogen absorption by copper in water}, series = {Scientific Reports}, volume = {6}, journal = {Scientific Reports}, number = {24234}, doi = {10.1038/srep24234}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-167730}, year = {2016}, abstract = {One of the most intricate issues of nuclear power is the long-term safety of repositories for radioactive waste. These repositories can have an impact on future generations for a period of time orders of magnitude longer than any known civilization. Several countries have considered copper as an outer corrosion barrier for canisters containing spent nuclear fuel. Among the many processes that must be considered in the safety assessments, radiation induced processes constitute a key-component. Here we show that copper metal immersed in water uptakes considerable amounts of hydrogen when exposed to γ-radiation. Additionally we show that the amount of hydrogen absorbed by copper depends on the total dose of radiation. At a dose of 69 kGy the uptake of hydrogen by metallic copper is 7 orders of magnitude higher than when the absorption is driven by H\(_{2}\)(g) at a pressure of 1 atm in a non-irradiated dry system. Moreover, irradiation of copper in water causes corrosion of the metal and the formation of a variety of surface cavities, nanoparticle deposits, and islands of needle-shaped crystals. Hence, radiation enhanced uptake of hydrogen by spent nuclear fuel encapsulating materials should be taken into account in the safety assessments of nuclear waste repositories.}, language = {en} } @article{MaaroufNeudorferElMajdoubetal.2016, author = {Maarouf, Mohammad and Neudorfer, Clemens and El Majdoub, Faycal and Lenartz, Doris and Kuhn, Jens and Sturm, Volker}, title = {Deep Brain Stimulation of Medial Dorsal and Ventral Anterior Nucleus of the Thalamus in OCD: A Retrospective Case Series}, series = {PLoS ONE}, volume = {11}, journal = {PLoS ONE}, number = {8}, doi = {10.1371/journal.pone.0160750}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166830}, pages = {e0160750}, year = {2016}, abstract = {Background The current notion that cortico-striato-thalamo-cortical circuits are involved in the pathophysiology of obsessive-compulsive disorder (OCD) has instigated the search for the most suitable target for deep brain stimulation (DBS). However, despite extensive research, uncertainty about the ideal target remains with many structures being underexplored. The aim of this report is to address a new target for DBS, the medial dorsal (MD) and the ventral anterior (VA) nucleus of the thalamus, which has thus far received little attention in the treatment of OCD. Methods In this retrospective trial, four patients (three female, one male) aged 31-48 years, suffering from therapy-refractory OCD underwent high-frequency DBS of the MD and VA. In two patients (de novo group) the thalamus was chosen as a primary target for DBS, whereas in two patients (rescue DBS group) lead implantation was performed in a rescue DBS attempt following unsuccessful primary stimulation. Results Continuous thalamic stimulation yielded no significant improvement in OCD symptom severity. Over the course of thalamic DBS symptoms improved in only one patient who showed "partial response" on the Yale-Brown Obsessive Compulsive (Y-BOCS) Scale. Beck Depression Inventory scores dropped by around 46\% in the de novo group; anxiety symptoms improved by up to 34\%. In the de novo DBS group no effect of DBS on anxiety and mood was observable. Conclusion MD/VA-DBS yielded no adequate alleviation of therapy-refractory OCD, the overall strategy in targeting MD/VA as described in this paper can thus not be recommended in DBS for OCD. The magnocellular portion of MD (MDMC), however, might prove a promising target in the treatment of mood related and anxiety disorders.}, language = {en} } @article{HellenbrandClausSchinketal.2016, author = {Hellenbrand, Wiebke and Claus, Heike and Schink, Susanne and Marcus, Ulrich and Wichmann, Ole and Vogel, Ulrich}, title = {Risk of Invasive Meningococcal Disease in Men Who Have Sex with Men: Lessons Learned from an Outbreak in Germany, 2012-2013}, series = {PLoS ONE}, volume = {11}, journal = {PLoS ONE}, number = {8}, doi = {10.1371/journal.pone.0160126}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166842}, pages = {e0160126}, year = {2016}, abstract = {Background We undertook investigations in response to an invasive meningococcal disease (IMD) outbreak in men who have sex with men (MSM) in Berlin 2012-2013 to better understand meningococcal transmission and IMD risk in MSM. Methods We retrospectively searched for further IMD cases in MSM in Germany through local health departments and undertook exploratory interviews. We performed antigen sequence typing, characterized fHbp and aniA genes of strains with the outbreak finetype and reviewed epidemiologically or spatiotemporally linked cases from 2002-2014. Results Among the 148 IMD-cases notified from 01.01.2012-30.09.2013 in 18-59 year-old men we identified 13 MSM in 6 federal states: 11 serogroup C (MenC, all finetype C:P1.5-1,10-8:F3-6), 2 MenB. Interviews with 7 MSM revealed frequent meeting of multiple partners online or via mobile apps and illicit drug use as potential risk factors. MenC incidence was 13-fold higher in MSM than non-MSM. MenC isolates from 9/11 MSM had a novel fHbp allele 766. All C:P1.5-1,10-8:F3-6 strains from MSM versus 16/23 from non-MSM had intact aniA genes (p = 0.04). Although definitive evidence for transmission among MSM in epidemiological or spatiotemporal clusters in 2002-2014 was lacking, clusters were more frequent in men aged 20-49 years. Molecular analysis of C:P1.5-1,10-8:F3-6 strains revealed cases with intact aniA since 2007, mainly associated with fHbp361, fHbp766 and fHbp813, all involving one or more MSM. Conclusions MenC incidence was elevated in MSM during the study period. Multiple casual sexual contacts and illicit drug use were common in affected MSM. In all strains from MSM we detected an intact aniA gene coding for a nitrite reductase, which permits survival in microanaerobic environments and could play a role in meningococcal transmission in MSM through urogenital colonization. Furthermore, meningococcal transmission among MSM may be sustained over large areas and thus require modified spatiotemporal scanning algorithms for timely detection and control.