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  • 1
    Publication Date: 2018-03-14
    Description: Motivation As whole-genome tumor sequence and biological annotation datasets grow in size, number and content, there is an increasing basic science and clinical need for efficient and accurate data management and analysis software. With the emergence of increasingly sophisticated data stores, execution environments and machine learning algorithms, there is also a need for the integration of functionality across frameworks. Results We present orchid, a python based software package for the management, annotation and machine learning of cancer mutations. Building on technologies of parallel workflow execution, in-memory database storage and machine learning analytics, orchid efficiently handles millions of mutations and hundreds of features in an easy-to-use manner. We describe the implementation of orchid and demonstrate its ability to distinguish tissue of origin in 12 tumor types based on 339 features using a random forest classifier. Availability and implementation Orchid and our annotated tumor mutation database are freely available at https://github.com/wittelab/orchid . Software is implemented in python 2.7, and makes use of MySQL or MemSQL databases. Groovy 2.4.5 is optionally required for parallel workflow execution. Contact JWitte@ucsf.edu Supplementary information Supplementary dataSupplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 2
    Abstract: Importance: Cancer is the second leading cause of death worldwide. Current estimates on the burden of cancer are needed for cancer control planning. Objective: To estimate mortality, incidence, years lived with disability (YLDs), years of life lost (YLLs), and disability-adjusted life-years (DALYs) for 32 cancers in 195 countries and territories from 1990 to 2015. Evidence Review: Cancer mortality was estimated using vital registration system data, cancer registry incidence data (transformed to mortality estimates using separately estimated mortality to incidence [MI] ratios), and verbal autopsy data. Cancer incidence was calculated by dividing mortality estimates through the modeled MI ratios. To calculate cancer prevalence, MI ratios were used to model survival. To calculate YLDs, prevalence estimates were multiplied by disability weights. The YLLs were estimated by multiplying age-specific cancer deaths by the reference life expectancy. DALYs were estimated as the sum of YLDs and YLLs. A sociodemographic index (SDI) was created for each location based on income per capita, educational attainment, and fertility. Countries were categorized by SDI quintiles to summarize results. Findings: In 2015, there were 17.5 million cancer cases worldwide and 8.7 million deaths. Between 2005 and 2015, cancer cases increased by 33%, with population aging contributing 16%, population growth 13%, and changes in age-specific rates contributing 4%. For men, the most common cancer globally was prostate cancer (1.6 million cases). Tracheal, bronchus, and lung cancer was the leading cause of cancer deaths and DALYs in men (1.2 million deaths and 25.9 million DALYs). For women, the most common cancer was breast cancer (2.4 million cases). Breast cancer was also the leading cause of cancer deaths and DALYs for women (523000 deaths and 15.1 million DALYs). Overall, cancer caused 208.3 million DALYs worldwide in 2015 for both sexes combined. Between 2005 and 2015, age-standardized incidence rates for all cancers combined increased in 174 of 195 countries or territories. Age-standardized death rates (ASDRs) for all cancers combined decreased within that timeframe in 140 of 195 countries or territories. Countries with an increase in the ASDR due to all cancers were largely located on the African continent. Of all cancers, deaths between 2005 and 2015 decreased significantly for Hodgkin lymphoma (-6.1% [95% uncertainty interval (UI), -10.6% to -1.3%]). The number of deaths also decreased for esophageal cancer, stomach cancer, and chronic myeloid leukemia, although these results were not statistically significant. Conclusion and Relevance: As part of the epidemiological transition, cancer incidence is expected to increase in the future, further straining limited health care resources. Appropriate allocation of resources for cancer prevention, early diagnosis, and curative and palliative care requires detailed knowledge of the local burden of cancer. The GBD 2015 study results demonstrate that progress is possible in the war against cancer. However, the major findings also highlight an unmet need for cancer prevention efforts, including tobacco control, vaccination, and the promotion of physical activity and a healthy diet.
    Type of Publication: Journal article published
    PubMed ID: 27918777
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  • 3
    ISSN: 0309-1651
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 78 (1989), S. 863-866 
    ISSN: 1432-2242
    Keywords: Medicago ; Alfalfa ; Plastid inheritance ; Organelle inheritance
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Plastids are plant cellular organelles that are generally inherited from the maternal parent in the angiosperms. Many species exhibit biparental inheritance of plastids, but usually with a predominantly maternal influence. In contrast to this, we report strong paternal inheritance of plastids in reciprocal crosses of alfalfa, Medicago sativa, by following restriction fragment length polymorphisms for plastid DNA in two normal green plastids. Mitochondrial inheritance remained exclusively maternal.
