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SPUTNIK: an R package for filtering of spatially related peaks in mass spectrometry imaging data

Paolo Inglese, Gonçalo Correia, Zoltan Takats, Jeremy K Nicholson, Robert C Glen, Robert Murphy
2018 Bioinformatics  
Split peaks estimation algorithm Split peaks estimation algorithm searches for candidate split peaks in the provided vector of the m/z values associated with the matched spectral peaks of the dataset.  ...  Maximum distance in ppm to consider two peaks contiguous. This should be lower or equal to the expected instrumental error;  ...  On the contrary, the RGB image corresponding to the removed peaks corresponds to an unstructured image for both the filters (D, I).  ... 
doi:10.1093/bioinformatics/bty622 pmid:30010780 fatcat:whjz6lyzwncsrfujht4ex5fcji

Colocalization features for classification of tumors using desorption electrospray ionization mass spectrometry imaging [article]

Paolo Inglese, Goncalo dos Santos Correia, Pamela Pruski, Robert C Glen, Zoltan Takats
2018 biorxiv/medrxiv   pre-print
Supervised modeling of mass spectrometry imaging (MSI) data is a crucial component for the detection of the distinct molecular characteristics of cancerous tissues.  ...  contained in the MSI data.  ...  Nicole Strittmatter for sharing the datasets used in their publications.  ... 
doi:10.1101/440057 fatcat:a4jrwoavvneidcerje5drl4oju

Colocalization features for classification of tumors using desorption electrospray ionization mass spectrometry imaging

Paolo Inglese, Gonçalo Correia, Pamela Pruski, Robert C Glen, Zoltan Takats
2019 Analytical Chemistry  
Supervised modeling of mass spectrometry imaging (MSI) data is a crucial component for the detection of the distinct molecular characteristics of cancerous tissues.  ...  contained in the MSI data.  ...  Tissue-unrelated peaks were filtered using the global reference and pixel count filters of the SPUTNIK package for R. 43 The parameters used are reported in the Supporting Information, Table S3 .  ... 
doi:10.1021/acs.analchem.8b05598 pmid:31013058 pmcid:PMC6533599 fatcat:wzfueyhftjerdc7i3wfjc26bx4

Mass recalibration for desorption electrospray ionization mass spectrometry imaging using endogenous reference ions

Paolo Inglese, Helen Xuexia Huang, Vincen Wu, Matthew R. Lewis, Zoltan Takats
2022 BMC Bioinformatics  
Background Mass spectrometry imaging (MSI) data often consist of tens of thousands of mass spectra collected from a sample surface.  ...  The procedure, tested on time-of-flight and Orbitrap mass spectrometry analyzers interfaced to a desorption electrospray ionization (DESI) source, improves the molecular annotation quality and the spatial  ...  Friis, Kyana Garza, Emrys Jones, James McKenzie, Nicole Strittmatter, Jialing Zhang, for sharing their datasets on METASPACE.  ... 
doi:10.1186/s12859-022-04671-5 pmid:35428194 pmcid:PMC9013061 fatcat:4ma6pjtyzrdljhh6aw6i2nvh5e

Mass recalibration for desorption electrospray ionization mass spectrometry imaging using endogenous reference ions [article]

Paolo Inglese, Helen Huang, Vincen Wu, Mathew R Lewis, Zoltan Takats
2021 bioRxiv   pre-print
Mass spectrometry imaging (MSI) data often consist of tens of thousands of mass spectra collected from a sample surface.  ...  During the time necessary to perform a single acquisition, it is likely that uncontrollable factors alter the validity of the initial mass calibration of the instrument, resulting in mass errors of magnitude  ...  James McKenzie for providing the public Orbitrap datasets on METASPACE. PI is supported by the NIHR Imperial Biomedical Research Centre (BRC). 9 References  ... 
doi:10.1101/2021.03.29.437482 fatcat:ahv2z3mx5fhwxnw4blgqib2rve

Multi-omics profiling of collagen-induced arthritis mouse model reveals early metabolic dysregulation via SIRT1 axis [article]

Lingzi Li, Janina Freitag, Christian Asbrand, Bogdan Munteanu, Bei-Tzu Wang, Ekaterina Zezina, Michel Didier, Gilbert Thill, Corinne Rocher, Matthias Herrmann, Nadine Biesemann
2022 bioRxiv   pre-print
We identified an early change in macrophage pathways which was accompanied by oxidative stress, a drop in NAD+ level and induction of glucose transporters.  ...  Therefore, we studied the longitudinal metabolic changes during the development of murine arthritis integrating metabolomics and bulk RNA-seq data.  ...  Acknowledgements We thank members of the  ... 
doi:10.1101/2022.03.09.483621 fatcat:a6qmkp5vlzfibicwvmwgh3rekm

Ion thrusters for electric propulsion: Scientific issues developing a niche technology into a game changer

K. Holste, P. Dietz, S. Scharmann, K. Keil, T. Henning, D. Zschätzsch, M. Reitemeyer, B. Nauschütt, F. Kiefer, F. Kunze, J. Zorn, C. Heiliger (+14 others)
2020 Review of Scientific Instruments  
This article describes how these changes related to new space affect various aspects that are important for the development of EP systems.  ...  In addition, aspects of thruster modeling and requirements for test facilities are discussed.  ...  The authors are also grateful for seed funding by the Research Campus of Central Hessen (RCCH) and for co-funding in frame of the funding scheme "Forschung für die Praxis 2018" of the Hessian Ministry  ... 
doi:10.1063/5.0010134 pmid:32611046 fatcat:cmqjccw5lnhklar7j4eduxgxwq

