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Search Results: 1 - 10 of 402663 matches for " Susanne M. Bailer "
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Single-Stranded DNA Catalyzes Hybridization of PCR-Products to Microarray Capture Probes
Simon Dally, Steffen Rupp, Karin Lemuth, Stefan C. Hartmann, Ekkehard Hiller, Susanne M. Bailer, Cornelius Knabbe, Jan Weile
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0102338
Abstract: Since its development, microarray technology has evolved to a standard method in the biotechnological and medical field with a broad range of applications. Nevertheless, the underlying mechanism of the hybridization process of PCR-products to microarray capture probes is still not completely understood, and several observed phenomena cannot be explained with current models. We investigated the influence of several parameters on the hybridization reaction and identified ssDNA to play a major role in the process. An increase of the ssDNA content in a hybridization reaction strongly enhanced resulting signal intensities. A strong influence could also be observed when unlabeled ssDNA was added to the hybridization reaction. A reduction of the ssDNA content resulted in a massive decrease of the hybridization efficiency. According to these data, we developed a novel model for the hybridization mechanism. This model is based on the assumption that single stranded DNA is necessary as catalyst to induce the hybridization of dsDNA. The developed hybridization model is capable of giving explanations for several yet unresolved questions regarding the functionality of microarrays. Our findings not only deepen the understanding of the hybridization process, but also have immediate practical use in data interpretation and the development of new microarrays.
The Herpes Simplex Virus Protein pUL31 Escorts Nucleocapsids to Sites of Nuclear Egress, a Process Coordinated by Its N-Terminal Domain
Christina Funk?,Melanie Ott?,Verena Raschbichler?,Claus-Henning Nagel?,Anne Binz?,Beate Sodeik?,Rudolf Bauerfeind?,Susanne M. Bailer
PLOS Pathogens , 2015, DOI: 10.1371/journal.ppat.1004957
Abstract: Progeny capsids of herpesviruses leave the nucleus by budding through the nuclear envelope. Two viral proteins, the membrane protein pUL34 and the nucleo-phosphoprotein pUL31 form the nuclear egress complex that is required for capsid egress out of the nucleus. All pUL31 orthologs are composed of a diverse N-terminal domain with 1 to 3 basic patches and a conserved C-terminal domain. To decipher the functions of the N-terminal domain, we have generated several Herpes simplex virus mutants and show here that the N-terminal domain of pUL31 is essential with basic patches being critical for viral propagation. pUL31 and pUL34 entered the nucleus independently of each other via separate routes and the N-terminal domain of pUL31 was required to prevent their premature interaction in the cytoplasm. Unexpectedly, a classical bipartite nuclear localization signal embedded in this domain was not required for nuclear import of pUL31. In the nucleus, pUL31 associated with the nuclear envelope and newly formed capsids. Viral mutants lacking the N-terminal domain or with its basic patches neutralized still associated with nucleocapsids but were unable to translocate them to the nuclear envelope. Replacing the authentic basic patches with a novel artificial one resulted in HSV1(17+)Lox-UL31-hbpmp1mp2, that was viable but delayed in nuclear egress and compromised in viral production. Thus, while the C-terminal domain of pUL31 is sufficient for the interaction with nucleocapsids, the N-terminal domain was essential for capsid translocation to sites of nuclear egress and a coordinated interaction with pUL34. Our data indicate an orchestrated sequence of events with pUL31 binding to nucleocapsids and escorting them to the inner nuclear envelope. We propose a common mechanism for herpesviral nuclear egress: pUL31 is required for intranuclear translocation of nucleocapsids and subsequent interaction with pUL34 thereby coupling capsid maturation with primary envelopment.
