Crystal chemistry and electronic properties of the n=2 Ruddlesden-Popper manganates: unconventional CMR materials

The crystallography and electronic properties of the Ln[sub 2- x]Sr[sub 1+x]Mn[sub 2]O[sub 7] manganese oxides adopting the n=2 Ruddlesden-Popper (RP) structure are discussed, focusing on the structural phase diagrams and electronic properties in the vicinity of the Mn +3.5 oxidation state and in particular the ease of synthesis of single phases of these materials

Magnetic field and chromospheric activity evolution of HD 75332 : a rapid magnetic cycle in an F star without a hot Jupiter

ELB is supported by an Australian Government Research Training Program (RTP) Scholarship. SJ acknowledges the support of the German Science Foundation (DFG) Research Unit FOR2544 ‘Blue Planets around Red Stars’ (project JE 701/3-1) and DFG priority program SPP 1992 ‘Exploring the Diversity of Extrasolar Planets’ (JE 701/5-1). AAV acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 817540, ASTROFLOW). VS acknowledges funding from the European Research Council (ERC) under the European Unions Horizon 2020 research and innovation programme (grant agreement No. 682393 AWESoMeStars).Studying cool star magnetic activity gives an important insight into the stellar dynamo and its relationship with stellar properties, as well as allowing us to place the Sun’s magnetism in the context of other stars. Only 61 Cyg A (K5V) and τ Boo (F8V) are currently known to have magnetic cycles like the Sun’s, where the large-scale magnetic field polarity reverses in phase with the star’s chromospheric activity cycles. τ Boo has a rapid ∼240 d magnetic cycle, and it is not yet clear whether this is related to the star’s thin convection zone or if the dynamo is accelerated by interactions between τ Boo and its hot Jupiter. To shed light on this, we studied the magnetic activity of HD 75332 (F7V) which has similar physical properties to τ Boo and does not appear to host a hot Jupiter. We characterized its long term chromospheric activity variability over 53 yrs and used Zeeman Doppler Imaging to reconstruct the large-scale surface magnetic field for 12 epochs between 2007 and 2019. Although we observe only one reversal of the large-scale magnetic dipole, our results suggest that HD 75332 has a rapid ∼1.06 yr solar-like magnetic cycle where the magnetic field evolves in phase with its chromospheric activity. If a solar-like cycle is present, reversals of the large-scale radial field polarity are expected to occur at around activity cycle maxima. This would be similar to the rapid magnetic cycle observed for τ Boo, suggesting that rapid magnetic cycles may be intrinsic to late-F stars and related to their shallow convection zones.Publisher PDFPeer reviewe

Interplay of spin and orbital ordering in the layered colossal magnetoresistance manganite La2-2xSr1+2xMn2O7 (0.5<=x<=1.0)

The crystallographic and magnetic phase diagram of the n=2 layered manganite La2-2xSr1+2xMn2O7 in the region x=>0.5 has been studied using temperature dependent neutron powder diffraction. The magnetic phase diagram reveals a progression of ordered magnetic structures generally paralleling that of 3-D perovskites with similar electronic doping: A (0.5 C (0.75 G (0.90<=x<=1.0). However, the quasi-2-D structure amplifies this progression to expose features of manganite physics uniquely accessible in the layered systems: (a) a "frustrated" region between the A and C regimes where no long-range magnetic order is observed; (b) magnetic polytypism arising from weak inter-bilayer magnetic exchange in the Type-C regime; and (c) a tetragonal to orthorhombic phase transition whose temperature evolution directly measures ordering of d3y2-r2 orbitals in the a-b plane. This orbital-ordering transition is precursory to Type-C magnetic ordering, where ferromagnetic rods lie parallel to the b-axis. These observations support the notion that eg orbital polarisation is the driving force behind magnetic spin ordering. Finally, in the crossover region between Type-C and Type-G states, we see some evidence for the development of local Type-C clusters embedded in a Type-G framework, directly addressing proposals of similar short-range magnetic ordering in highly-doped La1-xCaxMnO3 perovskites.Comment: 32 pages, 13 figures, submitted to Phys. Rev.

