Keep Calm and Fill in Your DMP: Lessons Learnt from a Swiss DMP-Template Initiative

Aligning with other funders such as Horizon 2020, the Swiss National Science Foundation (SNSF) requires researcherswho apply for project funding to provide a Data Management Plan (DMP) as an integral part of their research proposal.In an attempt to assist and guide researchers filling out this document, and to provide a service as efficient as possible, the libraries of the Ecole Polytechnique Fédérale de Lausanne (EPFL) and ETH Zurich took the lead to elaborate on a DMP template with content suggestions and recommendations. In this practice paper, we will describe the collaborative effort between the two Swiss federal institutes of technology, namely EPFL and ETH Zurich, as well as some partners of the national Data Life Cycle Management (DLCM) project, which resulted in a very helpful document as reported by our researchers

A MALDI-TOF MS approach for mammalian, human, and formula milks’ profiling

Human milk composition is dynamic, and substitute formulae are intended to mimic its protein content. The purpose of this study was to investigate the potentiality of matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS), followed by multivariate data analyses as a tool to analyze the peptide profiles of mammalian, human, and formula milks. Breast milk samples from women at different lactation stages (2 (n = 5), 30 (n = 6), 60 (n = 5), and 90 (n = 4) days postpartum), and milk from donkeys (n = 4), cows (n = 4), buffaloes (n = 7), goats (n = 4), ewes (n = 5), and camels (n = 2) were collected. Different brands (n = 4) of infant formulae were also analyzed. Protein content (<30 kDa) was analyzed by MS, and data were exported for statistical elaborations. The mass spectra for each milk closely clustered together, whereas different milk samples resulted in well-separated mass spectra. Human samples formed a cluster in which colostrum constituted a well-defined subcluster. None of the milk formulae correlated with animal or human milk, although they were specifically characterized and correlated well with each other. These findings propose MALDI-TOF MS milk profiling as an analytical tool to discriminate, in a blinded way, different milk types. As each formula has a distinct specificity, shifting a baby from one to another formula implies a specific proteomic exposure. These profiles may assist in milk proteomics for easiness of use and minimization of costs, suggesting that the MALDI-TOF MS pipelines may be useful for not only milk adulteration assessments but also for the characterization of banked milk specimens in pediatric clinical settings

Phylogenetic and Metabolic Tracking of Gut Microbiota during Perinatal Development

The colonization and development of gut microbiota immediately after birth is highly variable and depends on several factors, such as delivery mode and modality of feeding during the first months of life. A cohort of 31 mother and neonate pairs, including 25 at-term caesarean (CS) and 6 vaginally (V) delivered neonates (DNs), were included in this study and 121 meconium/faecal samples were collected at days 1 through 30 following birth. Operational taxonomic units (OTUs) were assessed in 69 stool samples by phylogenetic microarray HITChip and inter- and intra-individual distributions were established by inter-OTUs correlation matrices and OTUs co-occurrence or co-exclusion networks. H-1-NMR metabolites were determined in 70 stool samples, PCA analysis was performed on 55 CS DNs samples, and metabolome/OTUs co-correlations were assessed in 45 CS samples, providing an integrated map of the early microbiota OTUs-metabolome. A microbiota "core" of OTUs was identified that was independent of delivery mode and lactation stage, suggesting highly specialized communities that act as seminal colonizers of microbial networks. Correlations among OTUs, metabolites, and OTUs-metabolites revealed metabolic profiles associated with early microbial ecological dynamics, maturation of milk components, and host physiology.Peer reviewe

La comunicazione scientifica dal preprint al repository: il caso dello Scientific Information Service del CERN

Attraverso questa ricerca si è voluto affrontare il tema della comunicazione scientifica in relazione alle abitudini, alle necessità e al sistema di valori della comunità dei fisici, e in particolare dei fisici delle alte energie. Dall’analisi delle modalità sperimentali e innovative utilizzate in quest’ambito per la disseminazione dei risultati scientifici, messe a punto grazie anche a una stretta interazione tra i fisici e i bibliotecari, si è cercato di individuare le caratteristiche princ..

