The underappreciated diversity of bile acid modifications

The repertoire of modifications to bile acids and related steroidal lipids by host and microbial metabolism remains incompletely characterized. To address this knowledge gap, we created a reusable resource of tandem mass spectrometry (MS/MS) spectra by filtering 1.2 billion publicly available MS/MS spectra for bile-acid-selective ion patterns. Thousands of modifications are distributed throughout animal and human bodies as well as microbial cultures. We employed this MS/MS library to identify polyamine bile amidates, prevalent in carnivores. They are present in humans, and their levels alter with a diet change from a Mediterranean to a typical American diet. This work highlights the existence of many more bile acid modifications than previously recognized and the value of leveraging public large-scale untargeted metabolomics data to discover metabolites. The availability of a modification-centric bile acid MS/MS library will inform future studies investigating bile acid roles in health and disease.

Functional metabolomics of the human scalp: a metabolic niche for Staphylococcus epidermidis

Although metabolomics data acquisition and analysis technologies have become increasingly sophisticated over the past 5-10 years, deciphering a metabolite's function from a description of its structure and its abundance in a given experimental setting is still a major scientific and intellectual challenge. To point out ways to address this "data to knowledge" challenge, we developed a functional metabolomics strategy that combines state-of-the-art data analysis tools and applied it to a human scalp metabolomics data set: skin swabs from healthy volunteers with normal or oily scalp (Sebumeter score 60-120, n = 33; Sebumeter score > 120, n = 41) were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS), yielding four metabolomics data sets for reversed phase chromatography (C18) or hydrophilic interaction chromatography (HILIC) separation in electrospray ionization (ESI) + or - ionization mode. Following our data analysis strategy, we were able to obtain increasingly comprehensive structural and functional annotations, by applying the Global Natural Product Social Networking (M. Wang, J. J. Carver, V. V. Phelan, L. M. Sanchez, et al., Nat Biotechnol 34:828-837, 2016, https://doi.org/10.1038/nbt.3597), SIRIUS (K. Dührkop, M. Fleischauer, M. Ludwig, A. A. Aksenov, et al., Nat Methods 16:299-302, 2019, https://doi.org/10.1038/s41592-019-0344-8), and MicrobeMASST (S. ZuffaS, R. Schmid, A. Bauermeister, P. W, P. Gomes, et al., bioRxiv:rs.3.rs-3189768, 2023, https://doi.org/10.21203/rs.3.rs-3189768/v1) tools. We finally combined the metabolomics data with a corresponding metagenomic sequencing data set using MMvec (J. T. Morton, A. A. Aksenov, L. F. Nothias, J. R. Foulds, et. al., Nat Methods 16:1306-1314, 2019, https://doi.org/10.1038/s41592-019-0616-3), gaining insights into the metabolic niche of one of the most prominent microbes on the human skin, Staphylococcus epidermidis.IMPORTANCESystems biology research on host-associated microbiota focuses on two fundamental questions: which microbes are present and how do they interact with each other, their host, and the broader host environment? Metagenomics provides us with a direct answer to the first part of the question: it unveils the microbial inhabitants, e.g., on our skin, and can provide insight into their functional potential. Yet, it falls short in revealing their active role. Metabolomics shows us the chemical composition of the environment in which microbes thrive and the transformation products they produce. In particular, untargeted metabolomics has the potential to observe a diverse set of metabolites and is thus an ideal complement to metagenomics. However, this potential often remains underexplored due to the low annotation rates in MS-based metabolomics and the necessity for multiple experimental chromatographic and mass spectrometric conditions. Beyond detection, prospecting metabolites' functional role in the host/microbiome metabolome requires identifying the biological processes and entities involved in their production and biotransformations. In the present study of the human scalp, we developed a strategy to achieve comprehensive structural and functional annotation of the metabolites in the human scalp environment, thus diving one step deeper into the interpretation of "omics" data. Leveraging a collection of openly accessible software tools and integrating microbiome data as a source of functional metabolite annotations, we finally identified the specific metabolic niche of Staphylococcus epidermidis, one of the key players of the human skin microbiome.

microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data

microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbe-derived metabolites and relative producers without a priori knowledge will vastly enhance the understanding of microorganisms' role in ecology and human health.

Studying Plant Specialized Metabolites Using Computational Metabolomics Strategies

Plant specialized metabolites have diversified vastly over the course of plant evolution, and they are considered key players in complex interactions between plants and their environment. The chemical diversity of these metabolites has been widely explored and utilized in agriculture and crop enhancement, the food industry, and drug development, among other areas. However, the immensity of the plant metabolome can make its exploration challenging. Here we describe a protocol for exploring plant specialized metabolites that combines high-resolution mass spectrometry and computational metabolomics strategies, including molecular networking, identification of structural motifs, as well as prediction of chemical structures and metabolite classes.

Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics

Despite the increasing availability of tandem mass spectrometry (MS/MS) community spectral libraries for untargeted metabolomics over the past decade, the majority of acquired MS/MS spectra remain uninterpreted. To further aid in interpreting unannotated spectra, we created a nearest neighbor suspect spectral library, consisting of 87,916 annotated MS/MS spectra derived from hundreds of millions of MS/MS spectra originating from published untargeted metabolomics experiments. Entries in this library, or "suspects," were derived from unannotated spectra that could be linked in a molecular network to an annotated spectrum. Annotations were propagated to unknowns based on structural relationships to reference molecules using MS/MS-based spectrum alignment. We demonstrate the broad relevance of the nearest neighbor suspect spectral library through representative examples of propagation-based annotation of acylcarnitines, bacterial and plant natural products, and drug metabolism. Our results also highlight how the library can help to better understand an Alzheimer's brain phenotype. The nearest neighbor suspect spectral library is openly available for download or for data analysis through the GNPS platform to help investigators hypothesize candidate structures for unknown MS/MS spectra in untargeted metabolomics data.

[Interdisciplinary ultrasound-guided, minimally invasive autopsy in COVID-19-deceased patients in the intensive care unit of a university hospital : A proof-of-concept study]

In this feasibility study, we carried out in an interdisciplinary team standardised, ultrasound-guided, minimally invasive autopsy (US-MIA) directly at the bedside of patients who died of COVID-19 in the intensive care unit of the Rechts der Isar Hospital of the Technical University Munich (TUM). The aim of the study was to verify the feasibility, time efficiency and infection hygiene aspects of the process, as well as the quality of the tissue samples. Our results show that bedside US-MIA is suitable for obtaining tissue samples before the onset of postmortem autolysis, and that it can also be carried out quickly and safely. The potential of US-MIA, which has gained little recognition so far, deserves special attention in the context of postmortem diagnosis, research and quality assurance. In the future, these strengths of US-MIA could help to lead postmortem diagnosis into the modern age of pathological deep analytics ("omics").

On-tissue dataset-dependent MALDI-TIMS-MS2 bioimaging

Trapped ion mobility spectrometry (TIMS) adds an additional separation dimension to mass spectrometry (MS) imaging, however, the lack of fragmentation spectra (MS2) impedes confident compound annotation in spatial metabolomics. Here, we describe spatial ion mobility-scheduled exhaustive fragmentation (SIMSEF), a dataset-dependent acquisition strategy that augments TIMS-MS imaging datasets with MS2 spectra. The fragmentation experiments are systematically distributed across the sample and scheduled for multiple collision energies per precursor ion. Extendable data processing and evaluation workflows are implemented into the open source software MZmine. The workflow and annotation capabilities are demonstrated on rat brain tissue thin sections, measured by matrix-assisted laser desorption/ionisation (MALDI)-TIMS-MS, where SIMSEF enables on-tissue compound annotation through spectral library matching and rule-based lipid annotation within MZmine and maps the (un)known chemical space by molecular networking. The SIMSEF algorithm and data analysis pipelines are open source and modular to provide a community resource.

Evaluation of Data-Dependent MS/MS Acquisition Parameters for Non-Targeted Metabolomics and Molecular Networking of Environmental Samples: Focus on the Q Exactive Platform

Non-targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a widely used tool for metabolomics analysis, enabling the detection and annotation of small molecules in complex environmental samples. Data-dependent acquisition (DDA) of product ion spectra is thereby currently one of the most frequently applied data acquisition strategies. The optimization of DDA parameters is central to ensuring high spectral quality, coverage, and number of compound annotations. Here, we evaluated the influence of 10 central DDA settings of the Q Exactive mass spectrometer on natural organic matter samples from ocean, river, and soil environments. After data analysis with classical and feature-based molecular networking using MZmine and GNPS, we compared the total number of network nodes, multivariate clustering, and spectrum quality-related metrics such as annotation and singleton rates, MS/MS placement, and coverage. Our results show that automatic gain control, microscans, mass resolving power, and dynamic exclusion are the most critical parameters, whereas collision energy, TopN, and isolation width had moderate and apex trigger, monoisotopic selection, and isotopic exclusion minor effects. The insights into the data acquisition ergonomics of the Q Exactive platform presented here can guide new users and provide them with initial method parameters, some of which may also be transferable to other sample types and MS platforms.

A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data

MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbial-derived metabolites and relative producers, without a priori knowledge, will vastly enhance the understanding of microorganisms' role in ecology and human health.

Training in vascular trauma surgery for non-vascular surgeons: Vascular trauma surgery skills course

Background

The experience of general and trauma surgeons in vascular trauma management has decreased with sub-specialization of surgery and working hours restrictions. We introduce a vascular trauma surgery skills course established to train German military surgeons prior to their deployment to conflict areas.

