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Generic Software Frameworks for GC-MS Based Metabolomics [chapter]

Nils Hoffmann, Jens Stoye
2012 Metabolomics  
Metabolomics How to reference In order to correctly reference this scholarly work, feel free to copy and paste the following: Nils Hoffmann and Jens Stoye (2012).  ...  Peak alignment is based on a star-wise or tree-based application of an enhanced variant of pairwise dynamic time warping (DTW) (Hoffmann & Stoye, 2009 ).  ... 
doi:10.5772/31224 fatcat:dqt23nueeje53mm23zmbohbu54

Goslin - A Grammar of Succinct Lipid Nomenclature [article]

Dominik Kopczynski, Nils Hoffmann, Bing Peng, Robert Ahrends
2020 bioRxiv   pre-print
We introduce Goslin, a polyglot grammar for common lipid shorthand nomenclatures based on the LipidMaps nomenclature and the shorthand nomenclature established by Liebisch et al. and used by LipidHome and SwissLipids. Goslin was designed to address the following pressing issues in the lipidomics field: 1) to simplify the implementation of lipid name handling for developers of mass spectrometry-based lipidomics tools; 2) to offer a tool that unifies and normalizes the main existing lipid name
more » ... lects enabling a lipidomics analysis in a high-throughput fashion. We provide implementations of Goslin in four major programming languages, namely C++, Java, Python 3, and R to kick-start adoption and integration. Further, we set up a web service for users to work with Goslin directly. All implementations are available free of charge under a permissive open source license.
doi:10.1101/2020.04.17.046656 fatcat:yonxzkbshvdnrm5qdmnvwjnr6a

Substrate Elasticity Exerts Functional Effects on Primary Microglia

Stefan J. Blaschke, Seda Demir, Anna König, Jella-Andrea Abraham, Sabine U. Vay, Monika Rabenstein, Daniel N. Olschewski, Christina Hoffmann, Marco Hoffmann, Nils Hersch, Rudolf Merkel, Bernd Hoffmann (+3 others)
2020 Frontiers in Cellular Neuroscience  
Copyright © 2020 Blaschke, Demir, König, Abraham, Vay, Rabenstein, Olschewski, Hoffmann, Hoffmann, Hersch, Merkel, Hoffmann, Schroeter, Fink and Rueger.  ... 
doi:10.3389/fncel.2020.590500 pmid:33250714 pmcid:PMC7674555 fatcat:ssz5wp7fq5agxmf3ttenr5tqsu

Genetic dissection of the (poly)phenol profile of diploid strawberry ( Fragaria vesca ) fruits using a NIL collection

Maria Urrutia, Wilfried Schwab, Thomas Hoffmann, Amparo Monfort
2016 Plant Science  
Genotyping the NIL collection with the Axiom ® IStraw90 ® SNPs array, we were able to map 76 stable QTLs controlling accumulation of the (poly)-phenolic compounds.  ...  The metabolite profiling of a F. vesca near isogenic line (NIL) collection by LC-MS allowed the unambiguous identification of 22 (poly)-phenols, including anthocyanins, flavonols, flavan-3-ols, flavanones  ...  Distribution of total flavonols was fairly homogeneous among the NIL collection, except for a significant decline in NIL Fb1:26-61.  ... 
doi:10.1016/j.plantsci.2015.07.019 pmid:26566833 fatcat:hgtuy7dofvgtrdxewzeocjofua

Complex Size and Surface Charge Determine Nucleic Acid Transfer by Fusogenic Liposomes

Marco Hoffmann, Nils Hersch, Sven Gerlach, Georg Dreissen, Ronald Springer, Rudolf Merkel, Agnes Csiszár, Bernd Hoffmann
2020 International Journal of Molecular Sciences  
Highly efficient, biocompatible, and fast nucleic acid delivery methods are essential for biomedical applications and research. At present, two main strategies are used to this end. In non-viral transfection liposome- or polymer-based formulations are used to transfer cargo into cells via endocytosis, whereas viral carriers enable direct nucleic acid delivery into the cell cytoplasm. Here, we introduce a new generation of liposomes for nucleic acid delivery, which immediately fuse with the
more » ... lar plasma membrane upon contact to transfer the functional nucleic acid directly into the cell cytoplasm. For maximum fusion efficiency combined with high cargo transfer, nucleic acids had to be complexed and partially neutralized before incorporation into fusogenic liposomes. Among the various neutralization agents tested, small, linear, and positively charged polymers yielded the best complex properties. Systematic variation of liposomal composition and nucleic acid complexation identified surface charge as well as particle size as essential parameters for cargo-liposome interaction and subsequent fusion induction. Optimized protocols were tested for the efficient transfer of different kinds of nucleic acids like plasmid DNA, messenger RNA, and short-interfering RNA into various mammalian cells in culture and into primary tissues.
doi:10.3390/ijms21062244 pmid:32213928 fatcat:w3awxug2ibes5cdu6wb5gd3cqe

