Functional interpretation of single cell similarity maps.

We present Vision, a tool for annotating the sources of variation in single cell RNA-seq data in an automated and scalable manner. Vision operates directly on the manifold of cell-cell similarity and employs a flexible annotation approach that can operate either with or without preconceived stratification of the cells into groups or along a continuum. We demonstrate the utility of Vision in several case studies and show that it can derive important sources of cellular variation and link them to experimental meta-data even with relatively homogeneous sets of cells. Vision produces an interactive, low latency and feature rich web-based report that can be easily shared among researchers, thus facilitating data dissemination and collaboration

Effectively identifying regulatory hotspots while capturing expression heterogeneity in gene expression studies

Expression quantitative trait loci (eQTL) mapping is a tool that can systematically identify genetic variation affecting gene expression. eQTL mapping studies have shown that certain genomic locations, referred to as regulatory hotspots, may affect the expression levels of many genes. Recently, studies have shown that various confounding factors may induce spurious regulatory hotspots. Here, we introduce a novel statistical method that effectively eliminates spurious hotspots while retaining genuine hotspots. Applied to simulated and real datasets, we validate that our method achieves greater sensitivity while retaining low false discovery rates compared to previous methods

Lineage dynamics of murine pancreatic development at single-cell resolution.

Organogenesis requires the complex interactions of multiple cell lineages that coordinate their expansion, differentiation, and maturation over time. Here, we profile the cell types within the epithelial and mesenchymal compartments of the murine pancreas across developmental time using a combination of single-cell RNA sequencing, immunofluorescence, in situ hybridization, and genetic lineage tracing. We identify previously underappreciated cellular heterogeneity of the developing mesenchyme and reconstruct potential lineage relationships among the pancreatic mesothelium and mesenchymal cell types. Within the epithelium, we find a previously undescribed endocrine progenitor population, as well as an analogous population in both human fetal tissue and human embryonic stem cells differentiating toward a pancreatic beta cell fate. Further, we identify candidate transcriptional regulators along the differentiation trajectory of this population toward the alpha or beta cell lineages. This work establishes a roadmap of pancreatic development and demonstrates the broad utility of this approach for understanding lineage dynamics in developing organs

Effect of Asymmetric Anchoring Groups on Electronic Transport in Hybrid Metal/Molecule/Graphene Single Molecule Junctions.

A combined experimental and theoretical study on molecular junctions with asymmetry in both the electrode type and in the anchoring group type is presented. A scanning tunnelling microscope is used to create the "asymmetric" Au-S-(CH2 )n-COOH-graphene molecular junctions and determine their conductance. The measurements are combined with electron transport calculations based on density functional theory (DFT) to analyze the electrical conductance and its length attenuation factor from a series of junctions of different molecular length (n). These results show an unexpected trend with a rather high conductance and a smaller attenuation factor for the Au-S-(CH2 )n -COOH-graphene configuration compared to the equivalent junction with the "symmetrical" COOH contacting using the HOOC-(CH2 )n -COOH series. Owing to the effect of the graphene electrode, the attenuation factor is also smaller than the one obtained for Au/Au electrodes. These results are interpreted through the relative molecule/electrode couplings and molecular level alignments as determined with DFT calculations. In an asymmetric junction, the electrical current flows through the less resistive conductance channel, similarly to what is observed in the macroscopic regime

Anomalous Hall Effect and Skyrmion Number in Real- and Momentum-space

We study the anomalous Hall effect (AHE) for the double exchange model with the exchange coupling $|J_H|$ being smaller than the bandwidth $|t|$ for the purpose of clarifying the following unresolved and confusing issues: (i) the effect of the underlying lattice structure, (ii) the relation between AHE and the skyrmion number, (iii) the duality between real and momentum spaces, and (iv) the role of the disorder scatterings; which is more essential, $\sigma_H$ (Hall conductivity) or $\rho_H$ (Hall resistivity)? Starting from a generic expression for $\sigma_H$, we resolve all these issues and classify the regimes in the parameter space of $J_H \tau$ ($\tau$: elastic-scattering time), and $\lambda_{s}$ (length scale of spin texture). There are two distinct mechanisms of AHE; one is characterized by the real-space skyrmion-number, and the other by momentum-space skyrmion-density at the Fermi level, which work in different regimes of the parameter space.Comment: 4 pages, 1 figure, REVTe

