@article{ZahoGhirlandoAlfonsoetal.2015, author = {Zaho, Huaying and Ghirlando, Rodolfo and Alfonso, Carlos and Arisaka, Fumio and Attali, Ilan and Bain, David L. and Bakhtina, Marina M. and Becker, Donald F. and Bedwell, Gregory J. and Bekdemir, Ahmet and Besong, Tabot M. D. and Birck, Catherine and Brautigam, Chad A. and Brennerman, William and Byron, Olwyn and Bzowska, Agnieszka and Chaires, Jonathan B. and Chaton, Catherine T. and Coelfen, Helmbut and Connaghan, Keith D. and Crowley, Kimberly A. and Curth, Ute and Daviter, Tina and Dean, William L. and Diez, Ana I. and Ebel, Christine and Eckert, Debra M. and Eisele, Leslie E. and Eisenstein, Edward and England, Patrick and Escalante, Carlos and Fagan, Jeffrey A. and Fairman, Robert and Finn, Ron M. and Fischle, Wolfgang and Garcia de la Torre, Jose and Gor, Jayesh and Gustafsson, Henning and Hall, Damien and Harding, Stephen E. and Hernandez Cifre, Jose G. and Herr, Andrew B. and Howell, Elizabeth E. and Isaac, Richard S. and Jao, Shu-Chuan and Jose, Davis and Kim, Soon-Jong and Kokona, Bashkim and Kornblatt, Jack A. and Kosek, Dalibor and Krayukhina, Elena and Krzizike, Daniel and Kusznir, Eric A. and Kwon, Hyewon and Larson, Adam and Laue, Thomas M. and Le Roy, Aline and Leech, Andrew P. and Lilie, Hauke and Luger, Karolin and Luque-Ortega, Juan R. and Ma, Jia and May, Carrie A. and Maynard, Ernest L. and Modrak-Wojcik, Anna and Mok, Yee-Foong and M{\"u}cke, Norbert and Nagel-Steger, Luitgard and Narlikar, Geeta J. and Noda, Masanori and Nourse, Amanda and Obsil, Thomas and Park, Chad K and Park, Jin-Ku and Pawelek, Peter D. and Perdue, Erby E. and Perkins, Stephen J. and Perugini, Matthew A. and Peterson, Craig L. and Peverelli, Martin G. and Piszczek, Grzegorz and Prag, Gali and Prevelige, Peter E. and Raynal, Bertrand D. E. and Rezabkova, Lenka and Richter, Klaus and Ringel, Alison E. and Rosenberg, Rose and Rowe, Arthur J. and Rufer, Arne C. and Scott, David J. and Seravalli, Javier G. and Solovyova, Alexandra S. and Song, Renjie and Staunton, David and Stoddard, Caitlin and Stott, Katherine and Strauss, Holder M. and Streicher, Werner W. and Sumida, John P. and Swygert, Sarah G. and Szczepanowski, Roman H. and Tessmer, Ingrid and Toth, Ronald T. and Tripathy, Ashutosh and Uchiyama, Susumu and Uebel, Stephan F. W. and Unzai, Satoru and Gruber, Anna Vitlin and von Hippel, Peter H. and Wandrey, Christine and Wang, Szu-Huan and Weitzel, Steven E and Wielgus-Kutrowska, Beata and Wolberger, Cynthia and Wolff, Martin and Wright, Edward and Wu, Yu-Sung and Wubben, Jacinta M. and Schuck, Peter}, title = {A Multilaboratory Comparison of Calibration Accuracy and the Performance of External References in Analytical Ultracentrifugation}, series = {PLoS ONE}, volume = {10}, journal = {PLoS ONE}, number = {5}, doi = {10.1371/journal.pone.0126420}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-151903}, pages = {e0126420}, year = {2015}, abstract = {Analytical ultracentrifugation (AUC) is a first principles based method to determine absolute sedimentation coefficients and buoyant molar masses of macromolecules and their complexes, reporting on their size and shape in free solution. The purpose of this multi-laboratory study was to establish the precision and accuracy of basic data dimensions in AUC and validate previously proposed calibration techniques. Three kits of AUC cell assemblies containing radial and temperature calibration tools and a bovine serum albumin (BSA) reference sample were shared among 67 laboratories, generating 129 comprehensive data sets. These allowed for an assessment of many parameters of instrument performance, including accuracy of the reported scan time after the start of centrifugation, the accuracy of the temperature calibration, and the accuracy of the radial magnification. The range of sedimentation coefficients obtained