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  • 1
    Language: English
    In: Nucleic acids research, 18 March 2016, Vol.44(5), pp.2310-22
    Description: We analyzed a multi-drug resistant (MR) HIV-1 reverse transcriptase (RT), subcloned from a patient-derived subtype CRF02_AG, harboring 45 amino acid exchanges, amongst them four thymidine analog mutations (TAMs) relevant for high-level AZT (azidothymidine) resistance by AZTMP excision (M41L, D67N, T215Y, K219E) as well as four substitutions of the AZTTP discrimination pathway (A62V, V75I, F116Y and Q151M). In addition, K65R, known to antagonize AZTMP excision in HIV-1 subtype B was present. Although MR-RT harbored the most significant amino acid exchanges T215Y and Q151M of each pathway, it exclusively used AZTTP discrimination, indicating that the two mechanisms are mutually exclusive and that the Q151M pathway is obviously preferred since it confers resistance to most nucleoside inhibitors. A derivative was created, additionally harboring the TAM K70R and the reversions M151Q as well as R65K since K65R antagonizes excision. MR-R65K-K70R-M151Q was competent of AZTMP excision, whereas other combinations thereof with only one or two exchanges still promoted discrimination. To tackle the multi-drug resistance problem, we tested if the MR-RTs could still be inhibited by RNase H inhibitors. All MR-RTs exhibited similar sensitivity toward RNase H inhibitors belonging to different inhibitor classes, indicating the importance of developing RNase H inhibitors further as anti-HIV drugs.
    Keywords: Drug Resistance, Multiple, Viral -- Genetics ; Enzyme Inhibitors -- Pharmacology ; HIV Reverse Transcriptase -- Antagonists & Inhibitors ; HIV-1 -- Drug Effects ; Ribonuclease H, Human Immunodeficiency Virus -- Antagonists & Inhibitors
    ISSN: 03051048
    E-ISSN: 1362-4962
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  • 2
    Language: English
    In: Nature cell biology, November 2018, Vol.20(11), pp.1250-1255
    Description: Movement of cargos along microtubules plays key roles in diverse cellular processes, from signalling to mitosis. In cilia, rapid movement of ciliary components along the microtubules to and from the assembly site is essential for the assembly and disassembly of the structure itself. This bidirectional transport, known as intraflagellar transport (IFT), is driven by the anterograde motor kinesin-2 and the retrograde motor dynein-1b (dynein-2 in mammals). However, to drive retrograde transport, dynein-1b must first be delivered to the ciliary tip by anterograde IFT. Although, the presence of opposing motors in bidirectional transport processes often leads to periodic stalling and slowing of cargos, IFT is highly processive. Using cryo-electron tomography, we show that a tug-of-war between kinesin-2 and dynein-1b is prevented by loading dynein-1b onto anterograde IFT trains in an autoinhibited form and by positioning it away from the microtubule track to prevent binding. Once at the ciliary tip, dynein-1b must transition into an active form and engage microtubules to power retrograde trains. These findings provide a striking example of how coordinated structural changes mediate the behaviour of complex cellular machinery.
    Keywords: Cell Movement -- Physiology ; Cilia -- Physiology ; Cryoelectron Microscopy -- Methods ; Dyneins -- Metabolism
    ISSN: 14657392
    E-ISSN: 1476-4679
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  • 3
    Description: Multiple approaches to use deep learning for image restoration have recently been proposed. Training such approaches requires well registered pairs of high and low quality images. While this is easily achievable for many imaging modalities, e.g. fluorescence light microscopy, for others it is not. Cryo-transmission electron microscopy (cryo-TEM) could profoundly benefit from improved denoising methods, unfortunately it is one of the latter. Here we show how recent advances in network training for image restoration tasks, i.e. denoising, can be applied to cryo-TEM data. We describe our proposed method and show how it can be applied to single cryo-TEM projections and whole cryo-tomographic image volumes. Our proposed restoration method dramatically increases contrast in cryo-TEM images, which improves the interpretability of the acquired data. Furthermore we show that automated downstream processing on restored image data, demonstrated on a dense segmentation task, leads to improved results. Comment: This work has been submitted to the IEEE for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessible. This version fixed flipped graph labels in Figure 5
    Keywords: Computer Science - Computer Vision And Pattern Recognition ; Computer Science - Machine Learning
    Source: Cornell University
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  • 4
    Language: English
    In: International Journal of Oncology, August 2011, Vol.39(2), pp.515-520
    Description: We performed this study in order to evaluate the impact of the chemokine CXCL12 and its single-nucleotide polymorphism (SNP) rs1801157 on clinicopathological parameters and survival in patients undergoing surgery for esophagogastric cancer. The expression pattern of CXCL12 and its polymorphisms were analyzed by RT-PCR and PCR-RFLP in 69 consecutive fresh-frozen samples of human esophagogastric junction and gastric adenocarcinomas and statistically analyzed. Expression of the CXCL12 (SNP rs1801157) polymorphisms GA/AA significantly correlated with distant metastasis (P=0.026), but not with prognosis. However, CXCL12 expression was not significantly associated with the tumor infiltration depth, lymphatic metastasis and grading. As CXCL12 polymorphisms mediate tumor cell dissemination in esophagogastric cancer, they could represent a marker indicating advanced disease. Antagonists targeting the CXCL12/ CXCR4 axis may be a novel therapeutic option in this entity.
