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Critical Assessment of Small Molecule Identification 2016: automated methods

Emma L. Schymanski, Christoph Ruttkies, Martin Krauss, Céline Brouard, Tobias Kind, Kai Dührkop, Felicity Allen, Arpana Vaniya, Dries Verdegem, Sebastian Böcker, Juho Rousu, Huibin Shen (+5 others)
2017 Journal of Cheminformatics  
The fourth round of the Critical Assessment of Small Molecule Identification (CASMI) Contest (www. was held in 2016, with two new categories for automated methods.  ...  Conclusions: The improvement in (semi-)automated fragmentation methods for small molecule identification has been substantial.  ...  FA and TS acknowledge the contributions of Russ Greiner and David Wishart. MK acknowledges the help of Janek P. Dann with spectral acquisition.  ... 
doi:10.1186/s13321-017-0207-1 pmid:29086042 pmcid:PMC5368104 fatcat:uuvqxmusujhijjpmanptzbkj3i

Method for semi-automated microscopy of filtration-enriched circulating tumor cells

Emma Pailler, Marianne Oulhen, Fanny Billiot, Alexandre Galland, Nathalie Auger, Vincent Faugeroux, Corinne Laplace-Builhé, Benjamin Besse, Yohann Loriot, Maud Ngo-Camus, Merouan Hemanda, Colin R. Lindsay (+3 others)
2016 BMC Cancer  
Circulating tumor cell (CTC)-filtration methods capture high numbers of CTCs in non-small-cell lung cancer (NSCLC) and metastatic prostate cancer (mPCa) patients, and hold promise as a non-invasive technique  ...  We report the semi-automated microscopy method we developed to analyze filtration-enriched CTCs from NSCLC and mPCa patients.  ...  Acknowledgements We thank the patients and their families; Robert Sykes, Matthew Gorton and Karl Laczko (Leica Biosystems Richmond Inc.) for helping in the semi-automated method development.  ... 
doi:10.1186/s12885-016-2461-4 pmid:27417942 pmcid:PMC4946105 fatcat:y7cnb66uwbbrbetd7jpnirqgtm

A semi-automated Raman micro-spectroscopy method for morphological and chemical characterizations of microplastic litter

Frère L., Paul-Pont I., Moreau J., Soudant P., Lambert C., Huvet A., Rinnert E.
2016 Marine Pollution Bulletin  
The method was then applied to a larger environmental sample (n = 962 particles). The identification rate was 75% and significantly decreased as a function of particle size.  ...  identification rate (> 70%) ► Fast morphological and chemical characterization of environmental particles ► Efficient method for microplastics monitoring in marine environment  ...  The rapid analysis of large number of collected particles allows for an exhaustive assessment of large sample sizes and not only small subsamples.  ... 
doi:10.1016/j.marpolbul.2016.10.051 pmid:27837909 fatcat:ddb273rrf5cgpgs5oaumazzsca

Identification of Anthropogenic Compounds in Urban Environments and Evaluation of Automated Methods for Reading Fragmentation

Atsushi Yamamoto, Naoko Matsumoto, Hideya Kawasaki, Ryuichi Arakawa
2016 Mass Spectrometry  
In the identification process, two automated methods, MAGMa and MetFrag/MetFusion, for reading fragmentation were evaluated for the sixteen compounds.  ...  A workflow based on liquid chromatography/high-resolution mass spectrometry (LC/HR-MS) was applied for the identification of compounds in urban environments.  ...  are available on the Internet and they performed well in a public contest, CASMI2013 (Critical Assessment of Small Molecule Identi cation). 11) EXPERIMENTAL Sample preparation In February 2015, 500  ... 
doi:10.5702/massspectrometry.a0045 pmid:27313978 pmcid:PMC4894824 fatcat:ag27ccrrhnd6zh27na4qigj6ee

Comparison of different semi-automated cfDNA extraction methods in combination with UMI-based targeted sequencing

2019 OncoTarget  
Known oncogenic driver mutations were identified in 9 out of 12 patients with at least one of the cfDNA extraction methods, again favoring the extraction protocols from Qiagen and Promega.  ...  However, the critical bottleneck are sufficient cfDNA yields, which are essentially required to obtain meaningful test results.  ...  O.L. is the owner of TIB Molbiol.  ... 
doi:10.18632/oncotarget.27183 fatcat:q6x7wxf2zzharhtblhvshkx2va