for BSA monomer in different instruments and using different optical systems was from 3.655 S to 4.949 S, with a mean and standard deviation of (4.304\(\pm\)0.188) S (4.4\%). After the combined application of correction factors derived from the external calibration references for elapsed time, scan velocity, temperature, and radial magnification, the range of s-values was reduced 7-fold with a mean of 4.325 S and a 6-fold reduced standard deviation of \(\pm\)0.030 S (0.7\%). In addition, the large data set provided an opportunity to determine the instrument-to-instrument variation of the absolute radial positions reported in the scan files, the precision of photometric or refractometric signal magnitudes, and the precision of the calculated apparent molar mass of BSA monomer and the fraction of BSA dimers. These results highlight the necessity and effectiveness of independent calibration of basic AUC data dimensions for reliable quantitative studies.}, language = {en} } @article{StraubeReifRichteretal.2014, author = {Straube, B. and Reif, A. and Richter, J. and Lueken, U. and Weber, H. and Arolt, V. and Jansen, A. and Zwanzger, P. and Domschke, K. and Pauli, P. and Konrad, C. and Gerlach, A. L. and Lang, T. and Fydrich, T. and Alpers, G. W. and Stroehle, A. and Wittmann, A. and Pfleiderer, B. and Wittchen, H.-U. and Hamm, A. and Deckert, J. and Kircher, T.}, title = {The functional - 1019C/G HTR1A polymorphism and mechanisms of fear}, series = {Translational Psychiatry}, volume = {4}, journal = {Translational Psychiatry}, issn = {2158-3188}, doi = {10.1038/tp.2014.130}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-114369}, pages = {e490}, year = {2014}, abstract = {Serotonin receptor 1A gene (HTR1A) knockout mice show pronounced defensive behaviour and increased fear conditioning to ambiguous conditioned stimuli. Such behaviour is a hallmark of pathological human anxiety, as observed in panic disorder with agoraphobia (PD/AG). Thus, variations in HTR1A might contribute to neurophysiological differences within subgroups of PD/AG patients. Here, we tested this hypothesis by combining genetic with behavioural techniques and neuroimaging. In a clinical multicentre trial, patients with PD/AG received 12 sessions of manualized cognitive-behavioural therapy (CBT) and were genotyped for HTR1A rs6295. In four subsamples of this multicentre trial, exposure behaviour (n = 185), defensive reactivity measured using a behavioural avoidance test (BAT; before CBT: n = 245; after CBT: n = 171) and functional magnetic resonance imaging (fMRI) data during fear conditioning were acquired before and after CBT (n = 39). HTR1A risk genotype (GG) carriers more often escaped during the BAT before treatment. Exploratory fMRI results suggest increased activation of the amygdala in response to threat as well as safety cues before and after treatment in GG carriers. Furthermore, GG carriers demonstrated reduced effects of CBT on differential conditioning in regions including the bilateral insulae and the anterior cingulate cortex. Finally, risk genotype carriers demonstrated reduced self-initiated exposure behaviour to aversive situations. This study demonstrates the effect of HTR1A variation on defensive behaviour, amygdala activity, CBT-induced neural plasticity and normalization of defence behaviour in PD/AG. Our results, therefore, translate evidence from animal studies to humans and suggest a central role for HTR1A in differentiating subgroups of patients with anxiety disorders.}, language = {en} } @article{ZieglerRichterMahretal.2016, author = {Ziegler, C. and Richter, J. and Mahr, M. and Gajewska, A. and Schiele, M.A. and Gehrmann, A. and Schmidt, B. and Lesch, K.-P. and Lang, T. and Helbig-Lang, S. and Pauli, P. and Kircher, T. and Reif, A. and Rief, W. and Vossbeck-Elsebusch, A.N. and Arolt, V. and Wittchen, H.