scholarly journals The EU Child Cohort Network’s core data: establishing a set of findable, accessible, interoperable and re-usable (FAIR) variables

2021 ◽  
Author(s):  
Angela Pinot de Moira ◽  
◽  
Sido Haakma ◽  
Katrine Strandberg-Larsen ◽  
Esther van Enckevort ◽  
...  
Keyword(s):  
Statistical Power ◽  
Major Product ◽  
Multiple Birth ◽  
Birth Cohorts ◽  
Data Resource ◽  
Core Data ◽  
Number Of Children ◽  
Analysis Platform ◽  
Early Life Exposures ◽  
The Eu

AbstractThe Horizon2020 LifeCycle Project is a cross-cohort collaboration which brings together data from multiple birth cohorts from across Europe and Australia to facilitate studies on the influence of early-life exposures on later health outcomes. A major product of this collaboration has been the establishment of a FAIR (findable, accessible, interoperable and reusable) data resource known as the EU Child Cohort Network. Here we focus on the EU Child Cohort Network’s core variables. These are a set of basic variables, derivable by the majority of participating cohorts and frequently used as covariates or exposures in lifecourse research. First, we describe the process by which the list of core variables was established. Second, we explain the protocol according to which these variables were harmonised in order to make them interoperable. Third, we describe the catalogue developed to ensure that the network’s data are findable and reusable. Finally, we describe the core data, including the proportion of variables harmonised by each cohort and the number of children for whom harmonised core data are available. EU Child Cohort Network data will be analysed using a federated analysis platform, removing the need to physically transfer data and thus making the data more accessible to researchers. The network will add value to participating cohorts by increasing statistical power and exposure heterogeneity, as well as facilitating cross-cohort comparisons, cross-validation and replication. Our aim is to motivate other cohorts to join the network and encourage the use of the EU Child Cohort Network by the wider research community.

scholarly journals BRENDA, the ELIXIR core data resource in 2021: new developments and updates

2020 ◽  
Vol 49 (D1) ◽  
pp. D498-D508
Author(s):  
Antje Chang ◽  
Lisa Jeske ◽  
Sandra Ulbrich ◽  
Julia Hofmann ◽  
Julia Koblitz ◽  
...  
Keyword(s):  
Intracellular Localization ◽  
Easy Access ◽  
New Developments ◽  
Data Resource ◽  
Core Data ◽  
Related Data ◽  
Primary Literature ◽  
Ligand Interactions ◽  
Genome Annotations ◽  
Individual Enzyme

Abstract The BRENDA enzyme database (https://www.brenda-enzymes.org), established in 1987, has evolved into the main collection of functional enzyme and metabolism data. In 2018, BRENDA was selected as an ELIXIR Core Data Resource. BRENDA provides reliable data, continuous curation and updates of classified enzymes, and the integration of newly discovered enzymes. The main part contains >5 million data for ∼90 000 enzymes from ∼13 000 organisms, manually extracted from ∼157 000 primary literature references, combined with information of text and data mining, data integration, and prediction algorithms. Supplements comprise disease-related data, protein sequences, 3D structures, genome annotations, ligand information, taxonomic, bibliographic, and kinetic data. BRENDA offers an easy access to enzyme information from quick to advanced searches, text- and structured-based queries for enzyme-ligand interactions, word maps, and visualization of enzyme data. The BRENDA Pathway Maps are completely revised and updated for an enhanced interactive and intuitive usability. The new design of the Enzyme Summary Page provides an improved access to each individual enzyme. A new protein structure 3D viewer was integrated. The prediction of the intracellular localization of eukaryotic enzymes has been implemented. The new EnzymeDetector combines BRENDA enzyme annotations with protein and genome databases for the detection of eukaryotic and prokaryotic enzymes.

scholarly journals Epigenetics and DOHaD: from basics to birth and beyond

2017 ◽  
Vol 8 (5) ◽  
pp. 513-519 ◽  
Author(s):  
T. Bianco-Miotto ◽  
J. M. Craig ◽  
Y. P. Gasser ◽  
S. J. van Dijk ◽  
S. E. Ozanne
Keyword(s):  
Dna Methylation ◽  
Chronic Disease ◽  
Chronic Diseases ◽  
Early Life ◽  
Later Life ◽  
Metabolic Health ◽  
Number Of Children ◽  
Early Life Environment ◽  
Increased Risk ◽  
Early Life Exposures

