Combining Multiple Prevention Strategies in one Health Questionnaire: A Pilot Study

Abstract General practitioners are confronted with many required preventive interventions. A solution to this problem is comb ining several interventions in one questionnaire. Almost no research exists on this subject. In this pilot feasibility study we examine whether a prevention strategy based on a questionnaire increases the number of preventive items in the patient's records, and we examine the response rate when this questionnaire is given to patients during a routine consultation.An evidence based questionnaire containing 22 questions concerning 11 topics was used in a practice of general practit ioners in a semi-rural co mmunity. 26 items were studied: the answers to the 22 aforementioned questions plus four more items relating to multip le questions. All were rated before and after the intervention using strict criteria.Of the 104 included patients 46 participated.After the intervention the availability of most items increased but it was only significant for eight items. This unique pilot study clearly shows us that a questionnaire which comb ines multip le prevention interventions improves the quality of our records. Handing over this questionnaire to patients during routine visits gives a high response rate

CoPub Mapper: mining MEDLINE based on search term co-publication

BACKGROUND: High throughput microarray analyses result in many differentially expressed genes that are potentially responsible for the biological process of interest. In order to identify biological similarities between genes, publications from MEDLINE were identified in which pairs of gene names and combinations of gene name with specific keywords were co-mentioned. RESULTS: MEDLINE search strings for 15,621 known genes and 3,731 keywords were generated and validated. PubMed IDs were retrieved from MEDLINE and relative probability of co-occurrences of all gene-gene and gene-keyword pairs determined. To assess gene clustering according to literature co-publication, 150 genes consisting of 8 sets with known connections (same pathway, same protein complex, or same cellular localization, etc.) were run through the program. Receiver operator characteristics (ROC) analyses showed that most gene sets were clustered much better than expected by random chance. To test grouping of genes from real microarray data, 221 differentially expressed genes from a microarray experiment were analyzed with CoPub Mapper, which resulted in several relevant clusters of genes with biological process and disease keywords. In addition, all genes versus keywords were hierarchical clustered to reveal a complete grouping of published genes based on co-occurrence. CONCLUSION: The CoPub Mapper program allows for quick and versatile querying of co-published genes and keywords and can be successfully used to cluster predefined groups of genes and microarray data

Automatic metabolite annotation in complex LC-MS(n ≥ 2) data using MAGMa

Poster presented at the Analytical Tools for Cutting-edge Metabolomics meeting in London, 30 April 201

matchms - processing and similarity evaluation of mass spectrometry data

Mass spectrometry data is at the heart of numerous applications in the biomedical and lifesciences. With growing use of high-throughput techniques, researchers need to analyze largerand more complex datasets. In particular through joint effort in the research community,fragmentation mass spectrometry datasets are growing in size and number. Platforms such asMassBank (Horai et al., 2010), GNPS (Wang et al., 2016) or MetaboLights (Haug et al., 2020)serve as an open-access hub for sharing of raw, processed, or annotated fragmentation massspectrometry data. Without suitable tools, however, exploitation of such datasets remainsoverly challenging. In particular, large collected datasets contain data acquired using differentinstruments and measurement conditions, and can further contain a significant fraction ofinconsistent, wrongly labeled, or incorrect metadata (annotations)

Maatregel op de Kaart: Kansrijke landbouwmaatregelen per perceel voor schoner grond- en oppervlaktewater

De kwaliteit van het grond-en oppervlaktewater in Nederland is de afgelopen decennia weliswaar verbeterd, maar is op veel plekken nog niet op orde.De landbouwsector lanceerde daaromin 2017 een lijst met vrijwillige maatregelenom uitspoeling van meststoffen tegen te gaan. Om het nemen van maatregelen makkelijkerte maken is een kaart ontwikkeld die voor elk landbouwperceel in Nederland aangeeft welke vrijwillige maatregelen kansrijk zijn.Deze maatregelenkaart is voor iedereen beschikbaar en wordt in 2020 verder doorontwikkeld. De kaart biedt een basis om met verschillende partijen te werken aan een betere waterkwaliteit

Spec2Vec: improved mass spectral similarity scoring through learning of structural relationships

Spectral similarity is used as a proxy for structural similarity in many tandem mass spectrometry (MS/MS) based metabolomics analyses such as library matching and molecular networking. Although weaknesses in the relationship between spectral similarity scores and the true structural similarities have been described, little development of alternative scores has been undertaken. Here, we introduce Spec2Vec, a novel spectral similarity score inspired by a natural language processing algorithm—Word2Vec. Spec2Vec learns fragmental relationships within a large set of spectral data to derive abstract spectral embeddings that can be used to assess spectral similarities. Using data derived from GNPS MS/MS libraries including spectra for nearly 13,000 unique molecules, we show how Spec2Vec scores correlate better with structural similarity than cosine-based scores. We demonstrate the advantages of Spec2Vec in library matching and molecular networking. Spec2Vec is computationally more scalable allowing structural analogue searches in large databases within seconds

Lipid droplet degradation by autophagy connects mitochondria metabolism to Prox1-driven expression of lymphatic genes and lymphangiogenesis.

