TY - JOUR A1 - Bahram, Mohammad A1 - Anslan, Sten A1 - Hildebrand, Falk A1 - Bork, Peer A1 - Tedersoo, Leho T1 - Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment JF - Environmental Microbiology Reports N2 - High-throughput studies of microbial communities suggest that Archaea are a widespread component of microbial diversity in various ecosystems. However, proper quantification of archaeal diversity and community ecology remains limited, as sequence coverage of Archaea is usually low owing to the inability of available prokaryotic primers to efficiently amplify archaeal compared to bacterial rRNA genes. To improve identification and quantification of Archaea, we designed and validated the utility of several primer pairs to efficiently amplify archaeal 16S rRNA genes based on up-to-date reference genes. We demonstrate that several of these primer pairs amplify phylogenetically diverse Archaea with high sequencing coverage, outperforming commonly used primers. Based on comparing the resulting long 16S rRNA gene fragments with public databases from all habitats, we found several novel family- to phylum-level archaeal taxa from topsoil and surface water. Our results suggest that archaeal diversity has been largely overlooked due to the limitations of available primers, and that improved primer pairs enable to estimate archaeal diversity more accurately. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-221380 VL - 11 ER - TY - JOUR A1 - Hettich, Georg A1 - Schierjott, Ronja A. A1 - Ramm, Heiko A1 - Graichen, Heiko A1 - Jansson, Volkmar A1 - Rudert, Maximilian A1 - Traina, Francesco A1 - Grupp, Thomas M. T1 - Method for quantitative assessment of acetabular bone defects JF - Journal of Orthopaedic Research N2 - The objective of the study was to suggest a novel quantitative assessment of acetabular bone defects based on a statistical shape model, validate the method, and present preliminary results. Two exemplary CT-data sets with acetabular bone defects were segmented to obtain a solid model of each defect pelvis. The pathological areas around the acetabulum were excluded and a statistical shape model was fitted to the remaining healthy bone structures. The excluded areas were extrapolated such that a solid model of the native pelvis per specimen resulted (i.e., each pelvis without defect). The validity of the reconstruction was tested by a leave-one-out study. Validation results showed median reconstruction errors of 3.0 mm for center of rotation, 1.7 mm for acetabulum diameter, 2.1° for inclination, 2.5° for anteversion, and 3.3 mm3 for bone volume around the acetabulum. By applying Boolean operations on the solid models of defect and native pelvis, bone loss and bone formation in four different sectors were assessed. For both analyzed specimens, bone loss and bone formation per sector were calculated and were consistent with the visual impression. In specimen_1 bone loss was predominant in the medial wall (10.8 ml; 79%), in specimen_2 in the posterior column (15.6 ml; 46%). This study showed the feasibility of a quantitative assessment of acetabular bone defects using a statistical shape model-based reconstruction method. Validation results showed acceptable reconstruction accuracy, also when less healthy bone remains. The method could potentially be used for implant development, pre-clinical testing, pre-operative planning, and intra-operative navigation. © 2018 The Authors. Journal of Orthopaedic Research® Published by Wiley Periodicals, Inc. on behalf of Orthopaedic Research Society. J Orthop Res 9999:1–9, 2018. KW - acetabular bone defects KW - quantification KW - statistical shape model KW - volume analysis Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-320226 VL - 37 ER - TY - JOUR A1 - Greber, Johannes A1 - Polat, Bülent A1 - Flentje, Michael A1 - Bratengeier, Klaus T1 - Properties of the anisotropy of dose contributions: A planning study on prostate cases JF - Medical Physics N2 - Purpose To characterize the static properties of the anisotropy of dose contributions for different treatment techniques on real patient data (prostate cases). From this, we aim to define a class of treatment techniques with invariant anisotropy distribution carrying information of target coverage and organ-at-risk (OAR) sparing. The anisotropy presumably is a helpful quantity for plan adaptation problems. Methods The anisotropy field is analyzed for different intensity modulated radiotherapy (IMRT) and volumetric modulated arc therapy (VMAT) techniques for a total of ten planning CTs of prostate cases. Primary irradiation directions ranged from 5 to 15. The uniqueness of anisotropy was explored: In particular, the anisotropy distribution