Tracing magnetism and pairing in FeTe-based systems

In order to examine the interplay between magnetism and superconductivity, we monitor the non- superconducting chalcogenide FeTe and follow its transitions under insertion of oxygen, doping with Se and vacancies of Fe using spin-polarized band structure methods (LSDA with GGA) starting from the collinear and bicollinear magnetic arrangements. We use a supercell of Fe8Te8 as our starting point so that it can capture local changes in magnetic moments. The calculated values of magnetic moments agree well with available experimental data while oxygen insertions lead to significant changes in the bicollinear or collinear magnetic moments. The total energies of these systems indicate that the collinear-derived structure is the more favorable one prior to a possible superconducting transition. Using a 8-site Betts-cluster-based lattice and the Hubbard model, we show why this structure favors electron or hole pairing and provides clues to a common understanding of charge and spin pairing in the cuprates, pnictides and chalcogenides

How Cooper pairs vanish approaching the Mott insulator in Bi2Sr2CaCu2O8+d

The antiferromagnetic ground state of copper oxide Mott insulators is achieved by localizing an electron at each copper atom in real space (r-space). Removing a small fraction of these electrons (hole doping) transforms this system into a superconducting fluid of delocalized Cooper pairs in momentum space (k-space). During this transformation, two distinctive classes of electronic excitations appear. At high energies, the enigmatic 'pseudogap' excitations are found, whereas, at lower energies, Bogoliubov quasi-particles -- the excitations resulting from the breaking of Cooper pairs -- should exist. To explore this transformation, and to identify the two excitation types, we have imaged the electronic structure of Bi2Sr2CaCu2O8+d in r-space and k-space simultaneously. We find that although the low energy excitations are indeed Bogoliubov quasi-particles, they occupy only a restricted region of k-space that shrinks rapidly with diminishing hole density. Concomitantly, spectral weight is transferred to higher energy r-space states that lack the characteristics of excitations from delocalized Cooper pairs. Instead, these states break translational and rotational symmetries locally at the atomic scale in an energy independent fashion. We demonstrate that these unusual r-space excitations are, in fact, the pseudogap states. Thus, as the Mott insulating state is approached by decreasing the hole density, the delocalized Cooper pairs vanish from k-space, to be replaced by locally translational- and rotational-symmetry-breaking pseudogap states in r-space.Comment: This is author's version. See the Nature website for the published versio

Genotype-specific responses in Atlantic salmon (Salmo salar) subject to dietary fish oil replacement by vegetable oil: a liver transcriptomic analysis

<p>Abstract</p> <p>Background</p> <p>Expansion of aquaculture is seriously limited by reductions in fish oil (FO) supply for aquafeeds. Terrestrial alternatives such as vegetable oils (VO) have been investigated and recently a strategy combining genetic selection with changes in diet formulations has been proposed to meet growing demands for aquaculture products. This study investigates the influence of genotype on transcriptomic responses to sustainable feeds in Atlantic salmon.</p> <p>Results</p> <p>A microarray analysis was performed to investigate the liver transcriptome of two family groups selected according to their estimated breeding values (EBVs) for flesh lipid content, 'Lean' or 'Fat', fed diets containing either FO or a VO blend. Diet principally affected metabolism genes, mainly of lipid and carbohydrate, followed by immune response genes. Genotype had a much lower impact on metabolism-related genes and affected mostly signalling pathways. Replacement of dietary FO by VO caused an up-regulation of long-chain polyunsaturated fatty acid biosynthesis, but there was a clear genotype effect as fatty acyl elongase (elovl2) was only up-regulated and desaturases (Δ5 fad and Δ6 fad) showed a higher magnitude of response in Lean fish, which was reflected in liver fatty acid composition. Fatty acid synthase (FAS) was also up-regulated by VO and the effect was independent of genotype. Genetic background of the fish clearly affected regulation of lipid metabolism, as PPARα and PPARβ were down-regulated by the VO diet only in Lean fish, while in Fat salmon SREBP-1 expression was up-regulated by VO. In addition, all three genes had a lower expression in the Lean family group than in the Fat, when fed VO. Differences in muscle adiposity between family groups may have been caused by higher levels of hepatic fatty acid and glycerophospholipid synthesis in the Fat fish, as indicated by the expression of FAS, 1-acyl-sn-glycerol-3-phosphate acyltransferase and lipid phosphate phosphohydrolase 2.</p> <p>Conclusions</p> <p>This study has identified metabolic pathways and key regulators that may respond differently to alternative plant-based feeds depending on genotype. Further studies are required but data suggest that it will be possible to identify families better adapted to alternative diet formulations that might be appropriate for future genetic selection programmes.</p

