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  • 1
    Keywords: Proteomics ; Biochemistry ; Proteomics ; Protein Science ; Springer eBooks
    Description / Table of Contents: Pre- and Post-Analytical Factors in Biomarker Discovery -- Pre-Fractionation of Non-Circulating Biological Fluids to Improve Discovery of Clinically Relevant Protein Biomarkers -- Serum Exosome Isolation by Size-Exclusion Chromatography for the Discovery and Validation of Preeclampsia-Associated Biomarkers -- Protein Biomarker Discovery Using Human Blood Plasma Microparticles -- A Standardized and Reproducible Proteomics Protocol for Bottom-Up Quantitative Analysis of Protein Samples Using SP3 and Mass Spectrometry -- Analyzing Cerebrospinal Fluid Proteomes to Characterize Central Nervous System Disorders: A Highly Automated Mass Spectrometry-Based Pipeline for Biomarker Discovery -- Lys-C/Trypsin Tandem-Digestion Protocol for Gel-Free Proteomic Analysis of Colon Biopsies -- Tube-Gel: A Fast and Effective Sample Preparation Method for High-Throughput Quantitative Proteomics -- Protein Biomarker Discovery in Non-Depleted Serum by Spectral Library-Based Data-Independent Acquisition Mass Spectrometry -- Discovering Protein Biomarkers from Clinical Peripheral Blood Mononuclear Cells Using Data-Independent Acquisition Mass Spectrometry -- Intact Protein Analysis by LC-MS for Characterizing Biomarkers in Cerebrospinal Fluid -- Detection of Proteoforms Using Top-Down Mass Spectrometry and Diagnostic Ions -- Development of a Highly Multiplexed SRM Assay for Biomarker Discovery in Formalin-Fixed Paraffin-Embedded Tissues -- Development and Validation of Multiple Reaction Monitoring (MRM) Assays for Clinical Applications -- Protein-Level Statistical Analysis of Quantitative Label-Free Proteomics Data with ProStaR -- Computation and Selection of Optimal Biomarker Combinations by Integrative ROC Analysis using CombiROC -- PanelomiX for the Combination of Biomarkers -- Designing an In Silico Strategy to Select Tissue-Leakage Biomarkers Using the Galaxy Framework
    Abstract: This volume presents modern and enhanced methods that detail techniques to perform proteomics analyses dedicated to biomarker discovery for human health. Chapters guide readers through pre/post analytical factors, protocols for the preparation of extracellular vesicles and exosomes, and various analytical pipelines including Data Independent Acquisition (DIA), discovery, as well as targeted and top-down proteomics analysis workflows. Bioinformatics tools and workflows to select and evaluate candidate biomarkers or combinations of biomarkers are also presented. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Proteomics for Biomarker Discovery: Methods and Protocols aims to ensure successful results in the further study of this vital field
    Pages: XII, 292 p. 52 illus., 47 illus. in color. : online resource.
    ISBN: 9781493991648
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  • 2
    Call number: QZ365WP870:431
    Keywords: Biopsy / methods ; Breast Diseases / pathology ; Breast Neoplasms / pathology
    Pages: xii, 225 p. : ill. (some col.)
    ISBN: 9783540314035
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    QZ365WP870:431 available
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  • 3
    Keywords: Medicine ; Immunology ; Biomedicine ; Immunology ; Springer eBooks
    Description / Table of Contents: Vaccines and Vaccination for Veterinary Viral Diseases: A General Overview -- Using℗ IC-Tagging Methodology for Production and Purification of Epitope-Loaded Protein Microspheres for Vaccination -- Plant-Based Vaccine Antigen Production -- DNA Vaccines: Experiences in the Swine Model -- Novel Adjuvants and Immunomodulators for Veterinary Vaccines -- Polymerase Mechanism-Based Method of Viral Attenuation -- BacMam Platform for Vaccine Antigen Delivery -- Laboratory-Scale Production of Replication-Deficient Adenovirus Vectored Vaccines -- Generation of Recombinant Modified Vaccinia Virus Ankara Encoding VP2, NS1, and VP7 Proteins of Bluetongue Virus -- Generation of Recombinant Capripoxvirus Vectors for Vaccines and Gene Knockout Function Studies -- Recombinant Swinepox Virus for Veterinary Vaccine Development -- Generation and Selection of Orf Virus (ORFV) Recombinants -- Polycistronic Herpesvirus Amplicon Vectors for Veterinary Vaccine Development -- Construction and Application of Newcastle Disease Virus-Based Vector Vaccines -- Chimeric Pestivirus Experimental Vaccines -- Analysis of the Cellular Immune Responses to Vaccines
    Abstract: This detailed volume explores the most popular antigen production and delivery strategies that have been tested in veterinary species. Viral vectors as well as genetic and protein subunit vaccines or large scale protein production systems are considered as well as an updated view of most options available for vaccine development, including the data obtained through experimental trials which contributes to the exploration and understanding of the immune mechanisms and immune correlates relevant in protection among different animal species. Written for the highly successful Methods in Molecular Biology series, chapters include brief introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. ℗ Authoritative and practical, Vaccine Technologies for Veterinary Viral Diseases: Methods and Protocols facilitates access to well-established protocols to those beginning in this interesting and laborious field as well as providing important basic knowledge when attempting a novel vaccine design or platform
    Pages: XI, 265 p. 40 illus., 25 illus. in color. : online resource.