Keep calm and fill in your DMP: Lessons Learnt from a Swiss DMP-template initiative

Aligning with other funders such as Horizon 2020, the Swiss National Science Foundation (SNSF) requires researchers who apply for project funding to provide a Data Management Plan (DMP) as an integral part of their research proposal. In an attempt to assist and guide researchers filling out this document, and to provide a service as efficient as possible, the libraries of the Ecole Polytechnique Fédérale de Lausanne (EPFL) and ETH Zurich took the lead to elaborate on a DMP template with content suggestions and recommendations. In this practice paper, we will describe the collaborative effort between the two Swiss federal institutes of technology, namely EPFL and ETH Zurich, as well as some partners of the national Data Life Cycle Management (DLCM) project, which resulted in a very helpful document as reported by our researchers.ISSN:1746-825

Visible Data - Invisible Disparities : The politics of research data management in Switzerland

<p>This poster was presented during the 11th International Digital Curation Conference "Visible data, invisible infrastructure", 22 - 25 February 2016, in Amsterdam, Netherlands.</p

Docosahexaenoic acid supplementation during pregnancy: A potential tool to prevent membrane rupture and preterm labor

none8noPolyunsaturated fatty acids (PUFAs) are required to maintain the fluidity, permeability and integrity of cell membranes. Maternal dietary supplementation with ω-3 PUFAs during pregnancy has beneficial effects, including increased gestational length and reduced risk of pregnancy complications. Significant amounts of ω-3 docosahexaenoic acid (DHA) are transferred from maternal to fetal blood, hence ensuring high levels of DHA in the placenta and fetal bloodstream and tissues. Fetal DHA demand increases exponentially with gestational age, especially in the third trimester, due to fetal development. According to the World Health Organization (WHO) and the Food and Agriculture Organization of the United Nations (FAO), a daily intake of DHA is recommended during pregnancy. Omega-3 PUFAs are involved in several anti-inflammatory, pro-resolving and anti-oxidative pathways. Several placental disorders, such as intrauterine growth restriction, premature rupture of membranes (PROM) and preterm-PROM (pPROM), are associated with placental inflammation and oxidative stress. This pilot study reports on a preliminary evaluation of the significance of the daily DHA administration on PROM and pPROM events in healthy pregnant women. Further extensive clinical trials will be necessary to fully elucidate the correlation between DHA administration during pregnancy and PROM/pPROM occurrence, which is related in turn to gestational duration and overall fetal health. © 2014 by the authors; licensee MDPI, Basel, Switzerland.mixedPietrantoni, Emanuela; Del Chierico, Federica; Rigon, Giuliano; Vernocchi, Pamela; Salvatori, Guglielmo; Manco, Melania; Signore, Fabrizio; Putignani, LorenzaPietrantoni, Emanuela; Del Chierico, Federica; Rigon, Giuliano; Vernocchi, Pamela; Salvatori, Guglielmo; Manco, Melania; Signore, Fabrizio; Putignani, Lorenz

A Parallel Tracking of Salivary and Gut Microbiota Profiles Can Reveal Maturation and Interplay of Early Life Microbial Communities in Healthy Infants

In this study, the onset and shaping of the salivary and gut microbiota in healthy newborns during the first period of life has been followed, evaluating the impact of salivary microbiota on the development of early fecal microbial communities. The microbiota of 80 salivary and 82 fecal samples that were collected from healthy newborns in the first six months of life, was investigated by 16S rRNA amplicon profiling. The microbial relationship within and between the saliva and gut ecosystems was determined by correlation heatmaps and co-occurrence networks. Streptococcus and Staphylococcus appeared as early commensals in the salivary microbiota, dominating this ecosystem through the time, while Fusobacterium, Prevotella, Porphyromonas, Granulicatella, and Veillonella were late colonizers. Enterobacteriaceae, Staphylococcus and Streptococcus were gut pioneers, followed by the anaerobic Bifidobacterium, Veillonella, Eggerthella, and Bacteroides. Streptococcus, Staphylococcus, and Veillonella were shared by the gut and saliva ecosystems. The saliva and gut microbiota seem to evolve independently, driven by local adaptation strategies, except for the oral Streptococcus and Veillonella that are involved in gut microbiota development as seeding species. This study offers a piece of knowledge on how the oral microbiota may affect the gut microbiota in healthy newborns, shedding light onto new microbial targets for the development of therapies for early life intestinal dysbiosis

An omic approach to congenital diaphragmatic hernia: a pilot study of genomic, microRNA, and metabolomic profiling

The omic approach can help identify a signature that can be potentially used as biomarkers in babies with congenital diaphragmatic hernia (CDH)