Department of Biomedicine: Nye registreringer
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Machine learning applications in proteomics research: How the past can boost the future
(Peer reviewed; Journal article, 2014)Machine learning is a subdiscipline within artificial intelligence that focuses on algorithms that allow computers to learn solving a (complex) problem from existing data. This ability can be used to generate a solution ... -
Discovery and initial verification of differentially abundant proteins between multiple sclerosis patients and controls using iTRAQ and SID-SRM
(Peer reviewed; Journal article, 2013-01)In the present study, we aimed to discover cerebrospinal fluid (CSF) proteins with significant abundance difference between early multiple sclerosis patients and controls, and do an initial verification of these proteins ... -
Viewing the proteome: How to visualize proteomics data?
(Peer reviewed; Journal article, 2015-04)Proteomics has become one of the main approaches for analyzing and understanding biological systems. Yet similar to other high-throughput analysis methods, the presentation of the large amounts of obtained data in easily ... -
Shedding light on black boxes in protein identification
(Peer reviewed; Journal article, 2014-05)Performing a well thought-out proteomics data analysis can be a daunting task, especially for newcomers to the field. Even researchers experienced in the proteomics field can find it challenging to follow existing publication ... -
Post-translational modifications of Annexin A2 are linked to its association with perinuclear nonpolysomal mRNP complexes
(Peer reviewed; Journal article, 2017-02)Various post-translational modifications (PTMs) regulate the localisation and function of the multifunctional protein Annexin A2 (AnxA2). In addition to its various tasks as a cytoskeletal- and membrane-associated protein, ... -
NK cells with KIR2DS2 immunogenotype have a functional activation advantage to efficiently kill glioblastoma and prolong animal survival
(Peer reviewed; Journal article, 2014-12)Glioblastomas (GBMs) are lethal brain cancers that are resistant to current therapies. We investigated the cytotoxicity of human allogeneic NK cells against patient-derived GBM in vitro and in vivo, as well as mechanisms ... -
Combining NK cells and mAb9.2.27 to combat NG2-dependent and anti-inflammatory signals in glioblastoma
(Peer reviewed; Journal article, 2014)Glioblastoma is a deadly brain cancer with limited treatment options. Targeting chondroitin sulfate proteoglycan 4 (CSPG4, best known as NG2) with the monoclonal antibody mAb9.2.27 and activated natural killer (NK) cells ... -
Insulin and GSK3β-inhibition abrogates the infarct sparing-effect of ischemic postconditioning in ex vivo rat hearts
(Peer reviewed; Journal article, 2017)Objectives. Pharmacological treatment of reperfusion injury using insulin and GSK3β inhibition has been shown to be cardioprotective, however, their interaction with the endogenous cardioprotective strategy, ischemic ... -
Therapeutic potential and challenges of natural killer cells in treatment of solid tumors
(Peer reviewed; Journal article, 2015-04-29)Natural killer (NK) cells are innate lymphoid cells that hold tremendous potential for effective immunotherapy for a broad range of cancers. Due to the mode of NK cell killing, requiring one-to-one target engagement and ... -
In-depth characterization of the cerebrospinal fluid (CSF) proteome displayed through the CSF proteome resource (CSF-PR)
(Peer reviewed; Journal article, 2014-11)In this study, the human cerebrospinal fluid (CSF) proteome was mapped using three different strategies prior to Orbitrap LC-MS/MS analysis: SDS-PAGE and mixed mode reversed phase-anion exchange for mapping the global CSF ... -
DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra
(Peer reviewed; Journal article, 2014)De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence database. Despite the strong potential of de novo sequencing algorithms, ... -
thermo-msf-parser: An Open Source Java Library to Parse and Visualize Thermo Proteome Discoverer msf Files
(Peer reviewed; Journal article, 2011)The Thermo Proteome Discoverer program integrates both peptide identification and quantification into a single workflow for peptide-centric proteomics. Furthermore, its close integration with Thermo mass spectrometers has ... -
The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium
(Peer reviewed; Journal article, 2012-12)The original PRIDE Converter tool greatly simplified the process of submitting mass spectrometry (MS)-based proteomics data to the PRIDE database. However, after much user feedback, it was noted that the tool had some ... -
High-salt diet causes osmotic gradients and hyperosmolality in skin without affecting interstitial fluid and lymph
(Peer reviewed; Journal article, 2017-04)The common notion is that the body Na+ is maintained within narrow limits for fluid and blood pressure homeostasis. Several studies have, however, shown that considerable amounts of Na+ can be retained or removed from the ... -
Induction of mitochondrial biogenesis and respiration is associated with mTOR regulation in hepatocytes of rats treated with the pan-PPAR activator tetradecylthioacetic acid (TTA)
(Peer reviewed; Journal article, 2013-01)The hypolipidemic effect of peroxisome proliferator-activated receptor (PPAR) activators has been explained by increasing mitochondrial fatty acid oxidation, as observed in livers of rats treated with the pan-PPAR activator ... -
Regulation and quantification of cellular mitochondrial morphology and content
(Peer reviewed; Journal article, 2014)Mitochondria play a key role in signal transduction, redox homeostasis and cell survival, which extends far beyond their classical functioning in ATP production and energy metabolism. In living cells, mitochondrial content ... -
Use of stable isotope dimethyl labeling coupled to selected reaction monitoring to enhance throughput by multiplexing relative quantitation of targeted proteins
(Peer reviewed; Journal article, 2012)In this manuscript, we present a proof-of-concept study for targeted relative protein quantitation workflow using chemical labeling in the form of dimethylation, coupled with selected reaction monitoring (dimethyl-SRM). ... -
Dwarfism in mice lacking collagen-binding integrins alpha 2 beta 1 and alpha 11 beta 1 is caused by severely diminished IGF-1 levels
(Peer reviewed; Journal article, 2012-02)Mice with a combined deficiency in the α2β1 and α11β1 integrins lack the major receptors for collagen I. These mutants are born with inconspicuous differences in size but develop dwarfism within the first 4 weeks of life. ... -
TNT-Induced Phagocytosis: Tunneling Nanotubes Mediate the Transfer of Pro-Phagocytic Signals From Apoptotic to Viable Cells
(Peer reviewed; Journal article, 2017-09)The exposure of phosphatidylserine (PS) on the surface membrane of apoptotic cells triggers the recruitment of phagocytic receptors and subsequently results in uptake by phagocytes. Here we describe how apoptotic cells can ... -
Adult ADHD and Comorbid Somatic Disease: A Systematic Literature Review
(Peer reviewed; Journal article, 2016)Objective: To systematically review, synthesize, and appraise available evidence, connecting adult ADHD (aADHD) with somatic disease. Method: Embase, Psychinfo, and Medline databases were searched for studies published ...