    Edition: 1st ed. 2016.
    ISBN: 9781493930081
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  • 4
    ISSN: 1420-9071
    Keywords: Mesoderm induction ; Xenopus ; activin ; axes formation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Animal caps fromXenopus embryos at Stage 7/8 cultured in salt solution, were capable of elongating, and formed various embryonic tissues including axial mesoderm, nervous tissues and pigmented retina. In contrast, animal caps from Stage 9 only developed into permanent blastulae. Following exposure to PIF/activin, however, such animal caps displayed morphogenetic movements. They formed tube-shaped embryoids that frequently had one or more tails but no head. We conclude that animal caps from Stage 9 produce more reliable results than those from Stage 7/8 because the latter are most likely contaminated with mesodermal cells.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Amsterdam : Elsevier
    Computer Physics Communications 57 (1989), S. 235-238 
    ISSN: 0010-4655
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Computer Science , Physics
    Type of Medium: Electronic Resource
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  • 6
    Keywords: CANCER ; CELLS ; IN-VITRO ; AGENTS ; CELL ; Germany ; INHIBITION ; VITRO ; DNA ; MECHANISM ; DOMAIN ; BINDING ; ASSAY ; GLUTATHIONE-REDUCTASE ; CELL-LINE ; LINE ; CANCER-CELLS ; MAMMALIAN-CELLS ; DOMAINS ; CYTOTOXICITY ; CHEMISTRY ; DRUGS ; chloroquine ; GLIOBLASTOMA ; STRAIN ; AMODIAQUINE ; DEOXYRIBONUCLEIC ACID ; EFFLUX SYSTEM ; MALARIA PARASITES ; RESISTANT PLASMODIUM-FALCIPARUM
    Abstract: The synthesis and biological evaluation of new organic and organometallic dual drugs designed as potential antimalarial agents are reported. A series of 4-aminoquinoline-based Mannich bases with variations in the aliphatic amino side chain were prepared via a three-steps synthesis. These compounds were also tested against chloroquine-susceptible and chloroquine-resistant strains of Plasmodium falciparum and assayed for their ability to inhibit the formation of beta-hematin in vitro using a colorimetric beta-hematin inhibition assay. Several compounds showed a marked antimalarial activity, with IC50 and IC90 values in the low nM range but also a high cytotoxicity against mammalian cells, in particular a highly drug-resistant glioblastoma cell line. The newly designed compounds revealed high DNA binding properties, especially for the GC-rich domains. Altogether, these dual drugs seem to be more appropriate to be developed as antiproliferative agents against mammalian cancer cells than Plasmodium parasites
    Type of Publication: Journal article published
    PubMed ID: 20329733
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  • 7
    Keywords: VISUALIZATION ; MRI ; TRACT ; BRAIN-TUMOR SURGERY
    Abstract: BACKGROUND AND PURPOSE: Diffusion tensor imaging (DTI) tractography reconstruction of white matter pathways can help guide brain tumor resection. However, DTI tracts are complex mathematical objects and the validity of tractography-derived information in clinical settings has yet to be fully established. To address this issue, we initiated the DTI Challenge, an international working group of clinicians and scientists whose goal was to provide standardized evaluation of tractography methods for neurosurgery. The purpose of this empirical study was to evaluate different tractography techniques in the first DTI Challenge workshop. METHODS: Eight international teams from leading institutions reconstructed the pyramidal tract in four neurosurgical cases presenting with a glioma near the motor cortex. Tractography methods included deterministic, probabilistic, filtered, and global approaches. Standardized evaluation of the tracts consisted in the qualitative review of the pyramidal pathways by a panel of neurosurgeons and DTI experts and the quantitative evaluation of the degree of agreement among methods. RESULTS: The evaluation of tractography reconstructions showed a great interalgorithm variability. Although most methods found projections of the pyramidal tract from the medial portion of the motor strip, only a few algorithms could trace the lateral projections from the hand, face, and tongue area. In addition, the structure of disagreement among methods was similar across hemispheres despite the anatomical distortions caused by pathological tissues. CONCLUSIONS: The DTI Challenge provides a benchmark for the standardized evaluation of tractography methods on neurosurgical data. This study suggests that there are still limitations to the clinical use of tractography for neurosurgical decision making.
