University of Copenhagen

About: University of Copenhagen is a education organization based out in Copenhagen, Denmark. It is known for research contribution in the topics: Population & Galaxy. The organization has 57645 authors who have published 149740 publications receiving 5903093 citations. The organization is also known as: Copenhagen University & Københavns Universitet.

STRING v10: protein–protein interaction networks, integrated over the tree of life

Abstract: The many functional partnerships and interactions that occur between proteins are at the core of cellular processing and their systematic characterization helps to provide context in molecular systems biology. However, known and predicted interactions are scattered over multiple resources, and the available data exhibit notable differences in terms of quality and completeness. The STRING database (http://string-db.org) aims to provide a critical assessment and integration of protein-protein interactions, including direct (physical) as well as indirect (functional) associations. The new version 10.0 of STRING covers more than 2000 organisms, which has necessitated novel, scalable algorithms for transferring interaction information between organisms. For this purpose, we have introduced hierarchical and self-consistent orthology annotations for all interacting proteins, grouping the proteins into families at various levels of phylogenetic resolution. Further improvements in version 10.0 include a completely redesigned prediction pipeline for inferring protein-protein associations from co-expression data, an API interface for the R computing environment and improved statistical analysis for enrichment tests in user-provided networks.

Review of Particle Physics

Abstract: The Review summarizes much of particle physics and cosmology. Using data from previous editions, plus 3,283 new measurements from 899 Japers, we list, evaluate, and average measured properties of gauge bosons and the recently discovered Higgs boson, leptons, quarks, mesons, and baryons. We summarize searches for hypothetical particles such as heavy neutrinos, supersymmetric and technicolor particles, axions, dark photons, etc. All the particle properties and search limits are listed in Summary Tables. We also give numerous tables, figures, formulae, and reviews of topics such as Supersymmetry, Extra Dimensions, Particle Detectors, Probability, and Statistics. Among the 112 reviews are many that are new or heavily revised including those on: Dark Energy, Higgs Boson Physics, Electroweak Model, Neutrino Cross Section Measurements, Monte Carlo Neutrino Generators, Top Quark, Dark Matter, Dynamical Electroweak Symmetry Breaking, Accelerator Physics of Colliders, High-Energy Collider Parameters, Big Bang Nucleosynthesis, Astrophysical Constants and Cosmological Parameters.

Planetary boundaries: Guiding human development on a changing planet

Abstract: The planetary boundaries framework defines a safe operating space for humanity based on the intrinsic biophysical processes that regulate the stability of the Earth system. Here, we revise and update the planetary boundary framework, with a focus on the underpinning biophysical science, based on targeted input from expert research communities and on more general scientific advances over the past 5 years. Several of the boundaries now have a two-tier approach, reflecting the importance of cross-scale interactions and the regional-level heterogeneity of the processes that underpin the boundaries. Two core boundaries—climate change and biosphere integrity—have been identified, each of which has the potential on its own to drive the Earth system into a new state should they be substantially and persistently transgressed.

Stable isotopes in precipitation

Abstract: In chapter 2 the isotopic fractionation of water in some simple condensation-evaporation processes are considered quantitatively on the basis of the fractionation factors given in section 1.2. The condensation temperature is an important parameter, which has got some glaciological applications. The temperature effect (the δ's decreasing with temperature) together with varying evaporation and exchange appear in the “amount effect” as high δ's in sparse rain. The relative deuterium-oxygen-18 fractionation is not quite simple. If the relative deviations from the standard water (S.M.O.W.) are called δ D and δ 18 , the best linear approximation is δ D = 8 δ 18 . Chapter 3 gives some qualitative considerations on non-equilibrium (fast) processes. Kinetic effects have heavy bearings upon the effective fractionation factors. Such effects have only been demonstrated clearly in evaporation processes, but may also influence condensation processes. The quantity d = δ D −8 δ 18 is used as an index for non-equilibrium conditions. The stable isotope data from the world wide I.A.E.A.-W.M.O. precipitation survey are discussed in chapter 4. The unweighted mean annual composition of rain at tropical island stations fits the line δ D = 4.6 δ 18 indicating a first stage equilibrium condensation from vapour evaporated in a non-equilibrium process. Regional characteristics appear in the weighted means. The Northern hemisphere continental stations, except African and Near East, fit the line δ D = 8.0 δ 18 + 10 as far as the weighted means are concerned (δ D = 8.1 δ 18 + 11 for the unweighted) corresponding to an equilibrium Rayleigh condensation from vapour, evaporated in a non-equilibrium process from S.M.O.W. The departure from equilibrium vapour seems even higher in the rest of the investigated part of the world. At most stations the δ D and varies linearily with δ 18 with a slope close to 8, only at two stations higher than 8, at several lower than 8 (mainly connected with relatively dry climates). Considerable variations in the isotopic composition of monthly precipitation occur at most stations. At low latitudes the amount effect accounts for the variations, whereas seasonal variation at high latitudes is ascribed to the temperature effect. Tokyo is an example of a mid latitude station influenced by both effects. Some possible hydrological applications are outlined in chapter 5. DOI: 10.1111/j.2153-3490.1964.tb00181.x

Second-generation PLINK: rising to the challenge of larger and richer datasets

Abstract: Background: PLINK 1 is a widely used open-source C/C++ toolset for genome-wide association studies (GWAS) and research in population genetics. However, the steady accumulation of data from imputation and whole-genome sequencing studies has exposed a strong need for faster and scalable implementations of key functions, such as logistic regression, linkage disequilibrium estimation, and genomic distance evaluation. In addition, GWAS and population-genetic data now frequently contain genotype likelihoods, phase information, and/or multiallelic variants, none of which can be represented by PLINK 1’s primary data format. Findings: To address these issues, we are developing a second-generation codebase for PLINK. The first major release from this codebase, PLINK 1.9, introduces extensive use of bit-level parallelism, O √ n -time/constant-space Hardy-Weinberg equilibrium and Fisher’s exact tests, and many other algorithmic improvements. In combination, these changes accelerate most operations by 1-4 orders of magnitude, and allow the program to handle datasets too large to fit in RAM. We have also developed an extension to the data format which adds low-overhead support for genotype likelihoods, phase, multiallelic variants, and reference vs. alternate alleles, which is the basis of our planned second release (PLINK 2.0). Conclusions: The second-generation versions of PLINK will offer dramatic improvements in performance and compatibility. For the first time, users without access to high-end computing resources can perform several essential analyses of the feature-rich and very large genetic datasets coming into use.