Methods

The intention and implementation of the vascular trauma course for non-vascular surgeons is described in detail.

Results

In hands-on courses, participants learn and train basic vascular surgical techniques on more realistic extremity, neck, and abdominal models with pulsatile vessels. A fundamental and an advanced course each provide military as well as civilian surgeons from different non-vascular specialties with a surgical skill set including direct vessel sutures, patch angioplasty, anastomosis, thrombectomy, and resuscitative endovascular balloon occlusion of the aorta (REBOA) in order to render them capable of managing major vascular injuries.

Conclusion

The experiences of this vascular trauma surgical skills course, initially established for military surgeons, can also be of use to all civilian general, visceral, and trauma surgeons occasionally facing traumatic or iatrogenic vascular injuries. Thus, the introduced vascular trauma course is valuable for all surgeons working in trauma centers.

Comparison of Cosine, Modified Cosine, and Neutral Loss Based Spectrum Alignment For Discovery of Structurally Related Molecules

Spectrum alignment of tandem mass spectrometry (MS/MS) data using the modified cosine similarity and subsequent visualization as molecular networks have been demonstrated to be a useful strategy to discover analogs of molecules from untargeted MS/MS-based metabolomics experiments. Recently, a neutral loss matching approach has been introduced as an alternative to MS/MS-based molecular networking with an implied performance advantage in finding analogs that cannot be discovered using existing MS/MS spectrum alignment strategies. To comprehensively evaluate the scoring properties of neutral loss matching, the cosine similarity, and the modified cosine similarity, similarity measures of 955 228 peptide MS/MS spectrum pairs and 10 million small molecule MS/MS spectrum pairs were compared. This comparative analysis revealed that the modified cosine similarity outperformed neutral loss matching and the cosine similarity in all cases. The data further indicated that the performance of MS/MS spectrum alignment depends on the location and type of the modification, as well as the chemical compound class of fragmented molecules.

Analysis of a novel hydrophobic acrylic enhanced monofocal intraocular lens compared to its standard monofocal type on the optical bench

Introduction

The aim of this laboratory study is to objectively analyze the new hydrophobic, acrylic, enhanced monofocal intraocular lens Acunex Quantum (AN6Q) and compare it with the monofocal platform Acunex AN6. 

Methods

Two IOL models were analyzed (Acunex Quantum AN6Q and Acunex AN6, Teleon Surgical, Spankeren, Netherlands), each having the same refractive power of + 22.0 D, on the optical bench with the OptiSpheric IOL PRO 2. The measurements followed the guidelines of the International Standard Organization with following parameters: ISO 2 cornea (+ 0,28 µ), ISO 11979/2, lens placement in situ in NaCl with 35° temperature, 546 nm and selection of different aperture sizes (3.0 mm vs 4.5 mm). The aberrations of each IOL were evaluated by the WaveMaster IOL 2, a high-resolution Shack-Hartmann sensor in reverse projection setup. An in-situ model eye was used according to ISO 11979 in NaCl (n = 1.337) with 546 nm, mask width 4.51. Zernike polynomials up to 10th order were determined by means of the measured wavefront that describe the optical properties of the IOL.

Results

Through frequency modulation transfer function (mean) at 50 lp/mm (AN6Q/AN6 centered) was 0.687/0.731 (3.0 mm aperture) and 0.400/0.509 (4.5 mm aperture). The SR (mean) was 0.592/0.809 (3.0 mm) and 0.332/0.372 (4.5 mm). The MTF (mean) at 50 lp/mm (AN6Q/AN6 decentered by 1 mm) was 0.413/0.478 (3.0 mm) and 0.257/0.229 (4.5 mm). The SR (mean) was 0.393/0.404 (3.0 mm) and 0.183/0.212 (4.5 mm). The MTF (mean) at 50 lp/mm (AN6Q/AN6 tilted by 5°) was 0.508/0.710 (3.0 mm) and 0.337/0.513 (4.5 mm). The SR (mean) was 0.508/0.760 (3.0 mm) and 0.235/0.2372 (4.5 mm). AN6Q showed MTF peak of 0.55 with an enlarged depth of power of about 2.5 D and two cusps in the MTF curve. The spherical aberration Z 4–0 was about -0.21 µm and the secondary spherical aberration Z 6–0 was about 0.16 µm. No other relevant aberration showed up.

Conclusion

The new, enhanced monofocal AN6Q provides an extended range of focus with only slight decrease in contrast quality. Both types of the hydrophobic, acrylic Acunex IOL platform have its particular advantages in clinical settings and therefore its importance, respectively.