Evolutionarily Conserved Herpesviral Protein Interaction Networks
Even Fossum,Caroline C. Friedel,Seesandra V. Rajagopala,Bj?rn Titz,Armin Baiker,Tina Schmidt,Theo Kraus,Thorsten Stellberger,Christiane Rutenberg,Silpa Suthram,Sourav Bandyopadhyay,Dietlind Rose,Albrecht von Brunn,Mareike Uhlmann,Christine Zeretzke,Yu-An Dong,Hélène Boulet,Manfred Koegl,Susanne M. Bailer,Ulrich Koszinowski,Trey Ideker,Peter Uetz,Ralf Zimmer,Jürgen Haas
PLOS Pathogens , 2009, DOI: 10.1371/journal.ppat.1000570
Abstract: Herpesviruses constitute a family of large DNA viruses widely spread in vertebrates and causing a variety of different diseases. They possess dsDNA genomes ranging from 120 to 240 kbp encoding between 70 to 170 open reading frames. We previously reported the protein interaction networks of two herpesviruses, varicella-zoster virus (VZV) and Kaposi's sarcoma-associated herpesvirus (KSHV). In this study, we systematically tested three additional herpesvirus species, herpes simplex virus 1 (HSV-1), murine cytomegalovirus and Epstein-Barr virus, for protein interactions in order to be able to perform a comparative analysis of all three herpesvirus subfamilies. We identified 735 interactions by genome-wide yeast-two-hybrid screens (Y2H), and, together with the interactomes of VZV and KSHV, included a total of 1,007 intraviral protein interactions in the analysis. Whereas a large number of interactions have not been reported previously, we were able to identify a core set of highly conserved protein interactions, like the interaction between HSV-1 UL33 with the nuclear egress proteins UL31/UL34. Interactions were conserved between orthologous proteins despite generally low sequence similarity, suggesting that function may be more conserved than sequence. By combining interactomes of different species we were able to systematically address the low coverage of the Y2H system and to extract biologically relevant interactions which were not evident from single species.
A Preliminary Investigation of the Optimal Percentage Requirement in an Electricity Market with Tradable Green Certificates  [PDF]
Kevin M. Currier, Susanne Rassouli-Currier
Theoretical Economics Letters (TEL) , 2012, DOI: 10.4236/tel.2012.22039
Abstract: Around the world, energy markets are being liberalized with the goal of achieving fully competitive markets while at-taining environmental policy objectives. This paper considers a system of Tradable Green Certificates (TGCs)—a mar-ket based regulatory instrument designed to promote electricity generation from renewable energy sources. In a TGC program, the principal policy instrument is the “percentage requirement” which stipulates the percentage of total elec-tricity generation that must be obtained from renewable sources. This paper provides a preliminary investigation of the socially optimal choice of the percentage requirement in a Cournot duopoly setting. The paper discusses the problem geometrically and considers some of the practical difficulties associated with the determination of the optimal percent-age requirement. Several important avenues for generalization of the results are also discussed.
Bibliotherapie - kognitive Therapie in Buchform als Selbsthilfe bei Patienten mit teilremittierter Depression
Schl?gelhofer M,Aschauer H,Bailer U,Eder H
Journal für Neurologie, Neurochirurgie und Psychiatrie , 2003,
Abstract: Die Bibliotherapie ist eine kognitive Therapie in Buchform. Das Buch basiert auf der von A. Beck speziell zur Behandlung von Depressionen entwickelten kognitiven Theorie. Als therapeutische Intervention wird das Lesen des Buches betrachtet. Ein aktuelles Behandlungsprogramm an unserer Klinik überprüft die Wirksamkeit der Bibliotherapie in Kombination mit Psychopharmakotherapie bei Patient(inn)en mit teilremittierter Depression. Wir wollen von einem 59j hrigen Patienten berichten, bei dem trotz ad quater Therapie mit Antidepressiva weiterhin eine depressive Restsymptomatik bestand. Nach Abschlu der sechsw chigen Bibliotherapie konnte von einer Remission der Depression gesprochen werden, was auch mit psychometrischen Me werten belegt ist. Diese Besserung war auch bei einer Nachuntersuchung anhaltend. Die Kombination von Psychotherapie und Psychopharmakotherapie ist wahrscheinlich meist eine sehr wirkungsvolle Behandlung der Depression, auch bei Anwendung der sehr niederschwelligen Bibliotherapie.
Limits on the infrared photometric monitoring of brown dwarfs
C. A. L. Bailer-Jones,M. Lamm
Physics , 2002, DOI: 10.1046/j.1365-8711.2003.06189.x
Abstract: Recent monitoring programs of ultra cool field M and L dwarfs (low mass stars or brown dwarfs) have uncovered low amplitude photometric I-band variations which may be associated with an inhomogeneous distribution of photospheric condensates. Further evidence hints that this distribution may evolve on very short timescales, specifically of order a rotation period or less. In an attempt to study this behaviour in more detail, we have carried out a pilot program to monitor three L dwarfs in the near infrared where these objects are significantly brighter than at shorter wavelengths. We present a robust data analysis method for improving the precision and reliability of infrared photometry. No significant variability was detected in either the J or Km bands in 2M1439 and SDSS1203 above a peak-to-peak amplitude of 0.04 mag (0.08 mag for 2M1112). The main limiting factor in achieving lower detection limits is suspected to be second order extinction effects in the Earth's atmosphere, on account of the very different colours of the target and reference stars. Suggestions are given for overcoming such effects which should improve the sensitivity and reliability of infrared variability searches.