Developmental origins of health and disease (DOHaD) is the study of how the early life environment can impact the risk of chronic diseases from childhood to adulthood and the mechanisms involved. Epigenetic modifications such as DNA methylation, histone modifications and non-coding RNAs are involved in mediating how early life environment impacts later health. This review is a summary of the Epigenetics and DOHaD workshop held at the 2016 DOHaD Society of Australia and New Zealand Conference. Our extensive knowledge of how the early life environment impacts later risk for chronic disease would not have been possible without animal models. In this review we highlight some animal model examples that demonstrate how an adverse early life exposure results in epigenetic and gene expression changes that may contribute to increased risk of chronic disease later in life. Type 2 diabetes and cardiovascular disease are chronic diseases with an increasing incidence due to the increased number of children and adults that are obese. Epigenetic changes such as DNA methylation have been shown to be associated with metabolic health measures and potentially predict future metabolic health status. Although more difficult to elucidate in humans, recent studies suggest that DNA methylation may be one of the epigenetic mechanisms that mediates the effects of early life exposures on later life risk of obesity and obesity related diseases. Finally, we discuss the role of the microbiome and how it is a new player in developmental programming and mediating early life exposures on later risk of chronic disease.

scholarly journals BRENDA in 2019: a European ELIXIR core data resource

2018 ◽  
Vol 47 (D1) ◽  
pp. D542-D549 ◽  
Author(s):  
Lisa Jeske ◽  
Sandra Placzek ◽  
Ida Schomburg ◽  
Antje Chang ◽  
Dietmar Schomburg
Keyword(s):  
Data Resource ◽  
Core Data

scholarly journals Estimation of Cohort Fertility Using Parity Progression Ratio

2020 ◽  
pp. 18-28
Author(s):  
Dhanendra Veer Shakya
Keyword(s):  
Age Groups ◽  
Fertility Level ◽  
Parity Progression ◽  
Birth Cohorts ◽  
Number Of Children ◽  
Parity Progression Ratio ◽  
History Of ◽  
Cohort Fertility ◽  
Children Ever Born ◽  
Using Data

This study attempts to analyze the levels and patterns of cohort fertility in Nepal in 2016 using data on parity progression ratios (PPRs). Simple PPRs, rather than synthetic PPRs or birth history of women, are used in this study from distribution of women by age and children ever born. Data on PPRs are used from 2016 Nepal Demographic and Health Survey to estimate cohort fertility of currently married and all women separately. Fertility is analyzed for different birth cohorts of women, specifically for birth cohorts of age groups 45-49, 20-24, 25-29, and 30-34 years, beside overall span of reproductive ages (15-49) for different purposes. The PPRs data are employed in this study in three different ways such as PPRs itself, proportion of women with at least ‘N’ number of children ever born (CEB), and cohort fertility rates. All three measures are implied to estimate cohort fertility of both currently married and all women separately. Fertility patterns are almost similar in all the three methods and other the measures show that the level of cohort fertility is still a little higher in Nepal, although it is declining gradually over time. The completed cohort fertility is estimated at around 4 in Nepal in 2016. The contribution of this article will be to check fertility level by applying this simple, but less common, method in estimating cohort fertility.

Tertiary treatment of Berlin WWTP effluents with ferrate (Fe(VI))

2013 ◽  
Vol 68 (7) ◽  
pp. 1665-1671 ◽  
Author(s):  
U. Hübner ◽  
M. Jekel
Keyword(s):  
Surface Waters ◽  
Major Product ◽  
Advanced Treatment ◽  
Dual Function ◽  
Secondary Effluent ◽  
Tertiary Treatment ◽  
Efficient Removal ◽  
Promising Alternative ◽  
Secondary Effluents ◽  
The Eu

New and higher standards in the EU water framework directive necessitate advanced treatment of secondary effluents for reduction of trace organic compounds (TrOCs) and nutrients before the discharge into receiving surface waters. Due to its dual function as oxidant and coagulant, ferrate is considered as a promising alternative for tertiary treatment. The oxidation of selected TrOCs and simultaneous flocculation of phosphates by ferrate was tested in batch experiments with secondary effluent from Berlin Ruhleben. The concentrations of carbamazepine (CBZ) and diclofenac were reduced by >90% with ferrate dosages of 6 mg/L as Fe. CBZ was transformed to 1-(2-benzaldehyde)-4-hydro-(1H,3H)-quinazoline-2-one, which is known as the major product from the reaction of CBZ with ozone. In contrast to ozonation, no further transformation of this product was observed. The concentration of ibuprofen was not reduced by ferrate treatment. For efficient removal of 60–100 μg/L phosphate-P to values <20 μg/L, ferrate dosages of 3–4 mg/L as Fe were sufficient.

