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Computational analyses of mechanism of action (MoA): data, methods and integration

Maria-Anna Trapotsi, Layla Hosseini-Gerami, Andreas Bender
2022 RSC Chemical Biology  
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

EMBnet Journal
2012 EMBnet journal  
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]

Elisangela Bressan, Xylena Reed, Vikas Bansal, Elizabeth Hutchins, Melanie M. Cobb, Michelle G. Webb, Eric Alsop, Francis P. Grenn, Anastasia Illarionova, Natalia Savytska, Ivo Violich, Stefanie Broeer (+28 others)
2021 bioRxiv   pre-print
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  
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  
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]

CNR DTA-Dipartimento Terra E Ambiente
2020 Figshare  
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  
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  
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

Reza Mirnezami, Ara Darzi, Jeremy Nicholson, Robert Goldin, National Institute For Health Research (Great Britain)
2015
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  
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

Phorutai Pearngam
2022
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

Ksenia Katsanovskaja, David Klug, Keith Willison
2021
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

Claire Boulange, Marc Dumas, Nestlé
2015
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

Jonas Zaugg
2021
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

Tamara Alireza, David Dexter
2018
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