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Computational analyses of mechanism of action (MoA): data, methods and integration
2022
RSC Chemical Biology
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This review summarises different data, data resources and methods for computational mechanism of action (MoA) analysis, and highlights some case studies where integration of data types and methods enabled ...
as mass spectrometry-based targeted proteomics (LINCS P100)''. ...
each object and image. ...
doi:10.1039/d1cb00069a
pmid:35360890
pmcid:PMC8827085
fatcat:yqd77fs7nfdwdlbh437h23s2qm
EMBnet.journal 18 Suppl. A
2012
EMBnet journal
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Protein Structure and Function Acknowledgments This work was supported by NFSR of Bulgaria project DVU 01/197. ...
Availability http://www.bioblender.net/
Motivations Mass spectrometry (MS), one of the most recent high-throughput technologies, produces a high volume of data. ...
Calogero Molecular Biotechnology Center, University of Torino, Torino, Italy
Regularized network-based algorithm for predicting gene functions with high-imbalanced data M. Frasca , A. Bertoni, G. ...
doi:10.14806/ej.18.a.497
fatcat:2aexioifkfgfnipbo3btxqwvia
The Foundational data initiative for Parkinsons disease (FOUNDIN-PD): enabling efficient translation from genetic maps to mechanism
[article]
2021
bioRxiv
pre-print
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In the FOUNdational Data INitiative for Parkinsons Disease (FOUNDIN-PD) we sought to produce a multi-layered molecular dataset in a large cohort of 95 Induced pluripotent stem cells (iPSC) lines at multiple ...
a resource for understanding the molecular pathogenesis of PD. ...
Quantitative tandem mass tag proteomics preparation, mass spectrometry and dataprocessing Proteomics data were generated only for batch 1 (n=10) lines. ...
doi:10.1101/2021.06.03.446785
fatcat:7bqlqq6ml5anhnfv4sxw3fjcoy
Abstracts of the 87th Annual Meeting of the German Society for Experimental and Clinical Pharmacology and Toxicology (DGPT) with contribution of the Arbeitsgemeinschaft für Angewandte Humanpharmakologie e. V. (AGAH)
2021
Naunyn-Schmiedeberg's Archives of Pharmacology
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isotope dilution liquid chromatography tandem mass spectrometry. ...
A previous report has highlighted the use of plasma metabolomics, by gas-and liquid-chromatography-tandem mass spectrometry techniques, for an improved and mechanism-based identification of maternal toxicity ...
Two transitions per substance were used in multiple reaction monitor (MRM) mode of the tandem mass spectrometer. The supernatants of cell pellets of 106 cells were examined to quantify the dNTPs. ...
doi:10.1007/s00210-021-02066-6
pmid:33646325
fatcat:xm24ysqqcnevbdr3pdpaty5aje
New Developments in Science and Technology - 60th Anniversary Special Issue, Beihang University (BUAA)
2012
Science
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provides cutting-edge research and education in advanced structural and functional materials, nanomaterials, new materials for clean energy, polymers and composites, nonequilibrium fabrication, corrosion ...
We proposed a novel algorithm called COG (classification using local clustering) for rare class analysis (10) . ...
false positives (annotated by red rectangles). data sets with highly imbalanced classes, we further integrated the oversampling technique into COG, and proposed the COG-OS (COG with over-sampling) algorithm ...
doi:10.1126/science.338.6104.274-c
fatcat:iurk5neuwvh2jgbohwevb5dicy
DTA/29-2019 The Arctic as seen from Ny-Ålesund: research results, new proposals and overviews - Rome 18th and 19th March 2019
[article]
2020
Figshare
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ABSTRACTSThe workshop aims to highlight the state of the art of italian research activities at the CNR Arctic Station Dirigibile Italia Ny-Ålesund – Svalbard and to define common strategies to strengthen ...
Lastly, the relevant amount of data produced for the present research can serve as a useful reference for other research programs, as well as a baseline for medium-and longterm monitoring of environmental ...
The aim of the study was to collect behavioural and physiological data on biological rhythms of high arctic invertebrate Lepidurus arcticus (Branchiopoda, Nostostraca) to provide bases for further genetic ...
doi:10.6084/m9.figshare.11637738
fatcat:iayhyk454nat7jcbujhwz4i3mi
ETA Abstracts
[chapter]
2011
35th Annual Meeting of the European Thyroid Association
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OP06 Aims: A novel bioassay was developed for the detection of thyroidstimulating immunoglobulins (TSI) based on a CHO cell line (CHO-MC4) expressing a chimeric TSH-receptor (TSHR). ...
Objectives: To validate the use of the classical in vitro models of thyroid tumors for the analysis of microRNAs. ...