Birthweight Predicts IQ: Fact or Artefact?

2007 ◽  
Vol 10 (4) ◽  
pp. 581-586 ◽  
Author(s):  
Rhiannon Newcombe ◽  
Barry J. Milne ◽  
Avshalom Caspi ◽  
Richie Poulton ◽  
Terrie E. Moffitt
Keyword(s):  
Low Birthweight ◽  
Preventive Intervention ◽  
Environmental Influence ◽  
Birth Cohorts ◽  
Number Of Children ◽  
Point Increase ◽  
Or Genes ◽  
Lower Birthweight ◽  
Prospective Longitudinal ◽  
New Evidence

AbstractIt has been shown that lower birthweight is associated with lower IQ, but it remains unclear whether this association is causal or spurious. We examined the relationship between birthweight and IQ in two prospective longitudinal birth cohorts: a UK cohort of 1116 twin pairs (563 monozygotic [MZ] pairs), born in 1994–95, and a New Zealand cohort of 1037 singletons born in 1972–73. IQ was tested with the Wechsler Intelligence Scales for Children. Birthweight differences within MZ twin pairs predicted IQ differences within pairs, ruling out genetic and shared environmental explanations for the association. Birthweight predicted IQ similarly in the twin and nontwin cohorts after controlling for social disadvantage, attesting that the association generalized beyond twins. An increase of 1000 g in birthweight was associated with a 3 IQ point increase. Results from two cohorts add to evidence that low birthweight is a risk factor for compromised neurological health. Our finding that birthweight differences predict IQ differences within MZ twin pairs provides new evidence that the mechanism can be narrowed to an environmental effect during pregnancy, rather than any familial environmental influence shared by siblings, or genes. With the increasing numbers of low-birthweight infants, our results support the contention that birthweight could be a target for early preventive intervention to reduce the number of children with compromised IQ.

scholarly journals Child poverty policies across Europe

2009 ◽  
Vol 21 (2) ◽  
pp. 128-149
Author(s):  
Jonathan Bradshaw ◽  
Yekaterina Chzhen
Keyword(s):  
European Union ◽  
Child Poverty ◽  
Living Conditions ◽  
Family Type ◽  
The European Union ◽  
Number Of Children ◽  
Before And After ◽  
Children Education ◽  
Negative Effekte ◽  
The Eu

This article is in two parts. In the first part, we present the results of a comparative analysis of the European Union Statistics on Income and Living Conditions (SILC) to explore child poverty. Countries’ child poverty rates are compared using the conventional income definition and deprivation and economic strain. The extent of overlap in these different measures is explored. Variations in child poverty rates by employment, child age, number of children, education level of the parents and family type are explored. Then logistic regression is used to explore how countries’ child poverty varies having taken account of these characteristics. In the second part we explore how policy affects child poverty, presenting child poverty rates before and after transfers; analysis of spending and its relationship to child poverty; and the analysis of child benefit packages using model family methods. Child poverty is increasing in most EU countries. The article argues that the data available on what policies work is not really good enough. The OECD Benefits and Wages series is too limited and the EU should invest in a framework that collects data on how tax and benefit policies are working to combat child poverty across the EU. Zusammenfassung Im ersten der zwei Teile dieses Aufsatzes stellen wir die Ergebnisse einer vergleichenden Analyse der European Union Statistics on Income and Living Conditions (SILC) vor, um die Kinderarmut unter die Lupe zu nehmen. Die Kinderarmutsraten in den einzelnen Ländern werden mithilfe von einer konventionellen Einkommensdefinition, Mangelerscheinungen und wirtschaftlichen Zwängen miteinander verglichen. Dabei wird das Ausmaß der Überschneidungen der einzelnen Messungen und Variationen in der Kinderarmut aufgrund der Beschäftigungsverhältnisse, des Alters der Kinder, der Kinderzahl, des Bildungsniveaus der Eltern und des Familientyps untersucht. Danach kommt die logistische Regression zum Einsatz, um zu untersuchen, inwieweit die Kinderarmut in den jeweiligen Ländern variiert, wenn man all diese Ausprägungen berücksichtigt. Im zweiten Teil untersuchen wir, welchen Einfluss familienpolitische Maßnahmen auf die Kinderarmut haben, indem wir Kinderarmutsraten vor und nach der Einbeziehung von Transferleistungen vorstellen, die Staatsausgaben und ihr Verhältnis zur Kinderarmut und – mithilfe von Methoden der Modellierung von Familien – Kinderunterstützungspakete analysieren. Die Kinderarmut nimmt in den meisten EU-Ländern zu. Im Beitrag wird dann argumentiert, dass die Daten darüber, welchen familienpolitischen Maßnahmen funktionieren, nicht wirklich gut genug sind. Die Benefits and Wages-Zeitreihen der OECD sind Beschränkungen unterworfen – die EU sollte in ein Rahmenprogramm investieren, in signifikante negative Effekte vorausgegangener ökonomischer Deprivation auf das Wohlbefinden gibt, zusätzlich zu den Effekten des Bildungsniveaus der Eltern und der Familienformen. Diese Effekte waren bei Mädchen stärker ausgeprägt als bei Jungen. Ein eingeschränktes Wohlbefinden im Jahre 1996 trug nicht vollständig zur Erklärung von Langzeiteffekten ökonomischer Deprivation bei. Mütterliche Negativität erwies sich als stärkerer Mediator für die Reaktion von Mädchen auf ökonomischen Stress. Insgesamt legen die Daten nahe, dass ökonomische Deprivation ein signifikanter Risikofaktor mit negativen Langzeitfolgen, insbesondere für Mädchen, ist.