Subjective and Objective Results of Native Anterior Vaginal Wall Repair in Local Anesthesia: A 10-Year Follow-Up  [PDF]
Cecilie Hestbech Lundorff, Marianne Glavind-Kristensen, Susanne Maigaard Axelsen, Karl M?ller Bek, Susanne Greisen
Open Journal of Obstetrics and Gynecology (OJOG) , 2015, DOI: 10.4236/ojog.2015.513107
Abstract: Introduction and Hypothesis: This follow-up study evaluates long-term subjective and objective outcome of native tissue anterior vaginal wall repair using local anesthesia. Methods: 72 women were operated. At 10-year follow-up anatomical results were evaluated by clinical examination. Furthermore, the women filled in a validated symptom and quality of life questionnaire. Results: Forty women (56%) completed the 10-year follow-up. Eighteen women (25%) had died within the ten-year follow-up period and fourteen women (19%) were lost to follow-up. Six (15%) of the women who came for follow-up had been reoperated for anterior vaginal wall prolapse within the 10-year follow-up period and were analysed as a separate group. Of the 40 women who came for the 10-year clinical examination none had stage 0 pelvic organ prolapse. Twenty (50%) women had stage 1, whereas, 13 (32%) had stage 2 and 1 (3%) had stage 3 pelvic organ prolapse. Ten years after surgery, 28 women (70%) had no bulge symptoms. Six (15%) of the women experienced bulge symptoms at the time of follow-up. Ten years postoperatively, 30 (75%) of the women in an overall quality of life assessment considered their condition improved after surgery. Conclusion: At 10-year follow-up 70% of women were relieved from their bulge symptoms and 75% still considered themselves better or much better than before the operation. However, 15% of women had been reoperated and 15% still experienced bulge symptoms.
Point estimation with exponentially tilted empirical likelihood
Susanne M. Schennach
Mathematics , 2007, DOI: 10.1214/009053606000001208
Abstract: Parameters defined via general estimating equations (GEE) can be estimated by maximizing the empirical likelihood (EL). Newey and Smith [Econometrica 72 (2004) 219--255] have recently shown that this EL estimator exhibits desirable higher-order asymptotic properties, namely, that its $O(n^{-1})$ bias is small and that bias-corrected EL is higher-order efficient. Although EL possesses these properties when the model is correctly specified, this paper shows that, in the presence of model misspecification, EL may cease to be root n convergent when the functions defining the moment conditions are unbounded (even when their expectations are bounded). In contrast, the related exponential tilting (ET) estimator avoids this problem. This paper shows that the ET and EL estimators can be naturally combined to yield an estimator called exponentially tilted empirical likelihood (ETEL) exhibiting the same $O(n^{-1})$ bias and the same $O(n^{-2})$ variance as EL, while maintaining root n convergence under model misspecification.
Accompanying document to "Point Estimation with Exponentially Tilted Empirical Likelihood"
Susanne M. Schennach
Mathematics , 2005,
Abstract: Parameters defined via General Estimating Equations (GEE) can be estimated by maximizing the Empirical Likelihood (EL). Newey and Smith (2004) have recently shown that this EL estimator exhibits desirable higher-order asymptotic properties, namely, that its O(n^-1) bias is small and that bias-corrected EL is higher-order efficient. Although EL possesses these properties when the model is correctly specified, this paper shows that, in the presence of model misspecification, EL may cease to be root n convergent when the functions defining the moment conditions are unbounded (even when their expectations are bounded). In contrast, the related Exponential Tilting (ET) estimator avoids this problem. This paper shows that the ET and EL estimators can be naturally combined to yield an estimator called Exponentially Tilted Empirical Likelihood (ETEL) exhibiting the same O(n^-1) bias and the same O(n^-2) variance as EL, while maintaining root n convergence under model misspecification.
Regressions with Berkson errors in covariates - A nonparametric approach
Susanne M. Schennach
Quantitative Finance , 2013, DOI: 10.1214/13-AOS1122
Abstract: This paper establishes that so-called instrumental variables enable the identification and the estimation of a fully nonparametric regression model with Berkson-type measurement error in the regressors. An estimator is proposed and proven to be consistent. Its practical performance and feasibility are investigated via Monte Carlo simulations as well as through an epidemiological application investigating the effect of particulate air pollution on respiratory health. These examples illustrate that Berkson errors can clearly not be neglected in nonlinear regression models and that the proposed method represents an effective remedy.
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