    Keywords: Medicine;
    ISSN: 1019-6439
    E-ISSN: 17912423
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  • 5
    Language: English
    In: World Journal of Surgery, 2011, Vol.35(5), pp.1010-1016
    Description: BACKGROUNDThe present study was designed to evaluate the impact of the tyrosine kinase ligands VEGF-A/C/D, PDGF-A/B on tumor dissemination and survival in gastric cancer. This is the first study analyzing all these parameters in a homogeneous patient population undergoing surgery. METHODSThe expression pattern of VEGF-A/C/D and PDGF-A/B was analyzed by reverse transcriptase polymerase chain reaction (RT-PCR) in 69 samples of human gastric adenocarcinoma and correlated with tumor stage and survival. RESULTSExpression of the ligand VEGF-D significantly correlated with distant metastatic disease (P=0.00001) but not with patient survival. However, VEGF-A inversely correlated with M1 and grading, PDGF-A inversely correlated with pT and pN category. In contrast, VEGF-C and PDGF-B did not have an impact on clinicopathological parameters. CONCLUSIONSThe ligand VEGF-D, rather than the other ligands or tyrosine kinase receptors analyzed, is associated with progressive disease in gastric cancer patients undergoing surgery. The VEGF-D ligand might be a helpful marker indicating disseminated disease, and targeting VEGF-D may be a potential therapeutic strategy, although limitations imposed by the selected sample population have to be considered critically.
    Keywords: Adenocarcinoma–Mortality ; Adult–Pathology ; Aged–Surgery ; Aged, 80 and Over–Metabolism ; Female–Mortality ; Humans–Pathology ; Immunohistochemistry–Surgery ; Male–Metabolism ; Middle Aged–Metabolism ; Neoplasm Metastasis–Metabolism ; Platelet-Derived Growth Factor–Metabolism ; Reverse Transcriptase Polymerase Chain Reaction–Metabolism ; Stomach Neoplasms–Metabolism ; Vascular Endothelial Growth Factor A–Metabolism ; Vascular Endothelial Growth Factor C–Metabolism ; Vascular Endothelial Growth Factor D–Metabolism ; Platelet-Derived Growth Factor ; Vascular Endothelial Growth Factor A ; Vascular Endothelial Growth Factor C ; Vascular Endothelial Growth Factor D;
    ISSN: 0364-2313
    E-ISSN: 1432-2323
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  • 6
    Language: English
    In: Methods in cell biology, 2019, Vol.152, pp.179-195
    Description: In situ cryo-electron tomography (cryo-ET) and subtomogram averaging are powerful tools, able to provide 3D structures of biological samples at sub-nanometer resolution, while preserving information about cellular context and higher-order assembly. Best results are typically achieved, when applied to highly repetitive structures, such as viruses. Other typical examples are protein complexes that decorate long stretches along ciliary microtubules at stereotypical and precise repeats, such as axonemal dyneins. For such cases, a plethora of subtomogram averaging protocols exist. In this chapter, we show how we use cryo-ET and subtomogram averaging to study the architecture of the intraflagellar transport (IFT) machinery, a more challenging target that appears only in low copy numbers per tomogram. In the IFT trains, repeating units of IFT adaptor proteins engage two oppositely directed molecular motors to quickly shuttle ciliary building blocks and other proteins to the tip of the cilium and/or back to the base. This dynamic and sporadic nature of IFT trains poses challenges for determining the localization or precise orientation of the particles to be averaged. Solutions to these problems are described in this chapter.