inside the planning treatment volume (PTV) and in its vicinity was investigated. Furthermore, deviations of the anisotropy under beam rotations were explored by direct plan comparison as an indicating the susceptibility of each planned technique to changes in the geometric plan configuration. In addition, plan comparisons enabled the categorization of treatment techniques in terms of their anisotropy distribution. Results The anisotropy profile inside the PTV and in the transition between OAR and PTV is independent of the treatment technique as long as a sufficient number of beams contribute to the dose distribution. Techniques with multiple beams constitute a class of almost identical and technique-independent anisotropy distribution. For this class of techniques, substructures of the anisotropy are particularly pronounced in the PTV, thus offering good options for applying adaptation rules. Additionally, the techniques forming the mentioned class fortunately allow a better OAR sparing at constant PTV coverage. Besides the characterization of the distribution, a pairwise plan comparison reveals each technique's susceptibility to deviations which decreases for an increasing number of primary irradiation directions. Conclusions Techniques using many irradiation directions form a class of almost identical anisotropy distributions which are assumed to provide a basis for improved adaptation procedures. Encouragingly, these techniques deliver quite invariant anisotropy distributions with respect to rotations correlated with good plan qualities than techniques using few gantry angles. The following will be the next steps toward anisotropy-based adaptation: first, the quantification of anisotropy regarding organ deformations; and second, establishing the interrelation between the anisotropy and beam shaping. KW - adaptation KW - IMRT KW - radiotherapy KW - VMAT Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-228237 VL - 46 ER - TY - JOUR A1 - de Ruijter, Mylène A1 - Hrynevich, Andrei A1 - Haigh, Jodie N. A1 - Hochleitner, Gernot A1 - Castilho, Miguel A1 - Groll, Jürgen A1 - Malda, Jos A1 - Dalton, Paul D. T1 - Out-of-Plane 3D-Printed Microfibers Improve the Shear Properties of Hydrogel Composites JF - Small N2 - One challenge in biofabrication is to fabricate a matrix that is soft enough to elicit optimal cell behavior while possessing the strength required to withstand the mechanical load that the matrix is subjected to once implanted in the body. Here, melt electrowriting (MEW) is used to direct-write poly(ε-caprolactone) fibers “out-of-plane” by design. These out-of-plane fibers are specifically intended to stabilize an existing structure and subsequently improve the shear modulus of hydrogel–fiber composites. The stabilizing fibers (diameter = 13.3 ± 0.3 µm) are sinusoidally direct-written over an existing MEW wall-like structure (330 µm height). The printed constructs are embedded in different hydrogels (5, 10, and 15 wt% polyacrylamide; 65% poly(2-hydroxyethyl methacrylate) (pHEMA)) and a frequency sweep test (0.05–500 rad s−1, 0.01% strain, n = 5) is performed to measure the complex shear modulus. For the rheological measurements, stabilizing fibers are deposited with a radial-architecture prior to embedding to correspond to the direction of the stabilizing fibers with the loading of the rheometer. Stabilizing fibers increase the complex shear modulus irrespective of the percentage of gel or crosslinking density. The capacity of MEW to produce well-defined out-of-plane fibers and the ability to increase the shear properties of fiber-reinforced hydrogel composites are highlighted. KW - biofabrication KW - fiber reinforcement KW - hydrogels KW - mechanical properties KW - melt electrowriting Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-223666 VL - 14 ER - TY - JOUR A1 - Hrynevich, Andrei A1 - Elçi, Bilge Ş. A1 - Haigh, Jodie N. A1 - McMaster, Rebecca A1 - Youssef, Almoatazbellah A1 - Blum, Carina A1 - Blunk, Torsten A1 - Hochleitner, Gernot A1 - Groll, Jürgen A1 - Dalton, Paul D. T1 - Dimension-Based Design of Melt Electrowritten Scaffolds JF - Small N2 - The electrohydrodynamic stabilization of direct-written fluid jets is explored to design and manufacture tissue engineering scaffolds based on their desired fiber dimensions. It is demonstrated that melt electrowriting can fabricate a full spectrum of various fibers with discrete diameters (2–50 µm) using a single nozzle. This change in fiber diameter is digitally controlled by combining the mass flow rate to the nozzle with collector speed variations without changing the applied voltage. The greatest spectrum of fiber diameters was achieved by the simultaneous