Sepsis 2016 Paris

Marcia Ingles, Gary Crowfoot, Tamara V. Smelaya, Artem N. Kuzovlev, Lubov E. Salnikova, Raisa Bhikoo, Bodin Khwannimit, Rungsun Bhurayanontachai, Veerapong Vattanavanit, Emilie Tourteau, Amel Filali, Nicolas van Grunderbeeck (+125 others)
2016 Critical Care  
Aim of this study was the assessment of IL-35 and presepsin as prognostic sepsis markers in critical patients.  ...  The molecular pathogen identification method allows high multiplex, high sensitivity testing.  ... 
doi:10.1186/s13054-016-1518-8 fatcat:xc5r63mw4ffqzmzd2dvgma35zu

A Semi-automated Organoid Screening Method Demonstrates Epigenetic Control of Intestinal Epithelial Differentiation

Jenny Ostrop, Rosalie T. Zwiggelaar, Marianne Terndrup Pedersen, François Gerbe, Korbinian Bösl, Håvard T. Lindholm, Alberto Díez-Sánchez, Naveen Parmar, Silke Radetzki, Jens Peter von Kries, Philippe Jay, Kim B. Jensen (+2 others)
2021 Frontiers in Cell and Developmental Biology  
Here, we developed a semi-automated organoid screening method, which we applied to a library of highly specific chemical probes to identify epigenetic regulators of intestinal epithelial biology.  ...  Based on this resource dataset, we identified several targets that affected epithelial cell differentiation, including HDACs, EP300/CREBBP, LSD1, and type I PRMTs, which were verified by complementary methods  ...  METHODS Epigenetic Modifier Inhibitors The epigenetic modifier inhibitors in the screen experiment were part of the Structural Genomics Consortium Epigenetic Chemical Probes Collection as of March 2016  ... 
doi:10.3389/fcell.2020.618552 pmid:33575256 pmcid:PMC7872100 fatcat:rznqng7wujfw7gprvwrxnaaqgq

A semi-automated intestinal organoid screening method demonstrates epigenetic control of epithelial maturation [article]

Jenny Ostrop, Rosalie Zwiggelaar, Marianne Terndrup Pedersen, François Gerbe, Korbinian Bösl, Håvard T Lindholm, Alberto Díez-Sánchez, Naveen Parmar, Silke Radetzki, Jens Peter von Kries, Philippe Jay, Kim B Jensen (+2 others)
2020 biorxiv/medrxiv   pre-print
It consists of several epithelial cell lineages that are derived from LGR5+ intestinal stem cells.  ...  Yet, targeting of epigenetic regulatory enzymes may be relevant for new therapeutics, for example in cancer treatment.  ...  METHODS Epigenetic Modifier Inhibitors The epigenetic modifier inhibitors in the screen experiment were part of the Structural Genomics Consortium Epigenetic Chemical Probes Collection as of March 2016  ... 
doi:10.1101/2020.07.23.217414 fatcat:lkylrkvvljagzbghensjqdec6i

Joint Congress DGTI & DGI 2016, 7.-10. September 2016, Nürnberg, Abstracts

2016 Transfusion Medicine and Hemotherapy  
The appearance of advertisements in the journal is not a warranty, endorsement, or approval of the products or services advertised or of their effectiveness, quality or safety.  ...  The publisher and the editors disclaim responsibility for any injury to persons or property resulting form any ideas, methods, instructions or products referred to in the content or advertisements.  ...  Introduction: The quality of plasma for fractionation is of utmost importance.  ... 
doi:10.1159/000448382 fatcat:x74kjvwkqjg63bo67a5w77ltje

Immunotherapy biomarkers 2016: overcoming the barriers

James L. Gulley, Jay A. Berzofsky, Marcus O. Butler, Alessandra Cesano, Bernard A. Fox, Sacha Gnjatic, Sylvia Janetzki, Shyam Kalavar, Vaios Karanikas, Samir N. Khleif, Ilan Kirsch, Peter P. Lee (+9 others)
2017 Journal for ImmunoTherapy of Cancer  
This report summarizes the symposium, 'Immunotherapy Biomarkers 2016: Overcoming the Barriers', which was held on April 1, 2016 at the National Institutes of Health in Bethesda, Maryland.  ...  further progress, and recommendations for advancing the field of biomarker development.  ...  Availability of data and materials Not applicable.  ... 
doi:10.1186/s40425-017-0225-6 pmid:28653584 pmcid:PMC5359902 fatcat:mb2u576fkzgedjej3mvqcjgzru