    Type of Medium: Electronic Resource
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  • 5
    ISSN: 1432-2242
    Keywords: First-division restitution ; Tetrasomic inheritance ; Polyploidy ; RAPD markers
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract RAPD markers were used to determine the level of heterozygosity transmitted via 2n gametes from V. darrowi selection Florida 4B (Fla 4B) to inter-specific hybrids with tetraploid V. corymbosum cv Bluecrop. The tetraploid hybrid US 75 was found to contain about 70% of Fla 4B's heterozygosity, a value attributed to a first-division restitution (FDR) mode of 2n gamete production. Crossovers during 2n gamete formation were evidenced by the absence of 16 dominant alleles of Fla 4B in US 75, and direct tests of segregation in a diploid population involving Fla 4B. RAPD markers that were present in both Fla 4B and US 75 were used to determine the mode of inheritance in a segregating population of US 75xV. corymbosum cv Bluetta. Thirty-one duplex loci were identified which segregated in a 5∶1 ratio, indicating that US 75 undergoes tetrasomic inheritance.
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1432-2242
    Keywords: Mating systems ; Self-incompatibility ; Genetic load
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Tetraploid Vaccinium corymbosum genotypes exhibit wide variability in seed set following self- and cross-pollinations. In this paper, a post-zygotic mechanism (seed abortion) under polygenic control is proposed as the basis for fertility differences in this species. A pollen chase experiment indicated that self-pollen tubes fertilize ovules, but are also ‘outcompeted’ by foreign male gametes in pollen mixtures. Matings among cultivars derived from a pedigree showed a linear decrease in seed number per fruit, and increase in seed abortion, with increasing relatedness among parents. Selfed (S1) progeny from self-fertile parents were largely self-sterile. At zygotic levels of inbreeding of F〉0.3 there was little or no fertility, suggesting that an inbreeding threshold regulates reproductive success in V. corymbosum matings. Individuals below the threshold are facultative selfers, while those above it are obligate outcrossers. Inbreeding also caused a decrease in pollen viability, and reduced female fertility more rapidly than male fertility. These phenomena are discussed in terms of two models of genetic load: (1) mutational load — homozygosity for recessive embryolethal or sub-lethal mutations and (2) segregational load — loss of allelic interactions essential for embryonic vigor. Self-infertility in highbush blueberries is placed in the context of ‘late-acting’ self-incompatibility versus ‘early-acting’ inbreeding depression in angiosperms.
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 1432-2145
    Keywords: Keywords Vaccinium myrtilloides ; V. angustifolium ; V. corymbosum ; Autopolyploidy ; Genetic load ; Self-incompatibility.
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Greenhouse pollinations were performed to determine whether early-acting inbreeding depression is contributing to low levels of self-fertility in three Vaccinium species: V. myrtilloides Michaux, V. angustifolium Aiton, and V. corymbosum L. All three species showed a significant reduction in self fruit set and in the proportion of fertilized ovules that developed into mature seed in self compared to outcross fruit. Reductions were more severe in V. myrtilloides and V. angustifolium than in V. corymbosum; however, early-acting inbreeding depression appeared to be the primary factor limiting self-fertility in all three species. Evidence for early- acting inbreeding depression included the presence and higher proportion of aborted ovules in self fruit than in outcross fruit, a correlation between levels of self and outcross seed set, and pollen chase experiments demonstrating that self-pollen does fertilize the ovules. Self-fertility in the three species was probably influenced by levels of genetic load, ploidy level and outcrossing rates.
    Type of Medium: Electronic Resource
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  • 8
    ISSN: 1365-2478
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Geosciences , Physics
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 1615-6110
    Keywords: Angiosperms ; Malvaceae ; Hibiscus acetosella ; H. asper ; H. surattensis ; H. radiatus ; andH. cannabinus ; Allopolyploidy ; evolution of dosage compensation ; alcohol dehydrogenase ; malate dehydrogenase ; leucine aminopeptidase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Mature seeds of diploid and tetraploidHibiscus species were analyzed for enzyme activity (alcohol dehydrogenase, malate dehydrogenase, leucine aminopeptidase), total protein content, DNA amount and dry weight. The recently formed tetraploid,H. radiatus, generally had enzyme and protein levels very similar to the sum of its progenitors, while the more ancient speciesH. acetosella had several lower levels. This difference may reflect the greater amount of timeH. acetosella has had to evolve dosage compensations.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    [s.l.] : Nature Publishing Group
    Nature 355 (1992), S. 28-28 
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] SIR - Nelson et al.1 attempt to bring needed objectivity to an examination of the evolution of marine87Sr/86Sr near the Cretaceous/Tertiary (K/T) boundary. In our view, the complexity of their section, together with conflicts within their own biostratigraphy, invalidate their ...
    Type of Medium: Electronic Resource
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