Annotation of the Drosophila melanogaster euchromatic genome: a systematic review

BACKGROUND: The recent completion of the Drosophila melanogaster genomic sequence to high quality and the availability of a greatly expanded set of Drosophila cDNA sequences, aligning to 78% of the predicted euchromatic genes, afforded FlyBase the opportunity to significantly improve genomic annotations. We made the annotation process more rigorous by inspecting each gene visually, utilizing a comprehensive set of curation rules, requiring traceable evidence for each gene model, and comparing each predicted peptide to SWISS-PROT and TrEMBL sequences. RESULTS: Although the number of predicted protein-coding genes in Drosophila remains essentially unchanged, the revised annotation significantly improves gene models, resulting in structural changes to 85% of the transcripts and 45% of the predicted proteins. We annotated transposable elements and non-protein-coding RNAs as new features, and extended the annotation of untranslated (UTR) sequences and alternative transcripts to include more than 70% and 20% of genes, respectively. Finally, cDNA sequence provided evidence for dicistronic transcripts, neighboring genes with overlapping UTRs on the same DNA sequence strand, alternatively spliced genes that encode distinct, non-overlapping peptides, and numerous nested genes. CONCLUSIONS: Identification of so many unusual gene models not only suggests that some mechanisms for gene regulation are more prevalent than previously believed, but also underscores the complex challenges of eukaryotic gene prediction. At present, experimental data and human curation remain essential to generate high-quality genome annotations

Virtual Fly Brain—An interactive atlas of the Drosophila nervous system

As a model organism, Drosophila is uniquely placed to contribute to our understanding of how brains control complex behavior. Not only does it have complex adaptive behaviors, but also a uniquely powerful genetic toolkit, increasingly complete dense connectomic maps of the central nervous system and a rapidly growing set of transcriptomic profiles of cell types. But this also poses a challenge: Given the massive amounts of available data, how are researchers to Find, Access, Integrate and Reuse (FAIR) relevant data in order to develop an integrated anatomical and molecular picture of circuits, inform hypothesis generation, and find reagents for experiments to test these hypotheses? The Virtual Fly Brain (virtualflybrain.org) web application &amp; API provide a solution to this problem, using FAIR principles to integrate 3D images of neurons and brain regions, connectomics, transcriptomics and reagent expression data covering the whole CNS in both larva and adult. Users can search for neurons, neuroanatomy and reagents by name, location, or connectivity, via text search, clicking on 3D images, search-by-image, and queries by type (e.g., dopaminergic neuron) or properties (e.g., synaptic input in the antennal lobe). Returned results include cross-registered 3D images that can be explored in linked 2D and 3D browsers or downloaded under open licenses, and extensive descriptions of cell types and regions curated from the literature. These solutions are potentially extensible to cover similar atlasing and data integration challenges in vertebrates

Alliance of Genome Resources Portal: unified model organism research platform

The Alliance of Genome Resources (Alliance) is a consortium of the major model organism databases and the Gene Ontology that is guided by the vision of facilitating exploration of related genes in human and well-studied model organisms by providing a highly integrated and comprehensive platform that enables researchers to leverage the extensive body of genetic and genomic studies in these organisms. Initiated in 2016, the Alliance is building a central portal (www.alliancegenome.org) for access to data for the primary model organisms along with gene ontology data and human data. All data types represented in the Alliance portal (e.g. genomic data and phenotype descriptions) have common data models and workflows for curation. All data are open and freely available via a variety of mechanisms. Long-term plans for the Alliance project include a focus on coverage of additional model organisms including those without dedicated curation communities, and the inclusion of new data types with a particular focus on providing data and tools for the non-model-organism researcher that support enhanced discovery about human health and disease. Here we review current progress and present immediate plans for this new bioinformatics resource