Tattoo Pigment Identification in Inks and Skin Biopsies of Adverse Reactions by Complementary Elemental and Molecular Bioimaging with Mass Spectral Library Matching

Tattooing has become increasingly popular throughout society. Despite the recognized issue of adverse reactions in tattoos, regulations remain challenging with limited data available and a missing positive list. The diverse chemical properties of mostly insoluble inorganic and organic pigments pose an outstanding analytical challenge, which typically requires extensive sample preparation. Here, we present a multimodal bioimaging approach combining micro X-ray fluorescence (μXRF) and laser desorption ionization-mass spectrometry (LDI-MS) to detect the elemental and molecular composition in the same sample. The pigment structures directly absorb the laser energy, eliminating the need for matrix application. A computational data processing workflow clusters spatially resolved LDI-MS scans to merge redundant information into consensus spectra, which are then matched against new open mass spectral libraries of tattoo pigments. When applied to 13 tattoo inks and 68 skin samples from skin biopsies in adverse tattoo reactions, characteristic signal patterns of isotopes, ion adducts, and in-source fragments in LDI-MS¹ scans yielded confident compound annotations across various pigment classes. Combined with μXRF, pigment annotations were achieved for all skin samples with 14 unique structures and 2 inorganic pigments, emphasizing the applicability to larger studies. The tattoo-specific spectral libraries and further information are available on the tattoo-analysis.github.io website.

Native mass spectrometry-based metabolomics identifies metal-binding compounds

Although metals are essential for the molecular machineries of life, systematic methods for discovering metal-small molecule complexes from biological samples are limited. Here, we describe a two-step native electrospray ionization-mass spectrometry method, in which post-column pH adjustment and metal infusion are combined with ion identity molecular networking, a rule-based data analysis workflow. This method enabled the identification of metal-binding compounds in complex samples based on defined mass (m/z) offsets of ion species with the same chromatographic profiles. As this native electrospray metabolomics approach is suited to the use of any liquid chromatography-mass spectrometry system to explore the binding of any metal, this method has the potential to become an essential strategy for elucidating metal-binding molecules in biology.

Practice of radiation therapy for anal cancer in Austria-a survey on behalf of the Austrian radiation oncology society gastrointestinal tumor group (ÖGRO-GIT)

Purpose

We conducted a patterns-of-care survey on chemoradiation for locoregionally confined anal cancer in Austria to evaluate areas of disagreement and to identify possible targets for further standardization.

Methods

An anonymous questionnaire comprising 38 questions was sent to all Austrian radiation oncology departments. Results were analyzed descriptively and compared to two international guidelines.

Results

The response rate was 93%. Work-up generally includes DRE, endoscopy, and cross-sectional imaging of chest/abdomen and pelvis. PET-CT is used by 38%. Screening for HIV and biopsies of suspicious lymph nodes are infrequently used. All centers perform IMRT, mainly with daily IGRT. Median doses to the primary are 54.7 Gy (T1–2) and 59.4 Gy (T3–4). Suspicious nodes receive a boost (median dose 54 Gy), while elective nodal areas are mainly treated with 45–50.4 Gy. Target delineation of elective nodal areas seems generally uniform, although disagreement exists regarding inclusion of the common iliac nodes. No agreement was found for OAR-delineation and dose constraints. Concurrent chemotherapy is mitomycin and 5‑FU/capecitabine. Supportive care beyond skin care is infrequently offered. Intensive follow-up is performed for at least 5 years. Treatment of T1N0 shows considerable disagreement.

Conclusion

We found a high rate of agreement between the centers and concordance with major guidelines. PET-CT, routine HIV testing, and biopsies of suspicious LN seem underrepresented. The largest controversy regarding target volumes concerns inclusion of the common iliac nodes. Prescribed doses are generally in line with the recommendations or higher. OAR delineation, dose constraints, supportive care, and treatment of early anal cancer represent areas for further standardization.

Supplementary Information

The online version of this article (10.1007/s00066-021-01842-w) contains supplementary material, which is available to authorized users.

Neue Terminologie für Sprachentwicklungsstörungen?

Hintergrund

Sprachtherapeutisch-linguistische Fachkreise empfehlen die Anpassung einer von einem internationalen Konsortium empfohlenen Änderung der Nomenklatur für Sprachstörungen im Kindesalter, insbesondere für Sprachentwicklungsstörungen (SES), auch für den deutschsprachigen Raum.

Fragestellung

Ist eine solche Änderung in der Terminologie aus ärztlicher und psychologischer Sicht sinnvoll?

Material und Methode

Kritische Abwägung der Argumente für und gegen eine Nomenklaturänderung aus medizinischer und psychologischer Sicht eines Fachgesellschaften- und Leitliniengremiums.