-U. and Hamm, A.O. and Deckert, J. and Domschke, K.}, title = {MAOA gene hypomethylation in panic disorder-reversibility of an epigenetic risk pattern by psychotherapy}, series = {Translational Psychiatry}, journal = {Translational Psychiatry}, number = {6}, doi = {10.1038/tp.2016.41}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-164422}, pages = {e773}, year = {2016}, abstract = {Epigenetic signatures such as methylation of the monoamine oxidase A (MAOA) gene have been found to be altered in panic disorder (PD). Hypothesizing temporal plasticity of epigenetic processes as a mechanism of successful fear extinction, the present psychotherapy-epigenetic study for we believe the first time investigated MAOA methylation changes during the course of exposure-based cognitive behavioral therapy (CBT) in PD. MAOA methylation was compared between N=28 female Caucasian PD patients (discovery sample) and N=28 age- and sex-matched healthy controls via direct sequencing of sodium bisulfite-treated DNA extracted from blood cells. MAOA methylation was furthermore analyzed at baseline (T0) and after a 6-week CBT (T1) in the discovery sample parallelized by a waiting time in healthy controls, as well as in an independent sample of female PD patients (N=20). Patients exhibited lower MAOA methylation than healthy controls (P<0.001), and baseline PD severity correlated negatively with MAOA methylation (P=0.01). In the discovery sample, MAOA methylation increased up to the level of healthy controls along with CBT response (number of panic attacks; T0-T1: +3.37±2.17\%), while non-responders further decreased in methylation (-2.00±1.28\%; P=0.001). In the replication sample, increases in MAOA methylation correlated with agoraphobic symptom reduction after CBT (P=0.02-0.03). The present results support previous evidence for MAOA hypomethylation as a PD risk marker and suggest reversibility of MAOA hypomethylation as a potential epigenetic correlate of response to CBT. The emerging notion of epigenetic signatures as a mechanism of action of psychotherapeutic interventions may promote epigenetic patterns as biomarkers of lasting extinction effects.}, language = {en} } @article{ToussaintRichterManteletal.2016, author = {Toussaint, Andr{\´e} and Richter, Anne and Mantel, Frederick and Flickinger, John C. and Grills, Inga Siiner and Tyagi, Neelam and Sahgal, Arjun and Letourneau, Daniel and Sheehan, Jason P. and Schlesinger, David J. and Gerszten, Peter Carlos and Guckenberger, Matthias}, title = {Variability in spine radiosurgery treatment planning - results of an international multi-institutional study}, series = {Radiation Oncology}, volume = {11}, journal = {Radiation Oncology}, number = {57}, doi = {10.1186/s13014-016-0631-9}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-146687}, year = {2016}, abstract = {Background The aim of this study was to quantify the variability in spinal radiosurgery (SRS) planning practices between five international institutions, all member of the Elekta Spine Radiosurgery Research Consortium. Methods Four institutions provided one representative patient case each consisting of the medical history, CT and MR imaging. A step-wise planning approach was used where, after each planning step a consensus was generated that formed the basis for the next planning step. This allowed independent analysis of all planning steps of CT-MR image registration, GTV definition, CTV definition, PTV definition and SRS treatment planning. In addition, each institution generated one additional SRS plan for each case based on intra-institutional image registration and contouring, independent of consensus results. Results Averaged over the four cases, image registration variability ranged between translational 1.1 mm and 2.4 mm and rotational 1.1° and 2.0° in all three directions. GTV delineation variability