Survival probability of Baltic larval cod in relation to spatial overlap paterns with their prey obtained from drift model studies

Temporal mismatch between the occurrence of larvae and their prey potentially affects the spatial overlap and thus the contact rates between predator and prey. This might have important consequences for growth and survival. We performed a case study investigating the influence of circulation patterns on the overlap of Baltic cod larvae with their prey. A three-dimensional hydrodynamic model was used to analyse spatio-temporally resolved drift patterns of larval Baltic cod. A coefficient of overlap between modelled larval and idealized prey distributions indicated the probability of predator–prey overlap, dependent on the hatching time of cod larvae. By performing model runs for the years 1979–1998 investigated the intra- and interannual variability of potential spatial overlap between predator and prey. Assuming uniform prey distributions, we generally found the overlap to have decreased since the mid-1980s, but with the highest variability during the 1990s. Seasonally, predator–prey overlap on the Baltic cod spawning grounds was highest in summer and lowest at the end of the cod spawning season. Horizontally variable prey distributions generally resulted in decreased overlap coefficients. Finally, we related variations in overlap patterns to the variability of Baltic cod recruitment success

Production, partial cash flows and greenhouse gas emissions of simulated dairy herds with extended lactations

The transition period is the most critical period in the lactation cycle of dairy cows. Extended lactations reduce the frequency of transition periods, the number of calves and the related labour for farmers. This study aimed to assess the impact of 2 and 4 months extended lactations on milk yield and net partial cash flow (NPCF) at herd level, and on greenhouse gas (GHG) emissions per unit of fat- and protein-corrected milk (FPCM), using a stochastic simulation model. The model simulated individual lactations for 100 herds of 100 cows with a baseline lactation length (BL), and for 100 herds with lactations extended by 2 or 4 months for all cows (All+2 and All+4), or for heifers only (H+2 and H+4). Baseline lactation length herds produced 887 t (SD: 13) milk/year. The NPCF, based on revenues for milk, surplus calves and culled cows, and costs for feed, artificial insemination, calving management and rearing of youngstock, was k€174 (SD: 4)/BL herd per year. Extended lactations reduced milk yield of the herd by 4.1% for All+2, 6.9% for All+4, 1.1% for H+2 and 2.2% for H+4, and reduced the NPCF per herd per year by k€7 for All+2, k€12 for All+4, k€2 for H+2 and k€4 for H+4 compared with BL herds. Extended lactations increased GHG emissions in CO2-equivalents per t FPCM by 1.0% for All+2, by 1.7% for All+4, by 0.2% for H+2 and by 0.4% for H+4, but this could be compensated by an increase in lifespan of dairy cows. Subsequently, production level and lactation persistency were increased to assess the importance of these aspects for the impact of extended lactations. The increase in production level and lactation persistency increased milk production of BL herds by 30%. Moreover, reductions in milk yield for All+2 and All+4 compared with BL herds were only 0.7% and 1.1% per year, and milk yield in H+2 and H+4 herds was similar to BL herds. The resulting NPCF was equal to BL for All+2 and All+4 and increased by k€1 for H+2 and H+4 due to lower costs for insemination and calving management. Moreover, GHG emissions per t FPCM were equal to BL herds or reduced (0% to -0.3%) when lactations were extended. We concluded that, depending on lactation persistency, extending lactations of dairy cows can have a positive or negative impact on the NPCF and GHG emissions of milk production.</p

Quantum Mechanics from Focusing and Symmetry

A foundation of quantum mechanics based on the concepts of focusing and symmetry is proposed. Focusing is connected to c-variables - inaccessible conceptually derived variables; several examples of such variables are given. The focus is then on a maximal accessible parameter, a function of the common c-variable. Symmetry is introduced via a group acting on the c-variable. From this, the Hilbert space is constructed and state vectors and operators are given a clear interpretation. The Born formula is proved from weak assumptions, and from this the usual rules of quantum mechanics are derived. Several paradoxes and other issues of quantum theory are discussed.Comment: 26 page

Genomic basis for RNA alterations in cancer

Transcript alterations often result from somatic changes in cancer genomes. Various forms of RNA alterations have been described in cancer, including overexpression, altered splicing and gene fusions; however, it is difficult to attribute these to underlying genomic changes owing to heterogeneity among patients and tumour types, and the relatively small cohorts of patients for whom samples have been analysed by both transcriptome and whole-genome sequencing. Here we present, to our knowledge, the most comprehensive catalogue of cancer-associated gene alterations to date, obtained by characterizing tumour transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). Using matched whole-genome sequencing data, we associated several categories of RNA alterations with germline and somatic DNA alterations, and identified probable genetic mechanisms. Somatic copy-number alterations were the major drivers of variations in total gene and allele-specific expression. We identified 649 associations of somatic single-nucleotide variants with gene expression in cis, of which 68.4% involved associations with flanking non-coding regions of the gene. We found 1,900 splicing alterations associated with somatic mutations, including the formation of exons within introns in proximity to Alu elements. In addition, 82% of gene fusions were associated with structural variants, including 75 of a new class, termed 'bridged' fusions, in which a third genomic location bridges two genes. We observed transcriptomic alteration signatures that differ between cancer types and have associations with variations in DNA mutational signatures. This compendium of RNA alterations in the genomic context provides a rich resource for identifying genes and mechanisms that are functionally implicated in cancer