}, language = {en} } @article{MeierKruseButtlaretal.2016, author = {Meier, Doreen and Kruse, Janis and Buttlar, Jann and Friedrich, Michael and Zenk, Fides and Boesler, Benjamin and Forstner, Konrad U. and Hammann, Christian and Nellen, Wolfgang}, title = {Analysis of the Microprocessor in Dictyostelium: The Role of RbdB, a dsRNA Binding Protein}, series = {PLoS Genetics}, volume = {12}, journal = {PLoS Genetics}, number = {6}, doi = {10.1371/journal.pgen.1006057}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166687}, pages = {e1006057}, year = {2016}, abstract = {We identified the dsRNA binding protein RbdB as an essential component in miRNA processing in Dictyostelium discoideum. RbdB is a nuclear protein that accumulates, together with Dicer B, in nucleolar foci reminiscent of plant dicing bodies. Disruption of rbdB results in loss of miRNAs and accumulation of primary miRNAs. The phenotype can be rescued by ectopic expression of RbdB thus allowing for a detailed analysis of domain function. The lack of cytoplasmic dsRBD proteins involved in miRNA processing, suggests that both processing steps take place in the nucleus thus resembling the plant pathway. However, we also find features e.g. in the domain structure of Dicer which suggest similarities to animals. Reduction of miRNAs in the rbdB- strain and their increase in the Argonaute A knock out allowed the definition of new miRNAs one of which appears to belong to a new non-canonical class.}, language = {en} } @article{GoekbugetKelshChiaetal.2016, author = {G{\"o}kbuget, N. and Kelsh, M. and Chia, V. and Advani, A. and Bassan, R. and Dombret, H. and Doubek, M. and Fielding, A. K. and Giebel, S. and Haddad, V. and Hoelzer, D. and Holland, C. and Ifrah, N. and Katz, A. and Maniar, T. and Martinelli, G. and Morgades, M. and O'Brien, S. and Ribera, J.-M. and Rowe, J. M. and Stein, A. and Topp, M. and Wadleigh, M. and Kantarjian, H.}, title = {Blinatumomab vs historical standard therapy of adult relapsed/refractory acute lymphoblastic leukemia}, series = {Blood Cancer Journal}, volume = {6}, journal = {Blood Cancer Journal}, doi = {10.1038/bcj.2016.84}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-164495}, pages = {e473}, year = {2016}, abstract = {We compared outcomes from a single-arm study of blinatumomab in adult patients with B-precursor Ph-negative relapsed/refractory acute lymphoblastic leukemia (R/R ALL) with a historical data set from Europe and the United States. Estimates of complete remission (CR) and overall survival (OS) were weighted by the frequency distribution of prognostic factors in the blinatumomab trial. Outcomes were also compared between the trial and historical data using propensity score methods. The historical cohort included 694 patients with CR data and 1112 patients with OS data compared with 189 patients with CR and survival data in the blinatumomab trial. The weighted analysis revealed a CR rate of 24\% (95\% CI: 20-27\%) and a median OS of 3.3 months (95\% CI: 2.8-3.6) in the historical cohort compared with a CR/CRh rate of 43\% (95\% CI: 36-50\%) and a median OS of 6.1 months (95\% CI: 4.2-7.5) in the blinatumomab trial. Propensity score analysis estimated increased odds of CR/CRh (OR=2.68, 95\% CI: 1.67-4.31) and improved OS (HR=0.536, 95\% CI: 0.394-0.730) with blinatumomab. The analysis demonstrates the application of different study designs and statistical methods to compare novel therapies for R/R ALL with historical data.}, language = {en} } @article{KleberChenMichelsetal.2016, author = {Kleber, J{\"o}rg and Chen, Yi-Chun and Michels, Birgit and Saumweber, Timo and Schleyer, Michael and K{\"a}hne, Thilo and Buchner, Erich and Gerber, Bertram}, title = {Synapsin is required to "boost" memory strength for highly salient events}, series = {Learning and Memory}, volume = {23}, journal = {Learning and Memory}, number = {1}, doi = {10.1101/lm.039685.115}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-191440}, pages = {9-20}, year = {2016}, abstract = {Synapsin is an evolutionarily conserved presynaptic phosphoprotein. It is encoded by only one gene in the Drosophila genome and is expressed throughout the nervous system. It regulates the balance between reserve and releasable vesicles, is required to maintain transmission upon heavy demand, and is essential for proper memory function at the behavioral level. Task-relevant sensorimotor functions, however, remain intact in the absence of Synapsin. Using an odor-sugar reward associative learning paradigm in larval Drosophila, we show that memory scores in mutants lacking Synapsin (syn\(^{97}\)) are lower than in wild-type animals only when more salient, higher concentrations of odor or of the sugar reward are used. Furthermore, we show that Synapsin is selectively required for larval short-term memory. Thus, without Synapsin Drosophila larvae can learn and remember, but Synapsin is required to form memories that match in strength to event salience-in particular to a high saliency of odors, of rewards, or the salient recency of an event. We further show that the residual memory scores upon a lack of Synapsin are not further decreased by an additional lack of the Sap47 protein. In combination with mass spectrometry data showing an up-regulated phosphorylation of Synapsin in the larval nervous system upon a lack of Sap47, this is suggestive of a functional interdependence of Synapsin and Sap47.}, language = {en} }