alteration of those parameters during printing. The highest placement accuracy could be achieved when maintaining the collector speed slightly above the critical translation speed. This permits the fabrication of medical-grade poly(ε-caprolactone) into complex multimodal and multiphasic scaffolds, using a single nozzle in a single print. This ability to control fiber diameter during printing opens new design opportunities for accurate scaffold fabrication for biomedical applications. KW - biofabrication KW - electrohydrodynamic KW - melt electrospinning writing KW - scaffold design KW - tissue engineering Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-322677 VL - 14 ER - TY - JOUR A1 - Müller, Jörg A1 - Noss, Reed F. A1 - Thorn, Simon A1 - Bässler, Claus A1 - Leverkus, Alexandro B. A1 - Lindenmayer, David T1 - Increasing disturbance demands new policies to conserve intact forest JF - Conservation Letters N2 - Ongoing controversy over logging the ancient Białowieża Forest in Poland symbolizes a global problem for policies and management of the increasing proportion of the earth's intact forest that is subject to postdisturbance logging. We review the extent of, and motivations for, postdisturbance logging in protected and unprotected forests globally. An unprecedented level of logging in protected areas and other places where green-tree harvest would not normally occur is driven by economic interests and a desire for pest control. To avoid failure of global initiatives dedicated to reducing the loss of species, five key policy reforms are necessary: (1) salvage logging must be banned from protected areas; (2) forest planning should address altered disturbance regimes for all intact forests to ensure that significant areas remain undisturbed by logging; (3) new kinds of integrated analyses are needed to assess the potential economic benefits of salvage logging against its ecological, economic, and social costs; (4) global and regional maps of natural disturbance regimes should be created to guide better spatiotemporal planning of protected areas and undisturbed forests outside reserves; and (5) improved education and communication programs are needed to correct widely held misconceptions about natural disturbances. KW - anthropogenic disturbance KW - forestry KW - FSC KW - natural disturbance KW - protected area management KW - sanitary logging Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-224256 VL - 12 ER - TY - JOUR A1 - Steigerwald, Frank A1 - Timmermann, Lars A1 - Kühn, Andrea A1 - Schnitzler, Alfons A1 - Reich, Martin M. A1 - Kirsch, Anna Dalal A1 - Barbe, Michael Thomas A1 - Visser-Vandewalle, Veerle A1 - Hübl, Julius A1 - van Riesen, Christoph A1 - Groiss, Stefan Jun A1 - Moldovan, Alexia-Sabine A1 - Lin, Sherry A1 - Carcieri, Stephen A1 - Manola, Ljubomir A1 - Volkmann, Jens T1 - Pulse duration settings in subthalamic stimulation for Parkinson's disease JF - Movement Disorders N2 - Background Stimulation parameters in deep brain stimulation (DBS) of the subthalamic nucleus for Parkinson's disease (PD) are rarely tested in double-blind conditions. Evidence-based recommendations on optimal stimulator settings are needed. Results from the CUSTOM-DBS study are reported, comparing 2 pulse durations. Methods A total of 15 patients were programmed using a pulse width of 30 µs (test) or 60 µs (control). Efficacy and side-effect thresholds and unified PD rating scale (UPDRS) III were measured in meds-off (primary outcome). The therapeutic window was the difference between patients’ efficacy and side effect thresholds. Results The therapeutic window was significantly larger at 30 µs than 60 µs (P = ·0009) and the efficacy (UPDRS III score) was noninferior (P = .00008). Interpretation Subthalamic neurostimulation at 30 µs versus 60 µs pulse width is equally effective on PD motor signs, is more energy efficient, and has less likelihood of stimulation-related side effects. © 2017 The Authors. Movement Disorders published by Wiley Periodicals, Inc. on behalf of International Parkinson and Movement Disorder Society. KW - deep brain stimulation KW - Parkinson's disease; KW - pulse width KW - stimulation parameters KW - subthalamic Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-239402 VL - 33 ER - TY - JOUR A1 - Arlotti, Mattia A1 - Palmisano, Chiara A1 - Minafra, Brigida A1 - Todisco, Massimiliano A1 - Pacchetti, Claudio A1 - Canessa, Andrea A1 - Pozzi, Nicoló G. A1 - Cilia, Roberto A1 - Prenassi, Marco A1 - Marceglia, Sara A1 - Priori, Alberto A1 - Rampini, Paolo A1 - Barbieri, Sergio A1 - Servello, Domenico A1 - Volkmann, Jens A1 - Pezzoli, Gianni A1 - Isaias, Ioannis U. T1 - Monitoring subthalamic oscillations for 24 hours