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Motivation
The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.
Main types of variables included
The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.
Spatial location and grain
BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2).
Time period and grain
BioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.
Major taxa and level of measurement
BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.
Software format
.csv and .SQL.
Measles, mumps and rubella are viral infectious diseases that may cause severe and devastating complications among affected individuals. The disease burden of all three diseases is high, but could be reduced entirely through successful vaccination strategies. As such, the WHO has established the goal of globally eliminating measles and rubella and concomitantly controlling the frequently co-vaccinated mumps.
In 2010, the WHO European Region member states agreed to strengthen efforts to eliminate measles and rubella from Europe by the end of 2015. As this date draws closer, progress analyses become increasingly relevant. In this systematic literature review, the immunization strategies, vaccination coverages and disease incidences of eleven European nations were assessed and their progress towards disease elimination evaluated.
Successful prevention of the endemic transmission of measles, mumps, or rubella could be achieved in several nations, including Sweden, Croatia, Greece and Spain. Austria, France, Germany, Italy, Poland, Turkey and the United Kingdom of Great Britain and Northern Ireland, though having improved their overall immunization rates, have not yet been able to reach the elimination goals. In Turkey, Italy and Poland, sharp increases in case numbers during recent years are potentially threatening the successful measles, mumps and rubella control in Europe.
Pockets of susceptible population groups that may contribute to the perpetuation of the diseases have been identified. They include infants and young children, adolescents and young adults, adolescent and adult males, recent immigrants and refugees,and traveling ethnic minority groups. Reasons for the increased risk of infection among these groups are manifold and a result of various historic and current vaccination practices, cultural, political and religious differences, as well as individual believes and concerns. Travel and migration of infected individuals to and between the various European nations also play an essential role in the continual transmission of measles, mumps and rubella in Europe. Only an adequate population-wide immunity can prevent the occurrence of major outbreaks due to viral importation. Efforts should therefore be made to immunize all population members able to receive vaccinations and to offer additional immunization opportunities to those susceptible population subgroups that are difficult to reach through routine vaccination programs.
In countries struggling to meet the WHO elimination goals, alternative immunization practices may be necessary. A uniform, European-wide MMR vaccination schedule based on the successful immunization methods of countries that have eliminated measles, mumps and rubella may be an effective tool for improving the overall population-wide immunity and controlling the three diseases. A model for such a schedule was created and includes strategies for reaching population members regardless of age, gender or migratory background. The implementation of uniform immunization recommendations is challenging, but the advantages in terms of improved vaccination, surveillance and disease control methods may be worth at least considering such a strategy in Europe.
Measles, mumps and rubella elimination may be attainable in the WHO European Region. The current epidemiological situation suggests that the goal is unlikely to be reached by the end of 2015, but through continued international efforts and collaboration, effective disease control could be achieved in the near future. In the meantime, improvements in immunization strategies, vaccination coverages, supplementary campaigns as well as disease notification systems and confirmations should be made on a national and international level, so that an adequate population-wide immunity can be established and the disease elimination progresses effectively monitored within the entire European region.
Introduction: Several common alleles have been shown to be associated with breast and/or ovarian cancer risk for BRCA1 and BRCA2 mutation carriers. Recent genome-wide association studies of breast cancer have identified eight additional breast cancer susceptibility loci: rs1011970 (9p21, CDKN2A/B), rs10995190 (ZNF365), rs704010 (ZMIZ1), rs2380205 (10p15), rs614367 (11q13), rs1292011 (12q24), rs10771399 (12p11 near PTHLH) and rs865686 (9q31.2).
Methods: To evaluate whether these single nucleotide polymorphisms (SNPs) are associated with breast cancer risk for BRCA1 and BRCA2 carriers, we genotyped these SNPs in 12,599 BRCA1 and 7,132 BRCA2 mutation carriers and analysed the associations with breast cancer risk within a retrospective likelihood framework.
Results: Only SNP rs10771399 near PTHLH was associated with breast cancer risk for BRCA1 mutation carriers (per-allele hazard ratio (HR) = 0.87, 95% CI: 0.81 to 0.94, P-trend = 3 x 10\(^{-4}\)). The association was restricted to mutations proven or predicted to lead to absence of protein expression (HR = 0.82, 95% CI: 0.74 to 0.90, P-trend = 3.1 x 10\(^{-5}\), P-difference = 0.03). Four SNPs were associated with the risk of breast cancer for BRCA2 mutation carriers: rs10995190, P-trend = 0.015; rs1011970, P-trend = 0.048; rs865686, 2df P = 0.007; rs1292011 2df P = 0.03. rs10771399 (PTHLH) was predominantly associated with estrogen receptor (ER)-negative breast cancer for BRCA1 mutation carriers (HR = 0.81, 95% CI: 0.74 to 0.90, P-trend = 4 x 10\(^{-5}\)) and there was marginal evidence of association with ER- negative breast cancer for BRCA2 mutation carriers (HR = 0.78, 95% CI: 0.62 to 1.00, P-trend = 0.049).
Conclusions: The present findings, in combination with previously identified modifiers of risk, will ultimately lead to more accurate risk prediction and an improved understanding of the disease etiology in BRCA1 and BRCA2 mutation carriers.
Introduction:
Individuals carrying pathogenic mutations in the BRCA1 and BRCA2 genes have a high lifetime risk of breast cancer. BRCA1 and BRCA2 are involved in DNA double-strand break repair, DNA alterations that can be caused by exposure to reactive oxygen species, a main source of which are mitochondria. Mitochondrial genome variations affect electron transport chain efficiency and reactive oxygen species production. Individuals with different mitochondrial haplogroups differ in their metabolism and sensitivity to oxidative stress. Variability in mitochondrial genetic background can alter reactive oxygen species production, leading to cancer risk. In the present study, we tested the hypothesis that mitochondrial haplogroups modify breast cancer risk in BRCA1/2 mutation carriers.
Methods:
We genotyped 22,214 (11,421 affected, 10,793 unaffected) mutation carriers belonging to the Consortium of Investigators of Modifiers of BRCA1/2 for 129 mitochondrial polymorphisms using the iCOGS array. Haplogroup inference and association detection were performed using a phylogenetic approach. ALTree was applied to explore the reference mitochondrial evolutionary tree and detect subclades enriched in affected or unaffected individuals.
Results:
We discovered that subclade T1a1 was depleted in affected BRCA2 mutation carriers compared with the rest of clade T (hazard ratio (HR) = 0.55; 95% confidence interval (CI), 0.34 to 0.88; P = 0.01). Compared with the most frequent haplogroup in the general population (that is, H and T clades), the T1a1 haplogroup has a HR of 0.62 (95% CI, 0.40 to 0.95; P = 0.03). We also identified three potential susceptibility loci, including G13708A/rs28359178, which has demonstrated an inverse association with familial breast cancer risk.
Conclusions:
This study illustrates how original approaches such as the phylogeny-based method we used can empower classical molecular epidemiological studies aimed at identifying association or risk modification effects.