was 1.5 mm in axial and 1.6 mm in longitudinal direction averaged for the four cases. CTV delineation variability was 0.8 mm in axial and 1.2 mm in longitudinal direction. CTV-to-PTV margins ranged between 0 mm and 2 mm according to institutional protocol. Delineation variability was 1 mm in axial directions for the spinal cord. Average PTV coverage for a single fraction18 Gy prescription was 87 ± 5 \%; Dmin to the PTV was 7.5 ± 1.8 Gy averaged over all cases and institutions. Average Dmax to the PRV_SC (spinal cord + 1 mm) was 10.5 ± 1.6 Gy and the average Paddick conformity index was 0.69 ± 0.06. Conclusions Results of this study reflect the variability in current practice of spine radiosurgery in large and highly experienced academic centers. Despite close methodical agreement in the daily workflow, clinically significant variability in all steps of the treatment planning process was demonstrated. This may translate into differences in patient clinical outcome and highlights the need for consensus and established delineation and planning criteria.}, language = {en} } @article{SommerRichterRogauschetal.2011, author = {Sommer, Claudia and Richter, Helmut and Rogausch, Jan P. and Frettloh, Jule and Lungenhausen, Margitta and Maier, Christoph}, title = {A modified score to identify and discriminate neuropathic pain: a study on the German version of the neuropathic pain symptom inventory (NPSI)}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-68716}, year = {2011}, abstract = {Background: Neuropathic pain must be correctly diagnosed for optimal treatment. The questionnaire named Neuropathic Pain Symptom Inventory (NPSI) was developed in its original French version to evaluate the different symptoms of neuropathic pain. We hypothesized that the NPSI might also be used to differentiate neuropathic from non-neuropathic pain. Methods: We translated the NPSI into German using a standard forward-backward translation and administered it in a case-control design to patients with neuropathic (n = 68) and non-neuropathic pain (headache and osteoarthritis, n = 169) to validate it and to analyze its discriminant properties, its sensitivity to change, and to detect neuropathic pain subgroups with distinct profiles. Results: Using a sum score (the NPSI-G score), we found sensitivity to change (r between 0.37 and 0.5 for pain items of the graded chronic pain scale) and could distinguish between neuropathic and other pain on a group basis, but not for individual patients. Post hoc development of a discriminant score with optimized diagnostic properties to distinguish neuropathic pain from non-neuropathic pain resulted in an instrument with high sensitivity (91\%) and acceptable specificity (70\%). We detected six different pain profiles in the patient group with neuropathic pain; three profiles were found to be distinct. Conclusions: The NPSI-G potentially combines the properties of a diagnostic tool and an instrument to identify subtypes of neuropathic pain.}, subject = {Neuralgie}, language = {en} } @article{HegiUlrichSagelsdorffetal.1990, author = {Hegi, M. E. and Ulrich, D. and Sagelsdorff, P. and Richter, C. and Lutz, Werner K.}, title = {No measurable increase in thymidine glycol or 8-hydroxydeoxyguanosine in liver DNA of rats treated with nafenopin or choline-devoid low-methionine diet}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-60790}, year = {1990}, abstract = {Male rats were treated for 2 months with 1000 ppm nafenopin in the diet or for 4 or 7 days with a choline-devoid low-methionine diet. DNA was isolated from the livers and analyzed for the presence of cis-thymidine glycol-3'-phosphate (cis-dTGp) by 32P-postlabeling and for the Ievel of 8-hydroxy-deoxyguanosine (8-0H-dG) by electrochemical detection (ECD). In no DNA sample was the Ievel of cis-dTGp above the Iimit of detection of 1 modified thymidine per 106 nucleotides. With 8-0H-dG, a background Ievel of this modification of 20 8-0H-dG per 106 nucleosides was found in liver DNA of control rats, which was not affected by either treatment. It is postulated for thymidine glycol that a potential increase was below the Iimit of detection or was rapidly repaired in vivo and that the steady-state Ievel of endogenous 8-hydroxydeoxyguanosine appears not tobe influenced by the treatments chosen.