@phdthesis{Kapustjansky2011,
  author    = {Kapustjansky, Alexander},
  title     = {In vivo imaging and optogenetic approach to study the formation of olfactory memory and locomotor behaviour in Drosophila melanogaster},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-69535},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2011},
  abstract  = {Understanding of complex interactions and events in a nervous system, leading from the molecular level up to certain behavioural patterns calls for interdisciplinary interactions of various research areas. The goal of the presented work is to achieve such an interdisciplinary approach to study and manipulate animal behaviour and its underlying mechanisms. Optical in vivo imaging is a new constantly evolving method, allowing one to study not only the local but also wide reaching activity in the nervous system. Due to ease of its genetic accessibility Drosophila melanogaster represents an extraordinary experimental organism to utilize not only imaging but also various optogenetic techniques to study the neuronal underpinnings of behaviour. In this study four genetically encoded sensors were used to investigate the temporal dynamics of cAMP concentration changes in the horizontal lobes of the mushroom body, a brain area important for learning and memory, in response to various physiological and pharmacological stimuli. Several transgenic lines with various genomic insertion sites for the sensor constructs Epac1, Epac2, Epac2K390E and HCN2 were screened for the best signal quality, one line was selected for further experiments. The in vivo functionality of the sensor was assessed via pharmacological application of 8-bromo-cAMP as well as Forskolin, a substance stimulating cAMP producing adenylyl cyclases. This was followed by recording of the cAMP dynamics in response to the application of dopamine and octopamine, as well as to the presentation of electric shock, odorants or a simulated olfactory signal, induced by acetylcholine application to the observed brain area. In addition the interaction between the shock and the simulated olfactory signal by simultaneous presentation of both stimuli was studied. Preliminary results are supporting a coincidence detection mechanism at the level of the adenylyl cyclase as postulated by the present model for classical olfactory conditioning. In a second series of experiments an effort was made to selecticvely activate a subset of neurons via the optogenetic tool Channelrhodopsin (ChR2). This was achieved by recording the behaviour of the fly in a walking ball paradigm. A new method was developed to analyse the walking behaviour of the animal whose brain was made optically accessible via a dissection technique, as used for imaging, thus allowing one to target selected brain areas. Using the Gal4-UAS system the protocerebral bridge, a substructure of the central complex, was highlighted by expressing the ChR2 tagged by fluorescent protein EYFP. First behavioural recordings of such specially prepared animals were made. Lastly a new experimental paradigm for single animal conditioning was developed (Shock Box). Its design is based on the established Heat Box paradigm, however in addition to spatial and operant conditioning available in the Heat Box, the design of the new paradigm allows one to set up experiments to study classical and semioperant olfactory conditioning, as well as semioperant place learning and operant no idleness experiments. First experiments involving place learning were successfully performed in the new apparatus.},
  subject      = {Taufliege},
  language  = {en}
}
@phdthesis{Bonn2011,
  author    = {Bonn, Maria Roswitha},
  title     = {Zielstrukturen des serotonergen Systems in der laterobasalen Amygdala : Untersuchungen an Ratten und einem Mausmodell f{\"u}r emotionale Dysregulation},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-69494},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2011},
  abstract  = {Die Amygdala ist ein Kernkomplex, der dicht von serotonergen Afferenzen innerviert wird. Sowohl bei Tieren als auch beim Menschen spielen Interaktionen zwischen dem serotonergen System und der Amygdala bei der Verarbeitung von Reizen, die mit Angst oder Stress assoziiert sind, eine zentrale Rolle. Genetische Variationen im serotonergen System und/oder dauerhafter Stress k{\"o}nnen dazu f{\"u}hren, dass diese Verarbeitungsprozesse fehlerhaft ablaufen, wodurch Verhaltensanormalit{\"a}ten bzw. die Entstehung psychiatrischer Erkrankungen beg{\"u}nstigt werden. Die Zielneurone der serotonergen Transmission in der Amygdala, die molekularen Mechanismen m{\"o}glicher Interaktionen und strukturelle