Inhomogeneous ferromagnetism mimics signatures of the topological Hall effect in SrRuO3 films

Topological transport phenomena in magnetic materials are a major topic of current condensed matter research. One of the most widely studied phenomena is the topological Hall effect (THE), which is generated via spin-orbit interactions between conduction electrons and topological spin textures such as skyrmions. We report a comprehensive set of Hall effect and magnetization measurements on epitaxial films of the prototypical ferromagnetic metal SrRuO3 the magnetic and transport properties of which were systematically modulated by varying the concentration of Ru vacancies. We observe Hall effect anomalies that closely resemble signatures of the THE, but a quantitative analysis demonstrates that they result from inhomogeneities in the ferromagnetic magnetization caused by a nonrandom distribution of Ru vacancies. As such inhomogeneities are difficult to avoid and are rarely characterized independently, our results call into question the identification of topological spin textures in numerous prior transport studies of quantum materials, heterostructures, and devices. Firm conclusions regarding the presence of such textures must meet stringent conditions such as probes that couple directly to the noncollinear magnetization on the atomic scale

Strong-correlation effects in Born effective charges

Large values of Born effective charges are generally considered as reliable indicators of the genuine tendency of an insulator towards ferroelectric instability. However, these quantities can be very much influenced by strong electron correlation and metallic behavior, which are not exclusive properties of ferroelectric materials. In this paper we compare the Born effective charges of some prototypical ferroelectrics with those of magnetic, non-ferroelectric compounds using a novel, self-interaction free methodology that improves on the local-density approximation description of the electronic properties. We show that the inclusion of strong-correlation effects systermatically reduces the size of the Born effective charges and the electron localization lengths. Furthermore we give an interpretation of the Born effective charges in terms of band energy structure and orbital occupations which can be used as a guideline to rationalize their values in the general case.Comment: 10 pages, 4 postscript figure

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism

Screening selected myrtaceous tree species for production of essential oils in northern Queensland

Trials to identify alternative cropping options to Melaleuca alternifolia for northern Queensland essential oil growers were established at Dimbulah and Innot Hot Springs in 2001. Seed sources of Asteromyrtus symphyocarpa (1,8-cineole form), Eucalyptus staigeriana (citral), Melaleuca cajuputi subsp. cajuputi (trans-nerolidol), M. ericifolia (d-linalool), M. quinquenervia (trans-nerolidol and viridiflorol forms) and M. viridiflora (methyl cinnamate) with potential to produce commercial foliar oils were evaluated. Information was gathered on their adaptability, growth and oil yields over 49 months and 52 months (two harvests) from planting at Dimbulah and Innot Hot Springs, respectively. Of the species and chemotypes evaluated, M. quinquenervia showed potential for commercial production of trans-nerolidol, a compound used in perfumery. It had a very high survival rate (96%) and yields could be expected to improve dramatically from the average 100 kg/ha per harvest achieved in these trials with further research into selection of seed source, control of insect damage and breeding for genetic improvement. M. cajuputi subsp. cajuputi gave a similar performance to M. quinquenervia. The rarity of the trans-nerolidol form of this species and remoteness of its natural occurrence are impediments to further planting and research. E. staigeriana, with second harvest yields of ~600 kg/ha, performed exceptionally well on both sites but potential for development is limited by the ready availability of competitively priced E. staigeriana oil produced in South America. Survival of M. ericifolia ranged from 62% to 82% at 32 months (second harvest) at Innot Hot Springs and was deemed a failure at Dimbulah with poor growth and low survival, raising a major question about the suitability of this species for cultivation in the seasonally dry tropics. Planting of this species on a wider scale in northern Queensland cannot be recommended until more is known about factors affecting its survival. A. symphyocarpa and M. viridiflora were too slow-growing to warrant further consideration as potential oil-producing species at this time

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

10.1038/s41467-021-23143-7Nature Communications121329

An integrated encyclopedia of DNA elements in the human genome.

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research