}, subject = {Toxikologie}, language = {en} } @techreport{SchuesslervonGehlenMatthesetal.1991, author = {Sch{\"u}ssler, Ulrich and von Gehlen, K. and Matthes, S. and Okrusch, Martin and Richter, P. and R{\"o}hr, C.}, title = {Ultramafische Einschaltungen in Metabasiten der KTB-Vorbohrung}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-39206}, year = {1991}, abstract = {No abstract available}, subject = {Kontinentales Tiefbohrprogramm}, language = {de} } @inproceedings{SchuesslerOkruschRichter1987, author = {Sch{\"u}ssler, Ulrich and Okrusch, M. and Richter, P.}, title = {Amphibolites of the KTB target area Oberpfalz, Bavaria}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-38866}, year = {1987}, abstract = {No abstract available}, language = {en} } @inproceedings{SchuesslerOkruschRichteretal.1988, author = {Sch{\"u}ssler, Ulrich and Okrusch, M. and Richter, P. and Seidel, E.}, title = {Geochemistry of metabasites and element mobility}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-38880}, year = {1988}, abstract = {No abstract available}, language = {en} } @incollection{SchuesslerOkruschSeideletal.1989, author = {Sch{\"u}ssler, Ulrich and Okrusch, M. and Seidel, E. and Richter, P.}, title = {Geochemical characteristics of metabasites in different tectonic units of the North-East-Bavarian crystalline basement}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-39221}, publisher = {Universit{\"a}t W{\"u}rzburg}, year = {1989}, abstract = {Comprehensive geochemical investigations of rnetabasites yielded constraints for a correlation of, or discrimination between the different tectonic units within the northeast Bavarian crystalline basement. The M{\"u}nchberg nappe pile consists of at least five large tectonic units which exhibit differences in lithology, in part also in metamorphie grade and in metamorphie history. The metabasites in each of these nappes show their own, significant geochemical characteristics. The lowermost tectonic unit, the Bavarian lithofacies, includes the anchimetamorphie Ordovician Randschieferserie which contains alkaline basalts. In their geochemistry, they are sirnilar to the metabasites of the Fichtelgebirge crystalline complex in the autochthonous Saxo-thuringian. The next higher tectonic unit of the M{\"u}nchberg nappe pile, the Prasinit-Phyllit-Serie contains metabasites which can be derived from subalkaline basalts with a clear calc-alkaline tendency. There is a striking geochemical resemblance to the metabasites of the Erbendorf Greenschist Zone (EGZ) underscorinq the similar lithology of both allochthonous units which appear to be in a similar tectonic position. The Randamphibolit-Serie higher up in the M{\"u}nchberg nappe pile consists of metabasites with tholeiitic characteristics and a pronounced differentiation trend. The next higher tectonic unit, the Liegendserie of the M{\"u}nchberg gneiss cornplex s. str., contains metagabbros to metagabbronorites with a high-Al basaltic composition. The amphibolites and banded hornblende gneisses of the overlying Hangendserie are of subalkaline basaltic character with calc-alkaline affinity. The Zone Erbendorf-Vohenstrauss (ZEV) is currently regarded as an allochthonous unit equivalent to the higher crystalline nappes of the M{\"u}nchberg pile. However, the geochemical character of the metabasites do not encourage such a correlation. Neither the schistose