Konsequenzen der St{\"o}rungen dieser Interaktionen sind jedoch bis zum heutigen Zeitpunkt noch nicht vollst{\"a}ndig bekannt. Daher bestand ein Ziel der vorliegenden Arbeit darin, den Einfluss eines Ungleichgewichts im serotonergen System (5-Htt KO) sowie von wiederholtem, sozialem Stress auf die neuronale Morphologie der Amygdala zu analysieren und Zielneurone serotonerger Afferenzen zu identifizieren und zu charakterisieren, um die neuronalen Netzwerke der Emotionsverarbeitung besser verstehen zu k{\"o}nnen. Um vom 5-Htt-Genotyp abh{\"a}ngige und stressbedingte neuromorphologische Ver{\"a}nderungen zu untersuchen, wurden dreidimensionale Rekonstruktionen von Neuronen der laterobasalen Amygdala von m{\"a}nnlichen, adulten Wildtyp (WT)- und 5-Htt KO-M{\"a}usen angefertigt und bez{\"u}glich verschiedener morphologischer Parameter ausgewertet. An den Pyramidenzellen wurden nur geringf{\"u}gige Ver{\"a}nderungen der dendritischen Komplexit{\"a}t, jedoch, im Vergleich zu WT-M{\"a}usen, eine wesentliche Erh{\"o}hung der Dornendichte an spezifischen dendritischen Kompartimenten bei gestressten WT-M{\"a}usen, sowie nicht gestressten und gestressten 5-Htt KO-M{\"a}usen nachgewiesen. Im Vergleich zu nicht gestressten WT-M{\"a}usen war die dendritische Dornendichte aller anderen Gruppen gleichermaßen erh{\"o}ht. Die Sternzelle, zeigten bez{\"u}glich der untersuchten Parameter keine morphologischen Ver{\"a}nderungen auf. Eine besondere Subpopulation der Interneurone stellen die NeuropeptidY (NPY)-Neurone der laterobasalen Amygdala dar, da sie in diesen Nuclei anxiolytisch wirken. Es gibt nur wenige Anhaltspunkte dar{\"u}ber, durch welche Systeme NPY-Neurone moduliert werden. Da sowohl NPY-Neurone in der laterobasalen Amygdala als auch das serotonerge System an angstregulierenden Prozessen beteiligt sind, sollte im zweiten Teil der vorliegenden Arbeit untersucht werden, ob es sich bei diesen Neuronen um Zielstrukturen des serotonergen Systems handelt. Mittels licht- und elektronenmikroskopischer Analysen wurden synaptische Kontakte zwischen serotonergen Afferenzen und NPY-immunreaktiven Neuronen in der laterobasalen Amygdala von Ratten verifiziert. Da der funktionelle Einfluss der serotonergen Innervation auf diese Zielneurone von deren Serotoninrezeptor (5-HTR)-Ausstattung abh{\"a}ngt, wurden Koexpressionsanalysen von NPY mRNA mit den mRNAs verschiedener 5-HTR durchgef{\"u}hrt. Die Analysen ergaben, dass NPY mRNA-reaktive Neurone in der laterobasalen Amygdala 5-HT1A und 5-HT2C, jedoch nicht 5-HT3 mRNA koexprimieren. Die in der vorliegenden Arbeit erzielten Resultate liefern neue Erkenntnisse {\"u}ber den Einfluss des serotonergen Systems auf die laterobasale Amygdala von M{\"a}usen und Ratten. Bei den Ver{\"a}nderungen der dendritischen Dornendichte nach sozialen Stresserfahrungen k{\"o}nnte es sich um neuroadaptive bzw. kompensatorische Mechanismen der Pyramidenzellen handeln, die WT-M{\"a}usen eine Anpassung an sich {\"a}ndernde, negative Umweltbedingungen erm{\"o}glicht. Die erh{\"o}hte Dornendichte k{\"o}nnte dabei die Ausbildung eines „emotionalen Ged{\"a}chtnisses" repr{\"a}sentieren, das eine flexible Verhaltensantwort auf ein erneutes Auftauchen von Gefahr erlaubt. Eine solche Modulation der Erregbarkeit der laterobasalen Amygdala k{\"o}nnte beispielsweise {\"u}ber eine situationsentsprechende Hemmung des Outputs der Pyramidenzellen durch differentiell aktive inhibitorische Netzwerke erfolgen. Eine differentielle Aktivierung kann z. B. {\"u}ber unterschiedliche Rezeptorausstattungen, wie es in der Subpopulation der NPY-Neurone in der vorliegenden Arbeit nachgewiesen wurde, erfolgen. Das erh{\"o}hte angst{\"a}hnliche Verhalten der 5-Htt KO-M{\"a}use nach wiederholtem Stress k{\"o}nnte mit der Unf{\"a}higkeit zusammenh{\"a}ngen, in entsprechenden Situationen durch Neubildung von Dornen zu reagieren, da die Dornendichte bei diesen Tieren schon unter stressarmen Umweltbedingungen ihr Maximum erreicht hat. Sowohl Fehlfunktionen der neuronalen Plastizit{\"a}t als auch m{\"o}gliche Fehlfunktionen der differentiellen Inhibierung der Pyramidenzellen durch Interneurone, die durch genetische Variationen und/oder Stress bedingt sein k{\"o}nnen, k{\"o}nnten eine „offene T{\"u}r" repr{\"a}sentieren, die zu manifesten Auff{\"a}lligkeiten im Verhalten bei Tieren f{\"u}hrt bzw. auch zur Entstehung bestimmter psychiatrischer Erkrankungen beim Menschen beitr{\"a}gt.},
  subject      = {Angst},
  language  = {de}
}
@article{FriedrichRahmannWeigeletal.2010,
  author    = {Friedrich, Torben and Rahmann, Sven and Weigel, Wilfried and Rabsch, Wolfgang and Fruth, Angelika and Ron, Eliora and Gunzer, Florian and Dandekar, Thomas and Hacker, Joerg and Mueller, Tobias and Dobrindt, Ulrich},