CASMI 2016: A manual approach for dereplication of natural products using tandem mass spectrometry

Dejan Nikolić
2017 Phytochemistry Letters  
The Critical Assessment of Small Molecule Identification (CASMI) contest is an initiative designed as an unbiased test of manual and automated strategies for the identification of small molecules from  ...  CASMI 2016 is the fourth round of this contest in which the author participated in Category 1: Best Identification of Natural Products using a manual approach.  ...  Acknowledgments I would like to thank the organizers of the CASMI 2016 contest for their efforts in making this contest possible.  ... 
doi:10.1016/j.phytol.2017.01.006 pmid:28966697 pmcid:PMC5613954 fatcat:if4kmelvl5hrbl77vivlrijmca

Sepsis 2016 Agra, India

Surinder Kumar Sharma, Anurag Rohatgi, Mansi Bajaj, Charles L. Sprung, Ricardo Calderon Morales, Harvey Kasdan, Allon Reiter, Tobias Volker, Julien Meissonnier, Natalia Beloborodova, Viktor Moroz, Aleksandra Bedova (+78 others)
2016 Critical Care  
Critical Care 2016, 20(Suppl 1):P1 Background: The tools are currently limited in predicting which patients with an infection will progress to severe sepsis, shock, or death.  ...  Distribution of Organ Dysfunction across the range of D-dimer levels on day 2. (n = 60) Critical  ...  Acknowledgements This work was supported by an Intra-mural grant from the National Institute of Biomedical Genomics, Kalyani, India.  ... 
doi:10.1186/s13054-016-1204-x pmid:26996981 pmcid:PMC4895252 fatcat:ndpluarppbh67hp3qmnqsopvzq

Human genome meeting 2016

A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson, R. Polimanti, J. Gelernter, X. Lin (+828 others)
2016 Human Genomics  
Further, targeted quantitative analysis of a subset of discriminating metabolites using tandem mass spectrometry provided a reliable laboratory method to detect children with ASD.  ...  Methods Plasma samples from a clinically well-defined cohort of 100 male individuals, ages 2-16+ years, with ASD and 32 age-matched typically developing (TD) controls were subjected to global metabolomic  ...  However, the small number of these patients precludes a definitive assessment.  ... 
doi:10.1186/s40246-016-0063-5 pmid:27294413 pmcid:PMC4896275 fatcat:ycjj53ixrbauvnusibuz76y7bm

Interpol review of fibres and textiles 2016–2019

Laurent Lepot, Kyra Lunstroot, Kris De Wael
2020 Forensic Science International: Synergy  
This review paper covers the forensic-relevant literature in fibres and textiles from 2016 to 2019 as a part of the 19th Interpol International Forensic Science Managers Symposium.  ...  Identification of fibres Identification of vegetable fibres can sometimes cause difficulties.  ...  It is a continuation to our previous review [1] from 2016 and covers publications between June 2016 and the end of December 2018.  ... 
doi:10.1016/j.fsisyn.2020.01.014 pmid:33385143 pmcid:PMC7770456 fatcat:hrneuyolenfhvimkhivyphj4wm

Western Regional Meeting 2016, Carmel, California, January 28–30, 2016

2016 Journal of Investigative Medicine  
Methods Used We collected 6 minutes of resting state functional magnetic resonance imaging for 20 patients with CD/SUD and CU, 21 patients with CD/SUD without CU, and 22 controls (all males 14-18 years  ...  Such adolescents sometimes display high levels of callous-unemotional (CU) traits and recent work supports that the presence of CU identifies a distinct subgroup of youths with CD.  ...  Methods Used We retrospectively assessed time to organism identification (after growth on culture) and length of stay in all hospitalized children with bacteremia in 2011 utilizing the Phoenix automated  ... 
doi:10.1136/jim-d-15-00013.226 fatcat:fk6bo66fqbdbzch5ddirnkszzi
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