and striped amphibolites nor the flaseramphibolites of the ZEV with their N-KORB and E-MORB character respectively, find convincing counterparts in the crystalline nappes of the M{\"u}nchberg pile. However, an interestingly close resemblance exists between the schistose and striped amphibolites in the ZEV, on the one hand, and in the autochthonous Zone Tirschenreuth- M{\"a}hring (ZTM) and the adjacent Moldanubian sensu strictu, on the other. Owing to the absence of age criteria, our results cannot be used, so far, to reconstruct the paleogeographical position of the individual tectonic units, based on the geochemical characteristics of their respective metabasites.}, language = {en} } @inproceedings{SchuesslerOppermannSeideletal.1986, author = {Sch{\"u}ssler, Ulrich and Oppermann, U. and Seidel, E. and Okrusch, M. and Richter, P.}, title = {Vergleichende Untersuchungen an Metabasiten des ostbayerischen Kristallins}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-39212}, year = {1986}, abstract = {No abstract available}, subject = {Kontinentales Tiefbohrprogramm}, language = {de} } @article{SchuesslerRichterOkrusch1989, author = {Sch{\"u}ssler, Ulrich and Richter, P. and Okrusch, Martin}, title = {Metabasites from the KTB Oberpfalz target area, Bavaria - geochemical characteristics and examples of mobile behaviour of "immobile" elements}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-31021}, year = {1989}, abstract = {No abstract available}, language = {en} } @article{vonGehlenMatthesOkruschetal.1990, author = {von Gehlen, K. and Matthes, S. and Okrusch, Martin and Richter, P. and R{\"o}hr, C. and Sch{\"u}ssler, Ulrich}, title = {Metapyroxenite in der KTB-Vorbohrung}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-87539}, year = {1990}, abstract = {No abstract available.}, subject = {Kontinentales Tiefbohrprogramm der Bundesrepublik Deutschland}, language = {de} } @article{JiangOronClarketal.2016, author = {Jiang, Yuxiang and Oron, Tal Ronnen and Clark, Wyatt T. and Bankapur, Asma R. and D'Andrea, Daniel and Lepore, Rosalba and Funk, Christopher S. and Kahanda, Indika and Verspoor, Karin M. and Ben-Hur, Asa and Koo, Da Chen Emily and Penfold-Brown, Duncan and Shasha, Dennis and Youngs, Noah and Bonneau, Richard and Lin, Alexandra and Sahraeian, Sayed M. E. and Martelli, Pier Luigi and Profiti, Giuseppe and Casadio, Rita and Cao, Renzhi and Zhong, Zhaolong and Cheng, Jianlin and Altenhoff, Adrian and Skunca, Nives and Dessimoz, Christophe and Dogan, Tunca and Hakala, Kai and Kaewphan, Suwisa and Mehryary, Farrokh and Salakoski, Tapio and Ginter, Filip and Fang, Hai and Smithers, Ben and Oates, Matt and Gough, Julian and T{\"o}r{\"o}nen, Petri and Koskinen, Patrik and Holm, Liisa and Chen, Ching-Tai and Hsu, Wen-Lian and Bryson, Kevin and Cozzetto, Domenico and Minneci, Federico and Jones, David T. and Chapman, Samuel and BKC, Dukka and Khan, Ishita K. and Kihara, Daisuke and Ofer, Dan and Rappoport, Nadav and Stern, Amos and Cibrian-Uhalte, Elena and Denny, Paul and Foulger, Rebecca E. and Hieta, Reija and Legge, Duncan and Lovering, Ruth C. and Magrane, Michele and Melidoni, Anna N. and Mutowo-Meullenet, Prudence and Pichler, Klemens and Shypitsyna, Aleksandra and Li, Biao and Zakeri, Pooya and ElShal, Sarah and Tranchevent, L{\´e}on-Charles and Das, Sayoni and Dawson, Natalie L. and Lee, David and Lees, Jonathan G. and Sillitoe, Ian and Bhat, Prajwal and Nepusz, Tam{\´a}s and Romero, Alfonso E. and Sasidharan, Rajkumar and Yang, Haixuan and Paccanaro, Alberto and Gillis, Jesse and Sede{\~n}o-Cort{\´e}s, Adriana E. and Pavlidis, Paul and Feng, Shou and Cejuela, Juan M. and Goldberg, Tatyana and Hamp, Tobias and Richter, Lothar and Salamov, Asaf and Gabaldon, Toni and Marcet-Houben, Marina and Supek, Fran and Gong, Qingtian and Ning, Wei and Zhou, Yuanpeng and Tian, Weidong and Falda, Marco