  title     = {High-throughput microarray technology in diagnostics of enterobacteria based on genome-wide probe selection and regression analysis},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-67936},
  year      = {2010},
  abstract  = {The Enterobacteriaceae comprise a large number of clinically relevant species with several individual subspecies. Overlapping virulence-associated gene pools and the high overall genome plasticity often interferes with correct enterobacterial strain typing and risk assessment. Array technology offers a fast, reproducible and standardisable means for bacterial typing and thus provides many advantages for bacterial diagnostics, risk assessment and surveillance. The development of highly discriminative broad-range microbial diagnostic microarrays remains a challenge, because of marked genome plasticity of many bacterial pathogens. Results: We developed a DNA microarray for strain typing and detection of major antimicrobial resistance genes of clinically relevant enterobacteria. For this purpose, we applied a global genome-wide probe selection strategy on 32 available complete enterobacterial genomes combined with a regression model for pathogen classification. The discriminative power of the probe set was further tested in silico on 15 additional complete enterobacterial genome sequences. DNA microarrays based on the selected probes were used to type 92 clinical enterobacterial isolates. Phenotypic tests confirmed the array-based typing results and corroborate that the selected probes allowed correct typing and prediction of major antibiotic resistances of clinically relevant Enterobacteriaceae, including the subspecies level, e.g. the reliable distinction of different E. coli pathotypes. Conclusions: Our results demonstrate that the global probe selection approach based on longest common factor statistics as well as the design of a DNA microarray with a restricted set of discriminative probes enables robust discrimination of different enterobacterial variants and represents a proof of concept that can be adopted for diagnostics of a wide range of microbial pathogens. Our approach circumvents misclassifications arising from the application of virulence markers, which are highly affected by horizontal gene transfer. Moreover, a broad range of pathogens have been covered by an efficient probe set size enabling the design of high-throughput diagnostics.},
  subject      = {Mikroarray},
  language  = {en}
}
@article{LaisneyBraaschWalteretal.2010,
  author    = {Laisney, Juliette A. G. C. and Braasch, Ingo and Walter, Ronald B. and Meierjohann, Svenja and Schartl, Manfred},
  title     = {Lineage-specific co-evolution of the Egf receptor/ligand signaling system},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-67922},
  year      = {2010},
  abstract  = {Background: The epidermal growth factor receptor (Egfr) with its numerous ligands has fundamental roles in development, cell differentiation and physiology. Dysfunction of the receptor-ligand system contributes to many human malignancies. Consistent with such various tasks, the Egfr gene family has expanded during vertebrate evolution as a consequence of several rounds of whole genome duplication. Of particular interest is the effect of the fish-specific whole genome duplication (FSGD) on the ligand-receptor system, as it has supplied this largest group of vertebrates with additional opportunities for sub- and/or neofunctionalization in this signaling system. Results: We identified the predicted components of the Egf receptor-ligand signaling system in teleost fishes (medaka, platyfish, stickleback, pufferfishes and zebrafish). We found two duplicated egfr genes, egfra and egfrb, in all available teleost genomes. Surprisingly only one copy for each of the seven Egfr ligands could be identified in most fishes, with zebrafish hbegf being the only exception. Special focus was put on medaka, for which we more closely investigated all Egf receptors and Egfr ligands. The different expression patterns of egfra, egfrb and their ligands in medaka tissues and embryo stages suggest differences in role and function. Preferential co-expression of different subsets of Egfr ligands corroborates the possible subfunctionalization and specialization of the two receptors in adult tissues. Bioinformatic analyses of the ligand-receptor interface between Egfr and its ligands show a very weak evolutionary conservation within this region. Using in vitro analyses of medaka Egfra, we could show that this receptor is only activated by medaka ligands, but not by human EGF. Altogether, our data suggest a lineage-specific Egfr/Egfr ligand co-evolution. Conclusions: Our data indicate that medaka Egfr signaling occurs via its two copies, Egfra and Egfrb, each of them being preferentially coexpressed with different subsets of Egfr ligands. This fish-specific occurrence of Egf receptor specialization offers unique opportunities to study the functions of different Egf receptor-ligand combinations and their biological outputs in vertebrates. Furthermore, our results strongly support the use of homologous ligands in future studies, as sufficient cross-specificity is very unlikely for this ligand/receptor system.},