Chirality driven anomalous Hall effect in weak coupling regime

Anomalous Hall effect arising from non-trivial spin configuration (chirality) is studied based on the $s$-$d$ model. Considering a weak coupling case, the interaction is treated perturbatively. Scattering by normal impurities is included. Chirality is shown to drive locally Hall current and leads to overall Hall effect if there is a finite uniform chirality. This contribution is independent of the conventional spin-orbit contribution and shows distinct low temperature behavior. In mesoscopic spin glasses, chirality-induced anomalous Hall effect is expected below the spin-glass transition temperature. Measurement of Hall coefficient would be useful in experimentally confirming the chirality ordering

Anomalous Hall effect in ferromagnetic semiconductors

We present a theory of the anomalous Hall effect in ferromagnetic (Mn,III)V semiconductors. Our theory relates the anomalous Hall conductance of a homogeneous ferromagnet to the Berry phase acquired by a quasiparticle wavefunction upon traversing closed paths on the spin-split Fermi surface of a ferromagnetic state. It can be applied equally well to any itinerant electron ferromagnet. The quantitative agreement between our theory and experimental data in both (In,Mn)As and (Ga,Mn)As systems suggests that this disorder independent contribution to the anomalous Hall conductivity dominates in diluted magnetic semiconductors.Comment: 4 pages, 2 figure

Magnetocrystalline Anisotropy in a Single Crystal of CeNiGe2

We report measurements on single crystals of orthorhombic CeNiGe2, which is found to exhibit highly anisotropic magnetic and transport properties. The magnetization ratio M(H//b)/M(H^b) at 2 K is observed to be about 18 at 4 T and the electrical resistivity ratio r//b/r^b is about 70 at room temperature. It is confirmed that CeNiGe2 undergoes two-step antiferromagnetic transition at 4 and 3 K, as reported for polycrystalline samples. The application of magnetic field along the b axis (the easy magnetization axis) stabilizes a ferromagnetic correlation between the Ce ions and enhances the hopping of carriers. This results in large negative magnetoresistance along the b axis.Comment: 24 pages, including 9 figure

Charge Transport in Manganites: Hopping Conduction, the Anomalous Hall Effect and Universal Scaling

The low-temperature Hall resistivity \rho_{xy} of La_{2/3}A_{1/3}MnO_3 single crystals (where A stands for Ca, Pb and Ca, or Sr) can be separated into Ordinary and Anomalous contributions, giving rise to Ordinary and Anomalous Hall effects, respectively. However, no such decomposition is possible near the Curie temperature which, in these systems, is close to metal-to-insulator transition. Rather, for all of these compounds and to a good approximation, the \rho_{xy} data at various temperatures and magnetic fields collapse (up to an overall scale), on to a single function of the reduced magnetization m=M/M_{sat}, the extremum of this function lying at m~0.4. A new mechanism for the Anomalous Hall Effect in the inelastic hopping regime, which reproduces these scaling curves, is identified. This mechanism, which is an extension of Holstein's model for the Ordinary Hall effect in the hopping regime, arises from the combined effects of the double-exchange-induced quantal phase in triads of Mn ions and spin-orbit interactions. We identify processes that lead to the Anomalous Hall Effect for localized carriers and, along the way, analyze issues of quantum interference in the presence of phonon-assisted hopping. Our results suggest that, near the ferromagnet-to-paramagnet transition, it is appropriate to describe transport in manganites in terms of carrier hopping between states that are localized due to combined effect of magnetic and non-magnetic disorder. We attribute the qualitative variations in resistivity characteristics across manganite compounds to the differing strengths of their carrier self-trapping, and conclude that both disorder-induced localization and self-trapping effects are important for transport.Comment: 29 pages, 20 figure