Programmable Current Source for Implantable Neural Stimulation Systems

Jonas Pistor, Nils Heidmann, Janpeter Höffmann, Steffen Paul
2014 Procedia Engineering  
doi:10.1016/j.proeng.2014.11.720 fatcat:lnr5has4wzhk3gbcxr4r3fy2xy

Perkutan Katheter-basiert implantierbare Herzschrittmacher

Christian Meyer, Christiane Jungen, Nils Gosau, Boris Hoffmann, Christian Eickholt, Stephan Willems
2016 Deutsche Medizinische Wochenschrift  
Die elektrische Stimulation des Herzens ist heute die Standardtherapie bei symptomatischen Bradykardien. Herzschrittmacher reduzieren Symptome, Synkopen und verlängern das Überleben von Hoch-Risiko-Patienten [1, 2]. Dennoch spielen insbesondere Elektroden-assoziierte Komplikationen eine bedeutsame Rolle. Eine neue Form von "elektrodenlosen" Schrittmachern könnte diese vermindern.
doi:10.1055/s-0041-107413 pmid:27078248 fatcat:vgycche6gveitpxuljq4fx3upa

Access site complications after transfemoral aortic valve implantation - a comparison of Manta and ProGlide

Pavel Hoffmann, Ahmed Al-Ani, Thomas von Lueder, Jenny Hoffmann, Peter Majak, Ove Hagen, Helga Loose, Nils Einar Kløw, Anders Opdahl
2018 CVIR Endovascular  
Despite decreasing sheath diameter, access site bleeding and vascular complications are still a major concern in transfemoral aortic valve implantation (TAVI), and may increase morbidity and even increase mortality. The aim was to compare safety of arterial closure in transfemoral TAVI with two different principles, pre-suture with ProGlide and collagen plug closure with Manta. Seventy-six patients treated with ProGlide and 75 with Manta were analysed. The endpoints were 1: access site vascular
more » ... complications and 2: non-planned vascular or endovascular surgery at the puncture site. Complications occurred in 2 (2.7%) ProGlide and in 8 (10.7%) Manta cases, p = 0.047. During the learning phase there were no significant differences. In the established phase there was one event (2%) in the ProGlide group, compared to 6 endpoints (12.0%), p = 0.047, in the Manta group.Unplanned surgery or intervention was seen in two (2.7%) ProGlide and in 7 (9.3%) Manta patients, p = ns. There were no significant differences during the learning phase. In established use, endpoints occurred more frequently in patients treated with the Manta device (12%), than in patients treated with the ProGlide (2%), p = 0.047. The ProGlide presuture closure device was associated with significantly lower rates of vascular complications and lower rates of surgery and interventions compared to the collagen plug Manta system. The data were collected from Internal quality control registry on treatment of patients with valvular heart disease with or without coronary artery disease, No 2014/17280, Oslo University Hospital, Ullevål.
doi:10.1186/s42155-018-0026-0 pmid:30652151 pmcid:PMC6319663 fatcat:i62tmeae5bashmtdigxhsubtba

Diatom frustules show increased mechanical strength and altered valve morphology under iron limitation

Susanne Wilken, Bernd Hoffmann, Nils Hersch, Norbert Kirchgessner, Sabine Dieluweit, Wolfgang Rubner, Linn J. Hoffmann, Rudolf Merkel, Ilka Peeken
2011 Limnology and Oceanography  
F. kerguelensis had been isolated during the iron-enrichment experiment EIFEX (Hoffmann et al. 2007 ).  ...  Nevertheless, the increase by a factor of 1.4 under iron limitation in F. kerguelensis is within the same range as reported for the same strain by Hoffmann et al. (2007) , and is high enough to account  ... 
doi:10.4319/lo.2011.56.4.1399 fatcat:jhfqxo6jsndyfoqb7azgslzlga

Der Defining-Issues-Tests (DIT) in der wirtschaftswissenschaftlichen Konsumforschung

Nils Christian Hoffmann, Sebastian Müller
2021 WiSt - Wirtschaftswissenschaftliches Studium  
Nils Christian Hoffmann ist wissenschaftlicher Mitarbeiter an der Professur für Marketing an der Christian-Albrechts-Universität zu Kiel.  ...  Hoffmann/Müller, Der Defining-Issues-Tests (DIT) in der wirtschaftswissenschaftlichen Konsumforschung miteinander vergleichbar (vgl. Rest et al., 1997) .  ... 
doi:10.15358/0340-1650-2021-9-4 fatcat:uqdzdvkksre3lhipwn6fmzxpii