  subject      = {Epidermaler Wachstumsfaktor-Rezeptor},
  language  = {en}
}
@article{BrocherVogelHock2010,
  author    = {Brocher, Jan and Vogel, Benjamin and Hock, Robert},
  title     = {HMGA1 down-regulation is crucial for chromatin composition and a gene expression profile permitting myogenic differentiation},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-67914},
  year      = {2010},
  abstract  = {Background: High mobility group A (HMGA) proteins regulate gene transcription through architectural modulation of chromatin and the formation of multi-protein complexes on promoter/enhancer regions. Differential expression of HMGA variants has been found to be important for distinct differentiation processes and deregulated expression was linked to several disorders. Here we used mouse C2C12 myoblasts and C2C12 cells stably over-expressing HMGA1a-eGFP to study the impact of deregulated HMGA1 expression levels on cellular differentiation. Results: We found that induction of the myogenic or osteogenic program of C2C12 cells caused an immediate down-regulation of HMGA1. In contrast to wild type C2C12 cells, an engineered cell line with stable overexpression of HMGA1a-eGFP failed to differentiate into myotubes. Immunolocalization studies demonstrated that sustained HMGA1a-eGFP expression prevented myotube formation and chromatin reorganization that normally accompanies differentiation. Western Blot analyses showed that elevated HMGA1a-eGFP levels affected chromatin composition through either down-regulation of histone H1 or premature expression of MeCP2. RT-PCR analyses further revealed that sustained HMGA1a expression also affected myogenic gene expression and caused either down-regulation of genes such as MyoD, myogenin, Igf1, Igf2, Igfbp1-3 or up-regulation of the transcriptional repressor Msx1. Interestingly, siRNA experiments demonstrated that knock-down of HMGA1a was required and sufficient to reactivate the myogenic program in induced HMGA1a over-expressing cells. Conclusions: Our data demonstrate that HMGA1 down-regulation after induction is required to initiate the myogenic program in C2C12 cells. Sustained HMGA1a expression after induction prevents expression of key myogenic factors. This may be due to specific gene regulation and/or global effects on chromatin. Our data further corroborate that altered HMGA1 levels influence the expression of other chromatin proteins. Thus, HMGA1 is able to establish a specific chromatin composition. This work contributes to the understanding of how differential HMGA1 expression is involved in chromatin organization during cellular differentiation processes and it may help to comprehend effects of HMGA1 over-expression occurring in malign or benign tumours.},
  subject      = {HMG-Proteine},
  language  = {en}
}
@article{TeutschbeinHaydnSamansetal.2010,
  author    = {Teutschbein, Janka and Haydn, Johannes M. and Samans, Birgit and Krause, Michael and Eilers, Martin and Schartl, Manfred and Meierjohann, Svenja},
  title     = {Gene expression analysis after receptor tyrosine kinase activation reveals new potential melanoma proteins},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-67900},
  year      = {2010},
  abstract  = {Background: Melanoma is an aggressive tumor with increasing incidence. To develop accurate prognostic markers and targeted therapies, changes leading to malignant transformation of melanocytes need to be understood. In the Xiphophorus melanoma model system, a mutated version of the EGF receptor Xmrk (Xiphophorus melanoma receptor kinase) triggers melanomagenesis. Cellular events downstream of Xmrk, such as the activation of Akt, Ras, B-Raf or Stat5, were also shown to play a role in human melanomagenesis. This makes the elucidation of Xmrk downstream targets a useful method for identifying processes involved in melanoma formation. Methods: Here, we analyzed Xmrk-induced gene expression using a microarray approach. Several highly expressed genes were confirmed by realtime PCR, and pathways responsible for their induction were revealed