The instrument suite of the European Spallation Source

An overview is provided of the 15 neutron beam instruments making up the initial instrument suite of the European Spallation Source (ESS), and being made available to the neutron user community. The ESS neutron source consists of a high-power accelerator and target station, providing a unique long-pulse time structure of slow neutrons. The design considerations behind the time structure, moderator geometry and instrument layout are presented. The 15-instrument suite consists of two small-angle instruments, two reflectometers, an imaging beamline, two single-crystal diffractometers; one for macromolecular crystallography and one for magnetism, two powder diffractometers, and an engineering diffractometer, as well as an array of five inelastic instruments comprising two chopper spectrometers, an inverse-geometry single-crystal excitations spectrometer, an instrument for vibrational spectroscopy and a high-resolution backscattering spectrometer. The conceptual design, performance and scientific drivers of each of these instruments are described. All of the instruments are designed to provide breakthrough new scientific capability, not currently available at existing facilities, building on the inherent strengths of the ESS long-pulse neutron source of high flux, flexible resolution and large bandwidth. Each of them is predicted to provide world-leading performance at an accelerator power of 2 MW. This technical capability translates into a very broad range of scientific capabilities. The composition of the instrument suite has been chosen to maximise the breadth and depth of the scientific impact o

Combination of searches for Higgs boson pairs in pp collisions at \sqrts = 13 TeV with the ATLAS detector

This letter presents a combination of searches for Higgs boson pair production using up to 36.1 fb(-1) of proton-proton collision data at a centre-of-mass energy root s = 13 TeV recorded with the ATLAS detector at the LHC. The combination is performed using six analyses searching for Higgs boson pairs decaying into the b (b) over barb (b) over bar, b (b) over barW(+)W(-), b (b) over bar tau(+)tau(-), W+W-W+W-, b (b) over bar gamma gamma and W+W-gamma gamma final states. Results are presented for non-resonant and resonant Higgs boson pair production modes. No statistically significant excess in data above the Standard Model predictions is found. The combined observed (expected) limit at 95% confidence level on the non-resonant Higgs boson pair production cross-section is 6.9 (10) times the predicted Standard Model cross-section. Limits are also set on the ratio (kappa(lambda)) of the Higgs boson self-coupling to its Standard Model value. This ratio is constrained at 95% confidence level in observation (expectation) to -5.0 &lt; kappa(lambda) &lt; 12.0 (-5.8 &lt; kappa(lambda) &lt; 12.0). In addition, limits are set on the production of narrow scalar resonances and spin-2 Kaluza-Klein Randall-Sundrum gravitons. Exclusion regions are also provided in the parameter space of the habemus Minimal Supersymmetric Standard Model and the Electroweak Singlet Model. For complete list of authors see http://dx.doi.org/10.1016/j.physletb.2019.135103</p

Searches for lepton-flavour-violating decays of the Higgs boson in s=13\sqrt{s}=13 TeV pp\mathit{pp} collisions with the ATLAS detector

This Letter presents direct searches for lepton flavour violation in Higgs boson decays, H → eτ and H → μτ , performed with the ATLAS detector at the LHC. The searches are based on a data sample of proton–proton collisions at a centre-of-mass energy √s = 13 TeV, corresponding to an integrated luminosity of 36.1 fb−1. No significant excess is observed above the expected background from Standard Model processes. The observed (median expected) 95% confidence-level upper limits on the leptonflavour-violating branching ratios are 0.47% (0.34+0.13−0.10%) and 0.28% (0.37+0.14−0.10%) for H → eτ and H → μτ , respectively.publishedVersio

Search for flavour-changing neutral currents in processes with one top quark and a photon using 81 fb⁻¹ of pp collisions at \sqrts = 13 TeV with the ATLAS experiment

A search for flavour-changing neutral current (FCNC) events via the coupling of a top quark, a photon, and an up or charm quark is presented using 81 fb−1 of proton–proton collision data taken at a centre-of-mass energy of 13 TeV with the ATLAS detector at the LHC. Events with a photon, an electron or muon, a b-tagged jet, and missing transverse momentum are selected. A neural network based on kinematic variables differentiates between events from signal and background processes. The data are consistent with the background-only hypothesis, and limits are set on the strength of the tqγ coupling in an effective field theory. These are also interpreted as 95% CL upper limits on the cross section for FCNC tγ production via a left-handed (right-handed) tuγ coupling of 36 fb (78 fb) and on the branching ratio for t→γu of 2.8×10−5 (6.1×10−5). In addition, they are interpreted as 95% CL upper limits on the cross section for FCNC tγ production via a left-handed (right-handed) tcγ coupling of 40 fb (33 fb) and on the branching ratio for t→γc of 22×10−5 (18×10−5). © 2019 The Author(s

Genomic basis for RNA alterations in cancer

Transcript alterations often result from somatic changes in cancer genomes1. Various forms of RNA alterations have been described in cancer, including overexpression2, altered splicing3 and gene fusions4; however, it is difficult to attribute these to underlying genomic changes owing to heterogeneity among patients and tumour types, and the relatively small cohorts of patients for whom samples have been analysed by both transcriptome and whole-genome sequencing. Here we present, to our knowledge, the most comprehensive catalogue of cancer-associated gene alterations to date, obtained by characterizing tumour transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)5. Using matched whole-genome sequencing data, we associated several categories of RNA alterations with germline and somatic DNA alterations, and identified probable genetic mechanisms. Somatic copy-number alterations were the major drivers of variations in total gene and allele-specific expression. We identified 649 associations of somatic single-nucleotide variants with gene expression in cis, of which 68.4% involved associations with flanking non-coding regions of the gene. We found 1,900 splicing alterations associated with somatic mutations, including the formation of exons within introns in proximity to Alu elements. In addition, 82% of gene fusions were associated with structural variants, including 75 of a new class, termed ‘bridged’ fusions, in which a third genomic location bridges two genes. We observed transcriptomic alteration signatures that differ between cancer types and have associations with variations in DNA mutational signatures. This compendium of RNA alterations in the genomic context provides a rich resource for identifying genes and mechanisms that are functionally implicated in cancer