Planetary exploration - Earth's new horizon /12th von Karman Lecture/

H. M. SCHURMEIER
1975 Journal of Spacecraft and Rockets  
many images obtained in 1956 by R.  ...  Interest in the capability for high spatial and spectral resolution in these in- vestigations has led to the development of a considerable on- board sequencing, data-acquisition, and data-processing capability  ... 
doi:10.2514/3.27843 fatcat:2kz7hrwyb5f53ll35un2g5wzky

Active learning in optics and photonics: experiences in Africa

M. Alarcon, E. Arthurs, Z. Ben Lakhdar, I. Culaba, V. Lakshminarayanan, J. Maquiling, A. Mazzolini, J. Niemela, D. Sokoloff, François Flory
2005 Ninth International Topical Meeting on Education and Training in Optics and Photonics  
The student is under the conditions he can find in the real laboratory and can spend as long as he wishes, at any time.  ...  The teacher can track the student via a data base that includes the eventual missteps which the student would have committed.  ...  Xavier for compiling data for this paper. 238/416 Acknowledgement The Center for Biophotonics Science and Technology (CBST) is funded by the National Science Foundation and is managed by the University  ... 
doi:10.1117/12.2207699 fatcat:so5wxhilsvfbxafbjfvbiw64fu

46th ESAO Congress 3–7 September 2019 Hannover, Germany

2019 International Journal of Artificial Organs  
Finally, quantification of the uncertainties that are inherent to biomechanical modeling is an essential contribution to reliable patientspecific outcome prediction.  ...  Biomechanical modeling allows for patientspecific outcome prediction after surgical interventions and should become a routine practice in patient treatment.  ...  : IP@Leibniz Program of Leibniz University Hannover (DAAD project code 57156199) as well as Ways to Research Program of the Leibniz University Hannover (60442522).  ... 
doi:10.1177/0391398819860985 fatcat:s5xpxxvq2fhtdacxuf5iw6n3z4

The Trimeric Major Capsid Protein of Mavirus is stabilized by its Interlocked N-termini Enabling Core Flexibility for Capsid Assembly

Alexander Christiansen, Marie Weiel, Andreas Winkler, Alexander Schug, Jochen Reinstein
2021
Probing the dynamics of the capsomer with HDX mass spectrometry we observed differences in conformational flexibility between functional elements of the MCP trimer.  ...  Assessing the role of the N-terminal arm in maintaining capsomer stability showed that its detachment is required for capsomer dissociation, constituting a barrier towards capsomer monomerisation.  ...  Acknowledgments We thank Sabine Zimmermann, Susanne Eisel, and Ulrike Mersdorf for expert technical assistance, Diana Born for important insights and help with preparation of Figures 1 and 7 and Thomas  ... 
doi:10.5445/ir/1000130503 fatcat:fl55ip4lq5horcr7qfr5oio23i

The living universe: NASA and the development of astrobiology

2005 ChoiceReviews  
By the time the report was published in the summer of 1996, it included data for five possible planets around Sun-like stars and an HST image of a brown dwarf complete with a spectrum taken by the Keck  ...  CCD image of a disk around Beta Pictoris (1984) , early evidence for circumstellar material perhaps related to planet formation.  ...  Rummel resumed the position of planetary protection officer in 1997. Headquarters SETI Program Managers Dick Henry 1977 Henry -1978 Jeffrey D.  ... 
doi:10.5860/choice.42-4629 fatcat:36iiud3dufhifoqggbl6lr7e3m

Genetic and ultrastructural characterization of Cafeteria roenbergensis virus and its virophage Mavirus

Matthias Gunther Fischer
2011
Four genes contained an intein insertion and several genes have not been found before in viruses, including an isoleucyl-tRNA synthetase and a histone acetyltransferase.  ...  A 38 kilobase pair region of putative bacterial origin encoded predicted enzymes for the biosynthesis of 3-deoxy-D-manno-octulosonate, a key component of the bacterial lipopolysaccharide layer.  ...  Image data were recorded on an FEI Tecnai G2 20 TWIN transmission electron microscope at 80 kV for the 30-50 nm sections and 200 kV for the 200-300 nm sections.  ... 
doi:10.14288/1.0071637 fatcat:unaykgpwyfchnexyf5isooteri

Comets, Titan and Mars: Astrobiology and Space Projects [chapter]

Yves Bénilan, Hervé Cottin
Lectures in Astrobiology  
We also thank the editors of the book: Muriel Gargaud, Philippe Clays and Hervé Martin for their comments, encouragements and corrections. Hervé Martin did a wonderful job in processing the figures.  ...  Acknowledgements The authors wish to thank Antoine Jolly for a careful proofreading of the manuscript; his many comments and suggestions were a great help to improve the text.  ...  Table 13 .4 shows all the molecules detected with mass spectrometry in Halley's vicinity.  ... 
doi:10.1007/978-3-540-33693-8_13 fatcat:klwgy5trsrfspas3fe33h3ujzm

Deriving Protein Structures Efficiently by Integrating Experimental Data into Biomolecular Simulations

Marie Weiel-Potyagaylo
2021
Proteine sind molekulare Nanomaschinen in biologischen Zellen.  ...  In dieser Arbeit zeige ich, wie die entsprechenden Simulationsparameterräume mit Com [...]  ...  Hydrogen-Deuterium Exchange Coupled to Mass Spectrometry Hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) is a versatile technique to monitor the structure and dynamics of proteins in  ... 
doi:10.5445/ir/1000136249 fatcat:fyfpjea26bbijcwueo5bjqxig4
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