Ergebnisse

Die ICD-10-GM (Internationale statistische Klassifikation der Krankheiten und verwandter Gesundheitsprobleme, 10. Revision, German Modification) und eine S2k-Leitlinie unterteilen SES in umschriebene SES (USES) und SES assoziiert mit anderen Erkrankungen (Komorbiditäten). Die USES- wie auch die künftige SES-Definition der ICD-11 (International Classification of Diseases 11th Revision) fordern den Ausschluss von Sinnesbehinderungen, neurologischen Erkrankungen und einer bedeutsamen intellektuellen Einschränkung. Diese Definition erscheint weit genug, um leichtere nonverbale Einschränkungen einzuschließen, birgt nicht die Gefahr, Kindern Sprach- und weitere Therapien vorzuenthalten und erkennt das ICD(International Classification of Disease)-Kriterium, nach dem der Sprachentwicklungsstand eines Kindes bedeutsam unter der Altersnorm und unterhalb des seinem Intelligenzalter angemessenen Niveaus liegen soll, an. Die intendierte Ersetzung des Komorbiditäten-Begriffs durch verursachende Faktoren, Risikofaktoren und Begleiterscheinungen könnte die Unterlassung einer dezidierten medizinischen Differenzialdiagnostik bedeuten.

Schlussfolgerungen

Die vorgeschlagene Terminologie birgt die Gefahr, ätiologisch bedeutsame Klassifikationen und differenzialdiagnostische Grenzen zu verwischen und auf wertvolles ärztliches und psychologisches Fachwissen in Diagnostik und Therapie sprachlicher Störungen im Kindesalter zu verzichten.

Feature-based molecular networking for identification of organic micropollutants including metabolites by non-target analysis applied to riverbank filtration

Due to growing concern about organic micropollutants and their transformation products (TP) in surface and drinking water, reliable identification of unknowns is required. Here, we demonstrate how non-target liquid chromatography (LC)-high-resolution tandem mass spectrometry (MS/MS) and the feature-based molecular networking (FBMN) workflow provide insight into water samples from four riverbank filtration sites with different redox conditions. First, FBMN prioritized and connected drinking water relevant and seasonally dependent compounds based on a modification-aware MS/MS cosine similarity. Within the resulting molecular networks, forty-three compounds were annotated. Here, carbamazepine, sartans, and their respective TP were investigated exemplarily. With chromatographic information and spectral similarity, four additional TP (dealkylated valsartan, dealkylated irbesartan, two oxygenated irbesartan isomers) and olmesartan were identified and partly verified with an authentic standard. In this study, sartans and TP were investigated and grouped regarding their removal behavior under different redox conditions and seasons for the first time. Antihypertensives were grouped into compounds being well removed during riverbank filtration, those primarily removed under anoxic conditions, and rather persistent compounds. Observed seasonal variations were mainly limited to varying river water concentrations. FBMN is a powerful tool for identifying previously unknown or unexpected compounds and their TP in water samples by non-target analysis.

Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment

Molecular networking connects mass spectra of molecules based on the similarity of their fragmentation patterns. However, during ionization, molecules commonly form multiple ion species with different fragmentation behavior. As a result, the fragmentation spectra of these ion species often remain unconnected in tandem mass spectrometry-based molecular networks, leading to redundant and disconnected sub-networks of the same compound classes. To overcome this bottleneck, we develop Ion Identity Molecular Networking (IIMN) that integrates chromatographic peak shape correlation analysis into molecular networks to connect and collapse different ion species of the same molecule. The new feature relationships improve network connectivity for structurally related molecules, can be used to reveal unknown ion-ligand complexes, enhance annotation within molecular networks, and facilitate the expansion of spectral reference libraries. IIMN is integrated into various open source feature finding tools and the GNPS environment. Moreover, IIMN-based spectral libraries with a broad coverage of ion species are publicly available.

Spatially and size-resolved analysis of gold nanoparticles in rat spleen after intratracheal instillation by laser ablation-inductively coupled plasma-mass spectrometry

In a dual approach, laser ablation-inductively coupled plasma-mass spectrometry was applied to investigate spleen samples of rats after intratracheal instillation of polyvinylpyrrolidone-coated gold nanoparticles. First, spatially resolved imaging analysis was deployed to investigate gold translocation from the lungs to the spleen and to investigate the distribution pattern of gold in the spleen parenchyma itself. Using the same instrumental setup, laser ablation-inductively coupled plasma-mass spectrometry in single particle mode was applied to determine the species of translocated gold. Single particle analysis allows the determination of particle size distributions and therefore to distinguish between ionic species, intact nanoparticles, and agglomerates. A translocation of instilled gold from the lungs to the spleen was demonstrated for gold nanoparticles of 30 and 50 nm diameter. Furthermore single particle analysis revealed the translocation of intact gold nanoparticles in a non-agglomerated state.