Aim of the study was to assess the frequency of thyroid dysfunction in previously healthy adult population of Krakow. ...
doi:10.1159/000330565
fatcat:5qvmofknovblvcpzxr7jqog2ku
Supplementum 222: Joint annual meeting Swiss Society of Paediatrics and the Swiss Society for Allergology and Immunology, jointly organized with the 4th Lymphoid Tissue Meeting "Focus on Stromal Cells"
2017
Swiss Medical Weekly
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Specifically, FRC-derived IL-6 creates a supportive niche for activated T cells by enhancing their expression of IL-2 and TNF-alpha. ...
Human LNSCs cultured directly from freshly collected lymph node biopsies expressed TLR1-9 with exception of TLR7 and the strongest expression was observed for TLR3. ...
Meanwhile, the second method is based on in-tube immunomagnetic separation (IMS) with mass spectrometry identification (MALDI MS or peptide mass fingerprinting). ...
doi:10.4414/smw.2017.20424
pmid:33379860
fatcat:bpqm632nhffkjhzwtlemyopusa
Translational application of metabolic profiling technologies in the colorectal cancer clinical pathway
2015
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For this body of work I have designed and implemented a multi-axis metabolic profiling strategy for evaluation of fresh frozen CRC tissue; the study framework has been specifically designed to assess the ...
(iii) Desorption electrospray ionisation imaging MS (DESI-MSI) represents a more sophisticated method for histology-driven imaging mass spectrometry and permits 'chemical mapping' of the CRC tumour microenvironment ...
another in a sample suspended within a magnetic
Mass spectrometry
Basic principles of mass spectrometry (MS) Mass spectrometry (MS) encompasses a broad class of bio-analytical approaches that have ...
doi:10.25560/23997
fatcat:djins7yacrag7cyle3xjs3a6dq
ACNP 59th Annual Meeting: Poster Session III
2020
Neuropsychopharmacology
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As such, we assessed the relationship between CRP, PTSD and white matter structural integrity within two samples: a highly-traumatized population with chronic PTSD (Grady Trauma Project, GTP) and a population ...
Another exciting feature of the program that will be highlighted in this presentation will be assessment of abuse liability in the context of efficacy in pain endpoints. ...
PPL was determined from the blood samples using ultra-performance liquid chromatography and tandem mass spectrometry. ...
doi:10.1038/s41386-020-00892-5
pmid:33279936
pmcid:PMC7735201
fatcat:mip4ywutfnfwvmye4u65i6vgg4
Improvement of selection criteria and prioritisation for neoantigen prediction
2022
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MHCVision was built based on mathematical models including the beta distribution model and vi the EM algorithm. The script of this model was implemented using Python, as a command line application. ...
The classification model was trained from a set of features including physicochemical properties of amino acids in immunogenic and non-immunogenic peptides and a similarity between T cell epitopes and ...
(multi-allelic) mass spectrometry. ...
doi:10.17638/03150867
fatcat:ks2hu2x5wrawdfqdowxywgfkdy
Microfluidic methods for single cell analysis in clinically relevant samples
2021
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This thesis reports on attempts to obtain, concentrate and analyse CTCs from blood using a composite MAC-based device. ...
The ability to obtain and effectively analyse precious and scarce biomaterial from lungs, is greatly advantageous for both diagnosis and tracking of COPD. ...
flow cytometry and mass spectrometry (MS). ...
doi:10.25560/90491
fatcat:5rwpdngbobgqzicz4r4374eyau
Metabonomic investigations of the mammalian host-gut microbiome interactions in obesity and metabolic diseases
2015
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magnetic spectroscopy and mass spectrometry analysis were employed to measure the abundant metabolites in C57BL/6 mouse urine, feces, and plasma. ...
Genetic and environmental factors, (high calorie diet, lack of physical activity) strongly influence the onset of obesity and metabolic diseases. ...
mass spectrometry method. ...
doi:10.25560/24727
fatcat:tzkmx2fpcvg2pgnbqsus4ntozy
SLC transporter-mediated transfer of iron and amino acids across the placenta
2021
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Functional effects of a physiological gradient versus equimolar leucine concentrations were tested using in vitro uptake and Transwell®-based transfer assays. ...
A successful pregnancy and the birth of a healthy baby depends to a great extent on the controlled supply of essential nutrients via the placenta. ...
by tandem mass spectrometry. ...
doi:10.48549/307
fatcat:faucr26hxjglzol5bjhy23g5qa
Investigating the effects of the microglial inflammatory response on iron metabolism in dopaminergic neurons
2018
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Current research identifies iron accretion as a potential pathogenic factor. Iron is crucial for healthy cellular physiology, however, dysregulation can be highly neurotoxic. ...
Parkinson's disease (PD) is a chronic progressive neurodegenerative disorder characterised by selective loss of dopaminergic neurons in the substantia nigra. ...
by mass spectrometry at King's College London for hepcidin presence. ...
doi:10.25560/60641
fatcat:xnmx3pukqvfv7nyedsnktskyme