    Keywords: Cilia ; Cryo-Tomography ; Dynein ; Intraflagellar Transport ; Motors ; Subtomogram Averaging
    ISSN: 0091-679X
    Source: MEDLINE/PubMed (U.S. National Library of Medicine)
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  • 7
    Language: English
    In: 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019), April 2019, pp.502-506
    Description: Multiple approaches to use deep learning for image restoration have recently been proposed. Training such approaches requires well registered pairs of high and low quality images. While this is easily achievable for many imaging modalities, e.g. fluorescence light microscopy, for others it is not. Cryo-transmission electron microscopy (cryo-TEM) could profoundly benefit from improved denoising methods, unfortunately it is one of the latter. Here we show how recent advances in network training for image restoration tasks, i.e. denoising, can be applied to cryo-TEM data. We describe our proposed method and show how it can be applied to single cryo-TEM projections and whole cryo-tomographic image volumes. Our proposed restoration method dramatically increases contrast in cryo-TEM images, which improves the interpretability of the acquired data. Furthermore we show that automated downstream processing on restored image data, demonstrated on a dense segmentation task, leads to improved results.
    Keywords: Image Restoration ; Training ; Image Reconstruction ; Motion Pictures ; Electron Microscopy ; Tomography ; Image Restoration ; Cryo-Electron Microscopy ; Deep Learning ; Denoising
    E-ISSN: 1945-8452
    Source: IEEE Conference Publications
    Source: IEEE Xplore
    Source: IEEE Journals & Magazines 
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  • 8
    Language: English
    In: American Educational Research Journal, 2010, Vol.47(1), p.133
    Description: In both the United States and Europe, concerns have been raised about whether preservice and in-service training succeeds in equipping teachers with the professional knowledge they need to deliver consistently high-quality instruction. This article investigates the significance of teachers' content knowledge and pedagogical content knowledge for high-quality instruction and student progress in secondary-level mathematics. It reports findings from a 1-year study conducted in Germany with a representative sample of Grade 10 classes and their mathematics teachers. Teachers' pedagogical content knowledge was theoretically and empirically distinguishable from their content knowledge. Multilevel structural equation models revealed a substantial positive effect of pedagogical content knowledge on students' learning gains that was mediated by the provision of cognitive activation and individual learning support. (Contains 7 tables, 3 figures and 3 notes.)
    Keywords: Mathematics Education ; Structural Equation Models ; Foreign Countries ; Mathematics Teachers ; Grade 10 ; Pedagogical Content Knowledge ; Teacher Effectiveness ; Instructional Effectiveness ; Knowledge Base for Teaching ; Achievement Gains ; Cognitive Ability ; Teacher Competency Testing ; Academic Achievement ; Teacher Education ; Germany ; Education
    ISSN: 0002-8312
    E-ISSN: 1935-1011
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  • 9
    Language: English
    In: American Educational Research Journal, March 2010, Vol.47(1), pp.133-180
    Description: In both the United States and Europe, concerns have been raised about whether preservice and in-service training succeeds in equipping teachers with the professional knowledge they need to deliver consistently high-quality instruction. This article investigates the significance of teachers’ content knowledge and pedagogical content knowledge for high-quality instruction and student progress in secondary-level mathematics. It reports findings from a 1-year study conducted in Germany with a representative sample of Grade 10 classes and their mathematics teachers. Teachers’ pedagogical content knowledge was theoretically and empirically distinguishable from their content knowledge. Multilevel structural equation models revealed a substantial positive effect of pedagogical content knowledge on students’ learning gains that was mediated by the provision of cognitive activation and individual learning support.
    Keywords: Teacher Knowledge ; Teacher Education ; Mathematics ; Instruction ; Cognitive Activation ; Hierarchical Modeling With Latent Variables ; Education
    ISSN: 0002-8312
    E-ISSN: 1935-1011
    Source: Sage Journals (Sage Publications)
    Source: SAGE HSS (Sage Publications)
    Source: SAGE Education (Sage Publications)
    Source: SAGE Journals (Sage Publications)
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  • 10
    Language: English
    In: American Educational Research Journal, Annual, 2010, Vol.47(1), p.133
    Description: In both the United States and Europe, concerns have been raised about whether preservice and in-service training succeeds in equipping teachers with the professional knowledge they need to deliver consistently high-quality instruction. This article investigates the significance of teachers' content knowledge and pedagogical content knowledge for high-quality instruction and student progress in secondary-level mathematics. It reports findings from a 1-year study conducted in Germany with a representative sample of Grade 10 classes and their mathematics teachers. Teachers' pedagogical content knowledge was theoretically and empirically distinguishable from their content knowledge. Multilevel structural equation models revealed a substantial positive effect of pedagogical content knowledge on students' learning gains that was mediated by the provision of cognitive activation and individual learning support. (Contains 7 tables, 3 figures and 3 notes.)
    Keywords: Teacher Evaluation -- Research ; Teaching Methods -- Quality Management
    ISSN: 0002-8312
    E-ISSN: 19351011
    Source: Cengage Learning, Inc.
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