[EUROCRINE®: adrenal surgery 2015-2019- surprising initial results]

Hintergrund

Seit 2015 erfolgt in Europa mithilfe des EUROCRINE®-Registers eine systematische Dokumentation endokrin-chirurgischer Operationen. Ziel dieser ersten Auswertung war eine Darstellung der Versorgungsrealität für Nebenniereneingriffe in einem homogenen Versorgungsumfeld, entsprechend des deutschsprachigen Raums – bzw. des Präsenzgebiets der Chirurgischen Arbeitsgemeinschaft Endokrinologie (CAEK) der Deutschen Gesellschaft für Allgemein- und Viszeralchirurgie (DGAV) – einschließlich einer Analyse der Adhärenz zu geltenden Therapieempfehlungen.

Methodik

Es erfolgte eine deskriptive Analyse der präoperativen Diagnostik, der angewandten Operationstechniken sowie der zugrunde liegenden histologischen Entitäten der zwischen den Jahren 2015 und 2019 über EUROCRINE® in Deutschland, Österreich und der Schweiz dokumentierten Nebennierenoperationen.

Ergebnisse

In den insgesamt 21 teilnehmenden Kliniken des deutschsprachigen EUROCRINE®-Gebiets wurden 658 Operationen an Nebennieren durchgeführt. In 90 % erfolgten unilaterale, in 3 % bilaterale Adrenalektomien und in 7 % andere Resektionsverfahren. Die in 41 % der Operationen dokumentierte histologische Hauptdiagnose war das adrenokortikale Adenom. In 15 % lagen maligne Befunde zugrunde (einschließlich 6 % Nebennierenrindenkarzinome (ACC) und 8 % Nebennierenmetastasen). 23 % der Operationen erfolgten bei Phäochromozytomen. Diese wurden zu 82 % minimal-invasiv operiert, Nebennierenrindenkarzinome lediglich zu 28 % und Nebennierenmetastasen zu 66 %.

Schlussfolgerung

Überraschenderweise wurden nach Nebennierenadenomen und Phäochromozytomen an dritthäufigster Stelle Nebennierenmetastasen unterschiedlicher Primärtumoren reseziert. 28 % der ACC waren für minimal-invasive Techniken vorgesehen, wobei 20 % dieser Fälle eine Konversion zur offenen Operation erforderten. Die aktuelle Analyse deckte Diskrepanzen zwischen Versorgungsrealität und Leitlinienempfehlungen auf, aus denen sich zahlreiche Fragestellungen ergeben, welche nun in ein überarbeitetes EUROCRINE®-Modul zur Dokumentation von Nebennierenoperationen einfließen werden.

Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data

We engineered a machine learning approach, MSHub, to enable auto-deconvolution of gas chromatography-mass spectrometry (GC-MS) data. We then designed workflows to enable the community to store, process, share, annotate, compare and perform molecular networking of GC-MS data within the Global Natural Product Social (GNPS) Molecular Networking analysis platform. MSHub/GNPS performs auto-deconvolution of compound fragmentation patterns via unsupervised non-negative matrix factorization and quantifies the reproducibility of fragmentation patterns across samples.

Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data

We engineered a machine learning approach, MSHub, to enable auto-deconvolution of gas chromatography-mass spectrometry (GC-MS) data. We then designed workflows to enable the community to store, process, share, annotate, compare and perform molecular networking of GC-MS data within the Global Natural Product Social (GNPS) Molecular Networking analysis platform. MSHub/GNPS performs auto-deconvolution of compound fragmentation patterns via unsupervised non-negative matrix factorization and quantifies the reproducibility of fragmentation patterns across samples.

[Oestrus suppression in a dairy herd by means of anti-GnRH vaccination Improvac®: A prospective field study]

INTRODUCTION

The aim of this study was to evaluate the duration of estrus suppression after a double administration of the anti-GnRH vaccine Improvac® (Zoetis Schweiz GmbH, 2800 Delémont) in cows. Furthermore, it should be investigated, if a third administration could prolong the effect of the cycle suppression. A total of 21 cows (more than four weeks post partum) were vaccinated twice, at least 35 days apart, with 2 ml Improvac® (0.4 mg of a GnRH-analogon) subcutaneously on one side of the neck. Over a period of 368 days and in the course of 18 farm visits these cows were examined gynecologically and re-vaccinated if they showed signs of estrus behaviour or ovarian activity. After the second vaccination the cycle of the cows was suppressed for an average period of 114 days (59-175 days) and the effect could be prolonged by a booster of the vaccine for another 127 days in three cows. Estrus behaviour was absent for a longer period than ovarian activity was. The vaccine was tolerated well: apart from slight swelling at the injection site, no side effects were observed. Our results demonstrate that two immunizations with Improvac® are an easily applicable method for the suppression of cyclic activity in cows for a mean period of 114 days. The duration of cycle suppression was prolonged by a booster of the vaccination.