HTPheno: An image analysis pipeline for high-throughput plant phenotyping

Anja Hartmann, Tobias Czauderna, Roberto Hoffmann, Nils Stein, Falk Schreiber
2011 BMC Bioinformatics  
In the last few years high-throughput analysis methods have become state-of-the-art in the life sciences. One of the latest developments is automated greenhouse systems for high-throughput plant phenotyping. Such systems allow the non-destructive screening of plants over a period of time by means of image acquisition techniques. During such screening different images of each plant are recorded and must be analysed by applying sophisticated image analysis algorithms. Results: This paper presents
more » ... an image analysis pipeline (HTPheno) for high-throughput plant phenotyping. HTPheno is implemented as a plugin for ImageJ, an open source image processing software. It provides the possibility to analyse colour images of plants which are taken in two different views (top view and side view) during a screening. Within the analysis different phenotypical parameters for each plant such as height, width and projected shoot area of the plants are calculated for the duration of the screening. HTPheno is applied to analyse two barley cultivars. Conclusions: HTPheno, an open source image analysis pipeline, supplies a flexible and adaptable ImageJ plugin which can be used for automated image analysis in high-throughput plant phenotyping and therefore to derive new biological insights, such as determination of fitness.
doi:10.1186/1471-2105-12-148 pmid:21569390 pmcid:PMC3113939 fatcat:tpeurxtj3veuth6yd4ljvyl5ji

Health-related quality of life in adult survivors of childhood sarcoidosis

Nils Milman, Claus Bo Svendsen, Anne Lisbeth Hoffmann
2009 Respiratory Medicine  
Results Clinical presentation of sarcoidosis Clinical, laboratory and radiological features at the onset of disease have been described previously. 2 Table 1 (adapted from Milman and Hoffmann 12  ... 
doi:10.1016/j.rmed.2008.12.007 pmid:19155167 fatcat:zdy2drbwkzcf3nsvcvx7sg7uwi

Institutional entrepreneurship capabilities for interorganizational sustainable supply chain strategies

Nils J. Peters, Joerg S. Hofstetter, Volker H. Hoffmann
2011 International Journal of Logistics Management  
Purpose -The purpose of this paper is to address the implementation of proactive interorganizational sustainable supply chain strategies by empirically exploring the relationship between key (inter-)organizational resources of the initiating company and the establishment of widely accepted voluntary sustainability initiatives. Design/methodology/approach -The study is built on comparative case studies as well as literature on institutional entrepreneurship and the resource-based view. Findings
more » ... The authors identify capabilities that enable the creation and establishment of companydriven voluntary sustainability initiatives -namely external stakeholder integration, cross-functional integration, the management of loosely coupled business units, supply chain implementation, process improvement and cultural framing. Originality/value -With this study, the authors introduce institutional entrepreneurship theory to supply chain management literature and show that institutional entrepreneurship theory may contribute to the question of how organizations implement their interorganizational sustainable supply chain strategies. Specifically, the study derives propositions for key resources enabling the establishment of voluntary sustainability initiatives widely accepted by participants as well as initiative-external stakeholders.
doi:10.1108/09574091111127552 fatcat:7vp4rv2sz5co5oeq4dms3d5yoq

The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

Daniel Wibberg, Bérénice Batut, Peter Belmann, Jochen Blom, Frank Oliver Glöckner, Björn Grüning, Nils Hoffmann, Nils Kleinbölting, René Rahn, Maja Rey, Uwe Scholz, Malvika Sharan (+4 others)
2020 F1000Research  
The German Network for Bioinformatics Infrastructure (de.NBI) is a national and academic infrastructure funded by the German Federal Ministry of Education and Research (BMBF). The de.NBI provides (i) service, (ii) training, and (iii) cloud computing to users in life sciences research and biomedicine in Germany and Europe and (iv) fosters the cooperation of the German bioinformatics community with international network structures. The de.NBI members also run the German node (ELIXIR-DE) within
more » ... European ELIXIR infrastructure. The de.NBI / ELIXIR-DE training platform, also known as special interest group 3 (SIG 3) 'Training & Education', coordinates the bioinformatics training of de.NBI and the German ELIXIR node. The network provides a high-quality, coherent, timely, and impactful training program across its eight service centers. Life scientists learn how to handle and analyze biological big data more effectively by applying tools, standards and compute services provided by de.NBI. Since 2015, more than 300 training courses were carried out with about 6,000 participants and these courses received recommendation rates of almost 90% (status as of July 2020). In addition to face-to-face training courses, online training was introduced on the de.NBI website in 2016 and guidelines for the preparation of e-learning material were established in 2018. In 2016, ELIXIR-DE joined the ELIXIR training platform. Here, the de.NBI / ELIXIR-DE training platform collaborates with ELIXIR in training activities, advertising training courses via TeSS and discussions on the exchange of data for training events essential for quality assessment on both the technical and administrative levels. The de.NBI training program trained thousands of scientists from Germany and beyond in many different areas of bioinformatics.
doi:10.12688/f1000research.20244.2 fatcat:io4rgsengvddhlhwjgpqv5livu
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