Autophagy has vasculoprotective roles, but whether and how it regulates lymphatic endothelial cells (LEC) homeostasis and lymphangiogenesis is unknown. Here, we show that genetic deficiency of autophagy in LEC impairs responses to VEGF-C and injury-driven corneal lymphangiogenesis. Autophagy loss in LEC compromises the expression of main effectors of LEC identity, like VEGFR3, affects mitochondrial dynamics and causes an accumulation of lipid droplets (LDs) in vitro and in vivo. When lipophagy is impaired, mitochondrial ATP production, fatty acid oxidation, acetyl-CoA/CoA ratio and expression of lymphangiogenic PROX1 target genes are dwindled. Enforcing mitochondria fusion by silencing dynamin-related-protein 1 (DRP1) in autophagy-deficient LEC fails to restore LDs turnover and lymphatic gene expression, whereas supplementing the fatty acid precursor acetate rescues VEGFR3 levels and signaling, and lymphangiogenesis in LEC-Atg5-/- mice. Our findings reveal that lipophagy in LEC by supporting FAO, preserves a mitochondrial-PROX1 gene expression circuit that safeguards LEC responsiveness to lymphangiogenic mediators and lymphangiogenesis.We thank K. Rillaerts, J. Souffreau, and A. Bouche, for expert technical support and Dr. A. Luttun and Dr. A. Zijsen for sharing tools and advices. P.A. is supported by grants from the Flemish Research Foundation (FWO-Vlaanderen; G076617N, G049817N, G070115N), the EOS MetaNiche consortium N degrees 40007532, Stichting tegen Kanker (FAF-F/2018/1252) and the iBOF/21/053 ATLANTIS consortium with G.B. D.H. is the recipient of an FWO Doctoral Fellowship from the Flemish Research Foundation (FWO-Vlaanderen, 1186019N), Belgium. M.B. is supported by the `Fonds voor Wetenschappelijk Onderzoek' (FWO). K.J. is the recipient of an FWO Postdoctoral Fellowship from the Flemish Research Foundation (FWO-Vlaanderen). P.C. is supported by Methusalem funding by the Flemish government, and by an ERC Advanced Research Grant (EU-ERC269073).S

Microbiota-derived short chain fatty acids modulate microglia and promote Aβ plaque deposition.

Previous studies have identified a crucial role of the gut microbiome in modifying Alzheimer's disease (AD) progression. However, the mechanisms of microbiome-brain interaction in AD were so far unknown. Here, we identify microbiota-derived short chain fatty acids (SCFA) as microbial metabolites which promote Aβ deposition. Germ-free (GF) AD mice exhibit a substantially reduced Aβ plaque load and markedly reduced SCFA plasma concentrations; conversely, SCFA supplementation to GF AD mice increased the Aβ plaque load to levels of conventionally colonized (specific pathogen-free [SPF]) animals and SCFA supplementation to SPF mice even further exacerbated plaque load. This was accompanied by the pronounced alterations in microglial transcriptomic profile, including upregulation of ApoE. Despite increased microglial recruitment to Aβ plaques upon SCFA supplementation, microglia contained less intracellular Aβ. Taken together, our results demonstrate that microbiota-derived SCFA are critical mediators along the gut-brain axis which promote Aβ deposition likely via modulation of the microglial phenotype

Register: Language Users’ Knowledge of Situational-Functional Variation

The Collaborative Research Center 1412 “Register: Language Users’ Knowledge of Situational-Functional Variation” (CRC 1412) investigates the role of register in language, focusing in particular on what constitutes a language user’s register knowledge and which situational-functional factors determine a user’s choices. The following paper is an extract from the frame text of the proposal for the CRC 1412, which was submitted to the Deutsche Forschungsgemeinschaft in 2019, followed by a successful onsite evaluation that took place in 2019. The CRC 1412 then started its work on January 1, 2020. The theoretical part of the frame text gives an extensive overview of the theoretical and empirical perspectives on register knowledge from the viewpoint of 2019. Due to the high collaborative effort of all PIs involved, the frame text is unique in its scope on register research, encompassing register-relevant aspects from variationist approaches, psycholinguistics, grammatical theory, acquisition theory, historical linguistics, phonology, phonetics, typology, corpus linguistics, and computational linguistics, as well as qualitative and quantitative modeling. Although our positions and hypotheses since its submission have developed further, the frame text is still a vital resource as a compilation of state-of-the-art register research and a documentation of the start of the CRC 1412. The theoretical part without administrative components therefore presents an ideal starter publication to kick off the CRC’s publication series REALIS. For an overview of the projects and more information on the CRC, see https://sfb1412.hu-berlin.de/

Diagnostic exome sequencing in 266 Dutch patients with visual impairment

Inherited eye disorders have a large clinical and genetic heterogeneity, which makes genetic diagnosis cumbersome. An exome-sequencing approach was developed in which data analysis was divided into two steps: the vision gene panel and exome analysis. In the vision gene panel analysis, variants in genes known to cause inherited eye disorders were assessed for pathogenicity. If no causative variants were detected and when the patient consented, the entire exome data was analyzed. A total of 266 Dutch patients with different types of inherited eye disorders, including inherited retinal dystrophies, cataract, developmental eye disorders and optic atrophy, were investigated. In the vision gene panel analysis (likely), causative variants were detected in 49% and in the exome analysis in an additional 2% of the patients. The highest detection rate of (likely) causative variants was in patients with inherited retinal dystrophies, for instance a yield of 63% in patients with retinitis pigmentosa. In patients with developmental eye defects, cataract and optic atrophy, the detection rate was 50, 33 and 17%, respectively. An exome-sequencing approach enables a genetic diagnosis in patients with different types of inherited eye disorders using one test. The exome approach has the same detection rate as targeted panel sequencing tests, but offers a number of advantages. For instance, the vision gene panel can be frequently and easily updated with additional (novel) eye disorder genes. Determination of the genetic diagnosis improved the clinical diagnosis, regarding the assessment of the inheritance pattern as well as future disease perspective