Reproducible molecular networking of untargeted mass spectrometry data using GNPS

Global Natural Product Social Molecular Networking (GNPS) is an interactive online small molecule-focused tandem mass spectrometry (MS2) data curation and analysis infrastructure. It is intended to provide as much chemical insight as possible into an untargeted MS2 dataset and to connect this chemical insight to the user's underlying biological questions. This can be performed within one liquid chromatography (LC)-MS2 experiment or at the repository scale. GNPS-MassIVE is a public data repository for untargeted MS2 data with sample information (metadata) and annotated MS2 spectra. These publicly accessible data can be annotated and updated with the GNPS infrastructure keeping a continuous record of all changes. This knowledge is disseminated across all public data; it is a living dataset. Molecular networking-one of the main analysis tools used within the GNPS platform-creates a structured data table that reflects the molecular diversity captured in tandem mass spectrometry experiments by computing the relationships of the MS2 spectra as spectral similarity. This protocol provides step-by-step instructions for creating reproducible, high-quality molecular networks. For training purposes, the reader is led through a 90- to 120-min procedure that starts by recalling an example public dataset and its sample information and proceeds to creating and interpreting a molecular network. Each data analysis job can be shared or cloned to disseminate the knowledge gained, thus propagating information that can lead to the discovery of molecules, metabolic pathways, and ecosystem/community interactions.

Final results for the neutron -asymmetry parameter A0 from the UCNA experiment

The UCNA experiment was designed to measure the neutron β-asymmetry parameter A0 using polarized ultracold neutrons (UCN). UCN produced via downscattering in solid deuterium were polarized via transport through a 7 T magnetic field, and then directed to a 1 T solenoidal electron spectrometer, where the decay electrons were detected in electron detector packages located on the two ends of the spectrometer. A value for A0 was then extracted from the asymmetry in the numbers of counts in the two detector packages. We summarize all of the results from the UCNA experiment, obtained during run periods in 2007, 2008–2009, 2010, and 2011–2013, which ultimately culminated in a 0.67% precision result for A0.

Lipid Species Annotation at Double Bond Position Level with Custom Databases by Extension of the MZmine 2 Open-Source Software Package

In recent years, proprietary and open-source bioinformatics software tools have been developed for the identification of lipids in complex biological samples based on high-resolution mass spectrometry data. These existent software tools often rely on publicly available lipid databases, such as LIPID MAPS, which, in some cases, only contain a limited number of lipid species for a specific lipid class. Other software solutions implement their own lipid species databases, which are often confined regarding implemented lipid classes, such as phospholipids. To address these drawbacks, we provide an extension of the widely used open-source metabolomics software MZmine 2, which enables the annotation of detected chromatographic features as lipid species. The extension is designed for straightforward generation of a custom database for selected lipid classes. Furthermore, each lipid's sum formula of the created database can be rapidly modified to search for derivatization products, oxidation products, in-source fragments, or adducts. The versatility will be exemplified by a liquid chromatography-high resolution mass spectrometry data set with postcolumn Paternò-Büchi derivatization. The derivatization reaction was performed to pinpoint the double bond positions in diacylglyceryltrimethylhomoserine lipid species in a lipid extract of a green algae ( Chlamydomonas reinhardtii) sample. The developed Lipid Search module extension of MZmine 2 supports the identification of lipids as far as double bond position level.

Identification of potential human urinary biomarkers for tomato juice intake by mass spectrometry-based metabolomics

PURPOSE

Dietary biomarkers allow the accurate and objective determination of the dietary intake of humans and can thus be valuable for investigating the relation between consumption of foods and biochemical as well as physiological responses. The objective of this study was the identification of potential urinary biomarkers for consumption of tomato juice.

METHODS

In the course of a dietary intervention study, the human urine metabolome of a study cohort was compared between a tomato-free diet and after intake of tomato juice by application of an LC-HRMS-based metabolomics approach. The data acquisition was achieved using an orbitrap mass spectrometer, followed by multistage data processing and univariate as well as multivariate statistical analysis to identify discriminating features.

RESULTS

Statistical analysis revealed several unique features detectable after tomato juice intake. The most discriminating markers were putatively identified as hydroxylated and sulfonated metabolites of esculeogenin B, aglycone of the steroidal glycoalkaloid esculeoside B recently found in tomato juice. Furthermore, the β-carboline alkaloids tangutorid E and F and glucuronidated derivatives thereof were identified in urine.

CONCLUSIONS

Steroidal glycoalkaloids in tomato juice are cleaved after ingestion, and hydroxylated and sulfonated metabolites of their aglycones might serve as urinary biomarkers for tomato juice intake. Similarly, β-carboline alkaloids and glucuronidated derivatives were identified as potential urinary biomarkers. Both the aglycones of the steroidal alkaloids and the β-carboline alkaloids might exhibit biological activities worth investigating.