using small molecule inhibitors. The expression of these genes was also monitored in human melanoma cell lines, and the target gene FOSL1 was knocked down by siRNA. Proliferation and migration of siRNA-treated melanoma cell lines were then investigated. Results: Genes with the strongest upregulation after receptor activation were FOS-like antigen 1 (Fosl1), early growth response 1 (Egr1), osteopontin (Opn), insulin-like growth factor binding protein 3 (Igfbp3), dual-specificity phosphatase 4 (Dusp4), and tumor-associated antigen L6 (Taal6). Interestingly, most genes were blocked in presence of a SRC kinase inhibitor. Importantly, we found that FOSL1, OPN, IGFBP3, DUSP4, and TAAL6 also exhibited increased expression levels in human melanoma cell lines compared to human melanocytes. Knockdown of FOSL1 in human melanoma cell lines reduced their proliferation and migration. Conclusion: Altogether, the data show that the receptor tyrosine kinase Xmrk is a useful tool in the identification of target genes that are commonly expressed in Xmrk-transgenic melanocytes and melanoma cell lines. The identified molecules constitute new possible molecular players in melanoma development. Specifically, a role of FOSL1 in melanomagenic processes is demonstrated. These data are the basis for future detailed analyses of the investigated target genes.},
  language  = {en}
}
@article{GrimmGasserBueteretal.2010,
  author    = {Grimm, Martin and Gasser, Martin and Bueter, Marco and Strehl, Johanna and Wang, Johann and Nichiporuk, Ekaterina and Meyer, Detlef and Germer, Christoph T. and Waaga-Gasser, Ana M. and Thalheimer, Andreas},
  title     = {Evaluation of immunological escape mechanisms in a mouse model of colorectal liver metastases},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-67899},
  year      = {2010},
  abstract  = {Background: The local and systemic activation and regulation of the immune system by malignant cells during carcinogenesis is highly complex with involvement of the innate and acquired immune system. Despite the fact that malignant cells do have antigenic properties their immunogenic effects are minor suggesting tumor induced mechanisms to circumvent cancer immunosurveillance. The aim of this study is the analysis of tumor immune escape mechanisms in a colorectal liver metastases mouse model at different points in time during tumor growth. Methods: CT26.WT murine colon carcinoma cells were injected intraportally in Balb/c mice after median laparotomy using a standardized injection technique. Metastatic tumor growth in the liver was examined by standard histological procedures at defined points in time during metastatic growth. Liver tissue with metastases was additionally analyzed for cytokines, T cell markers and Fas/Fas-L expression using immunohistochemistry, immunofluorescence and RT-PCR. Comparisons were performed by analysis of variance or paired and unpaired t test when appropriate. Results: Intraportal injection of colon carcinoma cells resulted in a gradual and time dependent metastatic growth. T cells of regulatory phenotype (CD4+CD25+Foxp3+) which might play a role in protumoral immune response were found to infiltrate peritumoral tissue increasingly during carcinogenesis. Expression of cytokines IL-10, TGF-b and TNF-a were increased during tumor growth whereas IFN-g showed a decrease of the expression from day 10 on following an initial increase. Moreover, liver metastases of murine colon carcinoma show an up-regulation of FAS-L on tumor cell surface with a decreased expression of FAS from day 10 on. CD8+ T cells express FAS and show an increased rate of apoptosis at perimetastatic location. Conclusions: This study describes cellular and macromolecular changes contributing to immunological escape mechanisms during metastatic growth in a colorectal liver metastases mouse model simulating the situation in human cancer.},
  subject      = {Krebs <Medizin>},
  language  = {en}
}
@article{SchroepferKaemmererKappetal.2010,
  author    = {Schroepfer, Andrea and K{\"a}mmerer, Ulrike and Kapp, Michaela and Dietl, Johannes and Feix, Sonja and Anacker, Jelena},
  title     = {Expression pattern of matrix metalloproteinases in human gynecological cancer cell lines},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-67880},
  year      = {2010},