    Type of Publication: Journal article published
    PubMed ID: 26259925
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  • 8
    Keywords: CELLS ; Germany ; IN-VIVO ; SITE ; DNA ; DOMAIN ; STABILITY ; NUCLEOSOME CORE PARTICLE ; RE ; higher-order structure ; HELA-CELLS ; NUCLEOSOME ; analytical ultracentrifugation ; LEVEL ; HISTONE ACETYLATION ; LINKER DNA ; H1 ; NEUTRON-SCATTERING ; RECONSTITUTION ; TAILS
    Abstract: Using a previously described FRET technique, we measured the distance between the ends of DNA fragments on which nucleosomes were reconstituted from recombinant and native histories. This distance was analyzed in its dependence on the DNA fragment length, concentration of mono- and divalent counterions, presence of linker historic H1, and historic modifications. We found that the linker DNA arms do not cross under all conditions studied but diverge slightly as they leave the histone core surface. Historic H I leads to a global approach of the linker DNA arms, confirming the notion of a "stem structure". Increasing salt concentration also leads to an approach of the linker DNAs. To study the effect of acetylation, we compared chemically acetylated recombinant histories with histories prepared from HeLa cells, characterizing the sites of acetylation by mass spectroscopy. Nucleosomes from chemically acetylated histories have few modifications in the core domain and form nucleosomes normally. Acetylating all histories or selectively only H3 causes an opening of the nucleosome structure, indicated by the larger distances between the linker DNA ends. Selective acetylation of H4 distances the linker ends for short fragments but causes them to approach each other for fragments longer than 180 bp
    Type of Publication: Journal article published
    PubMed ID: 16460006
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  • 9
    Keywords: EXPRESSION ; GENE ; DIFFERENTIATION ; IDENTIFICATION ; EMBRYONIC STEM-CELLS ; HYPERMETHYLATION ; SUPPRESSOR ; methylome ; CANCER GENOME ; CPG ISLAND SHORES
    Abstract: Epigenetic alterations, that is, disruption of DNA methylation and chromatin architecture, are now acknowledged as a universal feature of tumorigenesis. Medulloblastoma, a clinically challenging, malignant childhood brain tumour, is no exception. Despite much progress from recent genomics studies, with recurrent changes identified in each of the four distinct tumour subgroups (WNT-pathway-activated, SHH-pathway-activated, and the less-well-characterized Group 3 and Group 4), many cases still lack an obvious genetic driver. Here we present whole-genome bisulphite-sequencing data from thirty-four human and five murine tumours plus eight human and three murine normal controls, augmented with matched whole-genome, RNA and chromatin immunoprecipitation sequencing data. This comprehensive data set allowed us to decipher several features underlying the interplay between the genome, epigenome and transcriptome, and its effects on medulloblastoma pathophysiology. Most notable were highly prevalent regions of hypomethylation correlating with increased gene expression, extending tens of kilobases downstream of transcription start sites. Focal regions of low methylation linked to transcription-factor-binding sites shed light on differential transcriptional networks between subgroups, whereas increased methylation due to re-normalization of repressed chromatin in DNA methylation valleys was positively correlated with gene expression. Large, partially methylated domains affecting up to one-third of the genome showed increased mutation rates and gene silencing in a subgroup-specific fashion. Epigenetic alterations also affected novel medulloblastoma candidate genes (for example, LIN28B), resulting in alternative promoter usage and/or differential messenger RNA/microRNA expression. Analysis of mouse medulloblastoma and precursor-cell methylation demonstrated a somatic origin for many alterations. Our data provide insights into the epigenetic regulation of transcription and genome organization in medulloblastoma pathogenesis, which are probably also of importance in a wider developmental and disease context.
    Type of Publication: Journal article published
    PubMed ID: 24847876
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  • 10
    ISSN: 0167-2738
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Physics
    Type of Medium: Electronic Resource
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