scholarly journals 1H-NMR metabolomics-based surrogates to impute common clinical risk factors and endpoints

2021 ◽  
Author(s):  
Daniele Bizzarri ◽  
Marcel J.T. Reinders ◽  
Marian Beekman ◽  
Pieternella Eline Slagboom ◽  
Erik B van den Akker ◽  
...  
Keyword(s):  
1H Nmr ◽  
Statistical Power ◽  
Association Studies ◽  
Epidemiological Studies ◽  
Medication Usage ◽  
Metabolomics Data ◽  
Data Resource ◽  
Nmr Metabolomics ◽  
Clinical Variables ◽  
Diabetes Status

Missing or incomplete phenotypic information can severely deteriorate the statistical power in epidemiological studies. High-throughput quantification of small-molecules in bio-samples, i.e. metabolomics, is steadily gaining popularity, as it is highly informative for various phenotypical characteristics. Here we aim to leverage metabolomics to impute missing data in clinical variables routinely assessed in large epidemiological and clinical studies. To this end, we have employed ~25,000 1H-NMR metabolomics samples from 28 Dutch cohorts collected within the BBMRI-NL consortium, to create 19 metabolomics-based predictors for clinical variables, including diabetes status (AUC5-Fold CV = 0.94) and lipid medication usage (AUC5-Fold CV = 0.90). Subsequent application in independent cohorts confirmed that our metabolomics-based predictors can indeed be used to impute a wide array of missing clinical variables from a single metabolomics data resource. In addition, application highlighted the potential use of our predictors to explore the effects of totally unobserved confounders in omics association studies. Finally, we show that our predictors can be used to explore risk factor profiles contributing to mortality in older participants. To conclude, we provide 1H-NMR metabolomics-based models to impute clinical variables routinely assessed in epidemiological studies and illustrate their merit in scenarios when phenotypic variables are partially incomplete or totally unobserved.

scholarly journals The Role of Fertility in the Demography of Grandparenthood: Evidence from Italy

2020 ◽  
Author(s):  
Giorgio Di Gessa ◽  
Valeria Bordone ◽  
Bruno Arpino
Keyword(s):  
Social Relations ◽  
Intergenerational Transfers ◽  
Later Life ◽  
Age At First Birth ◽  
Birth Cohorts ◽  
Number Of Children ◽  
Italian Survey ◽  
Fertility Differentials ◽  
Compositional Changes

Abstract Grandparents play an important role in their family’s lives. However, little is known about the demography of grandparenthood. Given dramatic recent changes in fertility, we explore the role of number of children and age at first birth in the timing of the transition into grandparenthood focusing on Italy, a country with well-known North-South fertility differentials. We used data from the 2009 Italian Survey ‘Family and Social Relations’ (N = 10,186) to estimate median ages of grandparenthood across three birth cohorts of parents (1920–29; 1930–39; 1940–49). Findings show an overall postponement of age of grandparenthood of 5 years, shifting for women from early to mid- or late-50s (in the South and North, respectively). Such postponement is largely driven by family compositional changes: although the age of grandparenthood among mothers of three or more children has not changed much over cohorts, the percentage of mothers with such characteristic decreased significantly. The heterogeneity in experiencing the transition to grandparenthood has implications for intergenerational transfers and other roles in later life.

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