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research

Seven decades of hydrogeomorphological changes in a near‐natural (Sense River) and a hydropower‐regulated (Sarine River) pre‐Alpine river floodplain in Western Switzerland

This is the peer reviewed version which has been published in final form at https://doi.org/10.1002/esp.5017 . This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions.Hydropower alteration of the natural flow and sediment regime can severely degrade hydromorphology, thereby threatening biodiversity and overall ecosystem processes of rivers and their floodplains. Using sequences of aerial images, we quantified seven decades (1938/1942–2013) of spatiotemporal changes in channel and floodplain morphology, as well as changes in the physical habitats, of three floodplain river reaches of the Swiss pre‐Alps, two hydropower‐regulated and one near‐natural. In the Sarine River floodplain, within the first decades of hydropower impairment, the magnitude and frequency of flood events (Q2, Q10, Q30) decreased substantially. As a result, the area of pioneer floodplain habitats that depend on flood activity and sediment dynamic, such as bare sediments, decreased dramatically by approximately 95%. However, by 2013 vegetated areas had generally increased in comparison to the pre‐regulation period in 1943, indicating general vegetative colonization. Between 1943 and 2013, the active channel underwent essential narrowing (up to 62% width reduction in the residual flow reach) and habitat turnover rates were very low (5% of the total floodplain area changed habitat type five to six times). In contrast, from the 1950s onwards, the near‐natural floodplain of the Sense River experienced recurrent narrowing and widening, and frequent changes between bare and vegetated areas, reflecting the shifting habitat mosaic concept typical for natural floodplains. In the three reaches investigated, we found that the active floodplain width and erosion of vegetated areas were primarily controlled by medium to large floods (Q10, Q30), which combined with reduced time intervals between ordinary floods ≥ Q2 most likely mobilized streambed sediments and limited the ability of vegetation to establish itself on bare gravel bars within the parafluvial zone. These findings can contribute to restoration action plans such as controlled flooding and sediment replenishments in the Sarine and other floodplain rivers of the Alps

Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-T <inf>c</inf> superconductors

An understanding of the missing antinodal electronic excitations in the pseudogap state is essential for uncovering the physics of the underdoped cuprate high temperature superconductors. The majority of high temperature experiments performed thus far, however, have been unable to discern whether the antinodal states are rendered unobservable due to their damping, or whether they vanish due to their gapping. Here we distinguish between these two scenarios by using quantum oscillations to examine whether the small Fermi surface pocket, found to occupy only 2% of the Brillouin zone in the underdoped cuprates, exists in isolation against a majority of completely gapped density of states spanning the antinodes, or whether it is thermodynamically coupled to a background of ungapped antinodal states. We find that quantum oscillations associated with the small Fermi surface pocket exhibit a signature sawtooth waveform characteristic of an isolated two-dimensional Fermi surface pocket. This finding reveals that the antinodal states are destroyed by a hard gap that extends over the majority of the Brillouin zone, placing strong constraints on a drastic underlying origin of quasiparticle disappearance over almost the entire Brillouin zone in the pseudogap regime.Royal Society Winton Programme for the Physics of Sustainability EPSRC studentship, grant number EP/P024947/1 EPSRC Strategic Equipment Grant EP/M000524/1 European Research Council ERC Grant Agreement number 772891 Leverhulme Trust - Philip Leverhulme Prize National Key Research and Development Program of China (Grant no. 2016YFA0401704) National Science Foundation Cooperative Agreement No. DMR-1644779 State of Florida U.S. Department of Energy US DOE BES ‘Science of 100 T’ progra