in a freely moving Parkinson's disease patient JF - Movement Disorders N2 - No abstract available Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-221249 VL - 34 ER - TY - JOUR A1 - Zeiner, Pia S. A1 - Preusse, Corinna A1 - Golebiewska, Anna A1 - Zinke, Jenny A1 - Iriondo, Ane A1 - Muller, Arnaud A1 - Kaoma, Tony A1 - Filipski, Katharina A1 - Müller-Eschner, Monika A1 - Bernatz, Simon A1 - Blank, Anna-Eva A1 - Baumgarten, Peter A1 - Ilina, Elena A1 - Grote, Anne A1 - Hansmann, Martin L. A1 - Verhoff, Marcel A. A1 - Franz, Kea A1 - Feuerhake, Friedrich A1 - Steinbach, Joachim P. A1 - Wischhusen, Jörg A1 - Stenzel, Werner A1 - Niclou, Simone P. A1 - Harter, Patrick N. A1 - Mittelbronn, Michel T1 - Distribution and prognostic impact of microglia/macrophage subpopulations in gliomas JF - Brain Pathology N2 - While the central nervous system is considered an immunoprivileged site and brain tumors display immunosuppressive features, both innate and adaptive immune responses affect glioblastoma (GBM) growth and treatment resistance. However, the impact of the major immune cell population in gliomas, represented by glioma-associated microglia/macrophages (GAMs), on patients’ clinical course is still unclear. Thus, we aimed at assessing the immunohistochemical expression of selected microglia and macrophage markers in 344 gliomas (including gliomas from WHO grade I–IV). Furthermore, we analyzed a cohort of 241 IDH1R132H-non-mutant GBM patients for association of GAM subtypes and patient overall survival. Phenotypical properties of GAMs, isolated from high-grade astrocytomas by CD11b-based magnetic cell sorting, were analyzed by immunocytochemistry, mRNA microarray, qRT-PCR and bioinformatic analyses. A higher amount of CD68-, CD163- and CD206-positive GAMs in the vital tumor core was associated with beneficial patient survival. The mRNA expression profile of GAMs displayed an upregulation of factors that are considered as pro-inflammatory M1 (eg, CCL2, CCL3L3, CCL4, PTGS2) and anti-inflammatory M2 polarization markers (eg, MRC1, LGMN, CD163, IL10, MSR1), the latter rather being associated with phagocytic functions in the GBM microenvironment. In summary, we present evidence that human GBMs contain mixed M1/M2-like polarized GAMs and that the levels of different GAM subpopulations in the tumor core are positively associated with overall survival of patients with IDH1R132H-non-mutant GBMs. KW - glioma KW - glioma-associated microglia and macrophages; KW - immune polarization KW - tumor microenvironment Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-233897 VL - 29 ER - TY - JOUR A1 - Ingendoh-Tsakmakidis, Alexandra A1 - Mikolai, Carina A1 - Winkel, Andreas A1 - Szafrański, Szymon P. A1 - Flak, Christine S. A1 - Rossi, Angela A1 - Walles, Heike A1 - Stiesch, Meike T1 - Commensal and pathogenic biofilms differently modulate peri-implant oral mucosa in an organotypic model JF - Cellular Microbiology N2 - The impact of oral commensal and pathogenic bacteria on peri-implant mucosa is not well understood, despite the high prevalence of peri-implant infections. Hence, we investigated responses of the peri-implant mucosa to Streptococcus oralis or Aggregatibacter actinomycetemcomitans biofilms using a novel in vitro peri-implant mucosa-biofilm model. Our 3D model combined three components, organotypic oral mucosa, implant material, and oral biofilm, with structural assembly close to native situation. S. oralis induced a protective stress response in the peri-implant mucosa through upregulation of heat shock protein (HSP70) genes. Attenuated inflammatory response was indicated by reduced cytokine levels of interleukin-6 (IL-6), interleukin-8 (CXCL8), and monocyte chemoattractant protein-1 (CCL2). The inflammatory balance was preserved through increased levels of tumor necrosis factor-alpha (TNF-α). A. actinomycetemcomitans induced downregulation of genes important for cell survival and host inflammatory response. The reduced cytokine levels of chemokine ligand 1 (CXCL1), CXCL8, and CCL2 also indicated a diminished inflammatory response. The induced immune balance by S. oralis may support oral health, whereas the reduced inflammatory response to A. actinomycetemcomitans may provide colonisation advantage and facilitate later tissue invasion. The comprehensive characterisation of peri-implant mucosa-biofilm interactions using our 3D model can provide new knowledge to improve strategies for prevention and therapy of peri-implant disease. KW - Aggregatibacter actinomycetemcomitans KW - dental implants KW - host modulation KW - organotypic oral mucosa KW - Streptococcus oralis Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-323077 VL - 21 ER -