  abstract  = {Background: Matrix metalloproteinases (MMPs) are involved in the degradation of protein components of the extracellular matrix and thus play an important role in tumor invasion and metastasis. Their expression is related to the progression of gynecological cancers (e.g. endometrial, cervical or ovarian carcinoma). In this study we investigated the expression pattern of the 23 MMPs, currently known in humans, in different gynecological cancer cell lines. Methods: In total, cell lines from three endometrium carcinomas (Ishikawa, HEC-1-A, AN3 CA), three cervical carcinomas (HeLa, Caski, SiHa), three chorioncarcinomas (JEG, JAR, BeWo), two ovarian cancers (BG-1, OAW-42) and one teratocarcinoma (PA-1) were examined. The expression of MMPs was analyzed by RT-PCR, Western blot and gelatin zymography. Results: We demonstrated that the cell lines examined can constitutively express a wide variety of MMPs on mRNA and protein level. While MMP-2, -11, -14 and -24 were widely expressed, no expression was seen for MMP-12, -16, -20, -25, -26, -27 in any of the cell lines. A broad range of 16 MMPs could be found in the PA1 cells and thus this cell line could be used as a positive control for general MMP experiments. While the three cervical cancer cell lines expressed 10-14 different MMPs, the median expression in endometrial and choriocarcinoma cells was 7 different enzymes. The two investigated ovarian cancer cell lines showed a distinctive difference in the number of expressed MMPs (2 vs. 10). Conclusions: Ishikawa, Caski, OAW-42 and BeWo cell lines could be the best choice for all future experiments on MMP regulation and their role in endometrial, cervical, ovarian or choriocarcinoma development, whereas the teratocarcinoma cell line PA1 could be used as a positive control for general MMP experiments.},
  subject      = {Krebs <Medizin>},
  language  = {en}
}
@article{VainshteinSanchezBrazmaetal.2010,
  author    = {Vainshtein, Yevhen and Sanchez, Mayka and Brazma, Alvis and Hentze, Matthias W. and Dandekar, Thomas and Muckenthaler, Martina U.},
  title     = {The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-67869},
  year      = {2010},
  abstract  = {Background: Gene expression studies greatly contribute to our understanding of complex relationships in gene regulatory networks. However, the complexity of array design, production and manipulations are limiting factors, affecting data quality. The use of customized DNA microarrays improves overall data quality in many situations, however, only if for these specifically designed microarrays analysis tools are available. Results: The IronChip Evaluation Package (ICEP) is a collection of Perl utilities and an easy to use data evaluation pipeline for the analysis of microarray data with a focus on data quality of custom-designed microarrays. The package has been developed for the statistical and bioinformatical analysis of the custom cDNA microarray IronChip but can be easily adapted for other cDNA or oligonucleotide-based designed microarray platforms. ICEP uses decision tree-based algorithms to assign quality flags and performs robust analysis based on chip design properties regarding multiple repetitions, ratio cut-off, background and negative controls. Conclusions: ICEP is a stand-alone Windows application to obtain optimal data quality from custom-designed microarrays and is freely available here (see "Additional Files" section) and at: http://www.alice-dsl.net/evgeniy. vainshtein/ICEP/},
  subject      = {Microarray},
  language  = {en}
}
@article{SchmidSchindelinCardonaetal.2010,
  author    = {Schmid, Benjamin and Schindelin, Johannes and Cardona, Albert and Longair, Martin and Heisenberg, Martin},
  title     = {A high-level 3D visualization API for Java and ImageJ},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-67851},
  year      = {2010},
  abstract  = {Background: Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set. Results: Here we present a platform-independent framework based on Java and Java 3D for accelerated rendering of biological images. Our framework is seamlessly integrated into ImageJ, a free image processing package with a vast collection of community-developed biological image analysis tools. Our framework enriches the ImageJ software libraries with methods that greatly reduce the complexity of developing image analysis tools in an interactive 3D visualization environment. In particular, we provide high-level access to volume rendering, volume editing, surface extraction, and image annotation. The ability to rely on a library that removes the low-level details enables concentrating software development efforts on the algorithm implementation parts. Conclusions: Our framework enables biomedical image software development to be built with 3D visualization capabilities with very little effort. We offer the source code and convenient binary packages along with extensive documentation at http://3dviewer.neurofly.de.},
  subject      = {Visualisierung},
  language  = {en}
}