Three-dimensional Kendrick mass plots as a tool for graphical lipid identification

RATIONALE

The rising field of lipidomics strongly relies on the identification of lipids in complex matrices. Recent technical advances regarding liquid chromatography (LC) and high-resolution mass spectrometry (HRMS) enable the mapping of the lipidome of an organism with short data acquisition times. However, interpretation and evaluation of resulting multidimensional datasets are challenging and this is still the bottleneck regarding overall analysis times.

METHODS

A novel adaption of Kendrick mass plot analysis is presented for a rapid and accurate analysis of lipids in complex matrices. Separation of lipids by their respective head group was achieved via hydrophilic interaction liquid chromatography (HILIC) coupled to HRMS. The resulting LC/HRMS datasets are processed to a list of chromatographically separated features by applying an optimized MZmine 2 workflow. All features are plotted in a three-dimensional Kendrick mass plot, which allows a fast identification of present lipid classes, based on equidistant features with fitting retention times and the same Kendrick mass defect. Suspected lipid classes are used for exact mass database matching to annotate features. A second three-dimensional Kendrick mass plot of annotated features of a single lipid class helps to reveal potential database mismatches, resulting in a curated list of identified lipid species.

RESULTS

The use of the novel adaption of the Kendrick mass plot has accelerated the identification of the relevant lipid species in the green alga Chlamydomonas reinhardtii. A total of 106 species were identified within the lipid classes: phosphatidylserine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, monogalactosyldiacylglycerol, digalactosyldiacylglycerol, and sulfoquinovosyldiacylglycerol.

CONCLUSIONS

This work shows how the addition of chromatographic information, i.e. the retention time, to a classical two-dimensional Kendrick mass plot enables rapid and accurate analysis of LC/HRMS datasets, exemplified on a green alga (C. reinhardtii) sample. Three-dimensional Kendrick mass plots have improved lipid class identification and fast spotting of falsely annotated lipid species.

Informatics and Medicine

Objectives: To clarify challenges and research topics for informatics in health and to describe new approaches for interdisciplinary collaboration and education. Methods: Research challenges and possible solutions were elaborated by scientists of two universities using an interdisciplinary approach, in a series of meetings over several months. Results and Conclusion: In order to translate scientific results from bench to bedside and further into an evidence-based and efficient health system, intensive collaboration is needed between experts from medicine, biology, informatics, engineering, public health, as well as social and economic sciences. Research challenges can be attributed to four areas: bioinformatics and systems biology, biomedical engineering and informatics, health informatics and individual healthcare, and public health informatics. In order to bridge existing gaps between different disciplines and cultures, we suggest focusing on interdisciplinary education, taking an integrative approach and starting interdisciplinary practice at early stages of education.

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[F-18]FDG imaging of head and neck tumors: Comparison of hybrid PET, dedicated PET and CT

Aim: Aim of the study was to evaluate [F-18] FDG imaging of head and neck tumors using a Hybrid-PET device of the 2nd or 3rd generation. Examinations were compared to dedicated PET and Spiral-CT. Methods: 54 patients suffering from head and neck tumors were examined using dedicated PET and Hybrid-PET after injection of 185-350 MBq [F-18] FDG. Examinations were carried out on the dedicated PET first followed by a scan on the Hybrid-PET. Dedicated PET was acquired in 3D mode, Hybrid-PET was performed in list mode using an axial filter. Reconstruction of data was performed itera-tively on both, dedicated PET and Hybrid-PET. All patients received a CT scan in multislice technique. All finding have been verified by the goldstandard histology or in case of negative histology by follow up. Results: Using dedicated PET the primary or recurrent lesion was correctly diagnosed in 47/48 patients, using Hybrid-PET in 46/ 48 patients and using CT in 25/48 patients. Metastatic disease in cervical lymph nodes was diagnosed in 17/ 18 patients with dedicated PET, in 16/18 patients with Hybrid-PET and in 15/18 with CT. False positive results with regard to lymph node metastasis were seen with one patient for dedicated PET and Hybrid-PET, respectively, and with 18 patients for CT. In a total of 11 patients unknown metastastic lesions were seen with dedicated PET and with Hybrid-PET elsewhere in the body. Additional malignant disease other than the head and neck tumor was found in 4 patients. Conclusion: Using Hybrid-PET for [F-18] FDG imaging reveals a loss of sensitivity and specificity of about 1-5% as compared to dedicated PET in head and neck tumors. [F-18] FDG PET with both, dedicated PET and Hybrid-PET is superior to CT in the diagnosis of primary or recurrent lesions as well as in the assessment of lymph node involvement.