Alliance of Genome Resources Portal: unified model organism research platform

The Alliance of Genome Resources (Alliance) is a consortium of the major model organism databases and the Gene Ontology that is guided by the vision of facilitating exploration of related genes in human and well-studied model organisms by providing a highly integrated and comprehensive platform that enables researchers to leverage the extensive body of genetic and genomic studies in these organisms. Initiated in 2016, the Alliance is building a central portal (www.alliancegenome.org) for access to data for the primary model organisms along with gene ontology data and human data. All data types represented in the Alliance portal (e.g. genomic data and phenotype descriptions) have common data models and workflows for curation. All data are open and freely available via a variety of mechanisms. Long-term plans for the Alliance project include a focus on coverage of additional model organisms including those without dedicated curation communities, and the inclusion of new data types with a particular focus on providing data and tools for the non-model-organism researcher that support enhanced discovery about human health and disease. Here we review current progress and present immediate plans for this new bioinformatics resource

Structural and magnetic states in layered manganites: An expanding view of the phase diagram

Colossal magnetoresistive (CMR) manganites display a spectacular range of structural, magnetic, and electronic phases as a function of hole concentration, temperature, magnetic field, etc. A1though the bulk of research has concentrated on the 3-D perovskite manganites, the ability to study anisotropic magnetic and electronic interactions made available in reduced dimensions has accelerated interest in the layered Ruddlesden-Popper (R-P) phases of the manganite class. The quest for understanding the coupling among lattice, spin, and electronic degrees of freedom (and dimensionality) is driven by the availability of high quality materials. In this talk, the authors will present recent results on synthesis and magnetic properties of layered manganites from the La{sub 2{minus}2x}Sr{sub 1+2x}Mn{sub 2}O{sub 7} series in the Mn{sup 4+}-rich regime x &gt;0.5. This region of the composition diagram is populated by antiferromagnetic structures that evolve from the A-type layered order to G-type ''rocksalt'' order as x increases. Between these two regimes is a wide region (0.7 &lt; x &lt; 0.9) where an incommensurate magnetic structure is observed. The IC structure joins spin canting and phase separation as a mode for mixed-valent manganites to accommodate FM/AF competition. Transport in these materials is dominated by highly insulating behavior, although a region close to x = 0.5 exhibits metal-nonmetal transitions and an extreme sensitivity to oxygen content. They suggest two possible explanations for this transport behavior at doping just above x = O.5: localization by oxygen defects or charge ordering of Mn{sup 3+}/Mn{sup 4+}sites

Magnetic phase diagram of layered manganites in the highly doped regime.

The naturally layered colossal magnetoresistive (CMR) manganites La{sub 2{minus}2x}Sr{sub 1+2x}Mn{sub 2}O{sub 7} exhibit an extremely varied range of magnetic and electronic behavior over a very narrow composition range between x = 0.3 and x = 0.5. The successful synthesis in our laboratories of compounds with nominally greater than 50 percent Mn{sup 4+} concentration has now allowed the study of this heretofore unexplored region of the phase diagram. Here we present detailed neutron diffraction measurements of these compounds with doping levels 0.5 &lt; x &lt;1.0. As predicted by simple theories, the type-A layered antiferromagnetic (AF) structure is found at x{approximately}0.5 and the type-G ''rocksalt'' AF structure at x = 1.0. Between these two extremes is found a C-type structure (ferromagnetic rods parallel to b coupled antiferromagnetically to all neighboring rods) stabilized by orbital ordering of y{sup 2} states. Also in this Mn{sup 4+}-rich regime is found a region in which no long-range magnetic order is observed. We discuss how semi-empirical models can explain the variety of magnetic structures and how structural trends as a function of doping corroborate the unifying notion of a shift from in-plane to axial orbital occupation as the Mn{sup 4+} concentration is decreased