and Fontana, Paolo and Lavezzo, Enrico and Toppo, Stefano and Ferrari, Carlo and Giollo, Manuel and Piovesan, Damiano and Tosatto, Silvio C. E. and del Pozo, Angela and Fern{\´a}ndez, Jos{\´e} M. and Maietta, Paolo and Valencia, Alfonso and Tress, Michael L. and Benso, Alfredo and Di Carlo, Stefano and Politano, Gianfranco and Savino, Alessandro and Rehman, Hafeez Ur and Re, Matteo and Mesiti, Marco and Valentini, Giorgio and Bargsten, Joachim W. and van Dijk, Aalt D. J. and Gemovic, Branislava and Glisic, Sanja and Perovic, Vladmir and Veljkovic, Veljko and Almeida-e-Silva, Danillo C. and Vencio, Ricardo Z. N. and Sharan, Malvika and Vogel, J{\"o}rg and Kansakar, Lakesh and Zhang, Shanshan and Vucetic, Slobodan and Wang, Zheng and Sternberg, Michael J. E. and Wass, Mark N. and Huntley, Rachael P. and Martin, Maria J. and O'Donovan, Claire and Robinson, Peter N. and Moreau, Yves and Tramontano, Anna and Babbitt, Patricia C. and Brenner, Steven E. and Linial, Michal and Orengo, Christine A. and Rost, Burkhard and Greene, Casey S. and Mooney, Sean D. and Friedberg, Iddo and Radivojac, Predrag and Veljkovic, Nevena}, title = {An expanded evaluation of protein function prediction methods shows an improvement in accuracy}, series = {Genome Biology}, volume = {17}, journal = {Genome Biology}, number = {184}, doi = {10.1186/s13059-016-1037-6}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166293}, year = {2016}, abstract = {Background A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent.}, language = {en} } @article{FuchsYoussefSeheretal.2019, author = {Fuchs, A. and Youssef, A. and Seher, A. and Hochleitner, G. and Dalton, P. D. and Hartmann, S. and Brands, R. C. and M{\"u}ller-Richter, U. D. A. and Linz, C,}, title = {Medical-grade polycaprolactone scaffolds made by melt electrospinning writing for oral bone regeneration - a pilot study in vitro}, series = {BMC Oral Health}, volume = {19}, journal = {BMC Oral Health}, doi = {10.1186/s12903-019-0717-5}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-200274}, pages = {28}, year = {2019}, abstract = {Background The spectrum of indications for the use of membranes and scaffolds in the field of oral and maxillofacial surgery includes, amongst others, guided bone regeneration (GBR). Currently available membrane systems face certain disadvantages such as difficult clinical handling, inconsistent degradation, undirected cell growth and a lack of stability that often complicate their application. Therefore, new membranes which can overcome these issues are of great interest in this field. Methods In this pilot study, we investigated polycaprolactone (PCL) scaffolds intended to enhance oral wound healing by means of melt electrospinning writing (MEW), which allowed for three-dimensional (3D) printing of micron scale fibers and very exact fiber placement. A singular set of box-shaped scaffolds of different sizes consisting of medical-grade PCL was examined and the scaffolds' morphology was evaluated via scanning electron microscopy (SEM). Each prototype sample with box sizes of 225 μm, 300 μm, 375 μm, 450 μm and 500 μm was assessed for cytotoxicity and cell growth by seeding each scaffold with human osteoblast-like cell line MG63. Results All scaffolds demonstrated good cytocompatibility according to cell viability, protein concentration, and cell number. SEM analysis revealed an exact fiber placement of the MEW scaffolds and the growth of viable MG63 cells on them. For the examined box-shaped scaffolds with pore sizes between 225 μm and 500 μm, a preferred box size for initial osteoblast attachment could not be found. Conclusions These well-defined 3D scaffolds consisting of medical-grade materials optimized for cell attachment and cell growth hold the key to a promising new approach in GBR in oral and maxillofacial surgery.}, language = {en} }