Origin of ferromagnetism in Cs2_2AgF4_4: importance of Ag - F covalency

The magnetic nature of Cs$_{2}$AgF$_{4}$, an isoelectronic and isostructural analogue of La$_2$CuO$_4$, is analyzed using density functional calculations. The ground state is found to be ferromagnetic and nearly half metallic. We find strong hybridization of Ag-$d$ and F-$p$ states. Substantial moments reside on the F atoms, which is unusual for the halides and reflects the chemistry of the Ag(II) ions in this compound. This provides the mechanism for ferromagnetism, which we find to be itinerant in character, a result of a Stoner instability enhanced by Hund's coupling on the F

Fermi Velocity Spectrum and Incipient Magnetism in TiBe2

We address the origin of the incipient magnetism in TiBe$_2$ through precise first principles calculations, which overestimate the ferromagnetic tendency and therefore require correction to account for spin fluctuations. TiBe$_2$ has sharp fine structure in its electronic density of states, with a van Hove singularity only 3 meV above the Fermi level. Similarly to the isovalent weak ferromagnet ZrZn$_2$, it is flat bands along the K-W-U lines of hexagonal face of the fcc Brillouin zone make the system prone to magnetism, and more so if electrons are added. We find that the Moriya $B$ coefficient (multiplying $\frac{\omega}{q}$ in the fluctuation susceptibility $\Delta \chi(q,\omega)$) is divergent when the velocity vanishes at a point on the Fermi surface, which is very close (3 meV) to occurring in TiBe$_2$. In exploring how the FM instability (the $q$=0 Stoner enhancement is $S\approx 60$) might be suppressed by fluctuations in TiBe$_2$, we calculate that the Moriya A coefficient (of $q^2$) is negative, so $q$=0 is not the primary instability. Explicit calculation of $\chi_o(q)$ shows that its maximum occurs at the X point $(1,0,0)\frac{2\pi}{a}$; TiBe$_2$ is thus an incipient {\it anti}ferromagnet rather than ferromagnet as has been supposed. We further show that simple temperature smearing of the peak accounts for most of the temperature dependence of the susceptibility, which previously had been attributed to local moments (via a Curie-Weiss fit), and that energy dependence of the density of states also strongly affects the magnetic field variation of $\chi$

A primary breast cancer with distinct foci of estrogen receptor-alpha positive and negative cells derived from the same clonal origin as revealed by whole exome sequencing

© 2018, Springer Science+Business Media, LLC, part of Springer Nature. Background/purpose: Tumor heterogeneity is a now well-recognized phenomenon that can affect the classification, prognosis and treatment of human cancers. Heterogeneity is often described in primary breast cancers based upon histologic subtypes, hormone- and HER2-receptor status, and immunolabeling for various markers, which can be seen within a single tumor as mixed cellular populations, or as separate discrete foci. Experimental design/methods: Here, we present a case report of a patient’s primary breast cancer that had two separate but adjacent histologic components, one that was estrogen receptor (ER) positive, and the other ER negative. Each component was subjected to whole exome sequencing and compared for gene identity to determine clonal origin. Results: Using prior bioinformatic tools, we demonstrated that both the ER positive and negative components shared many variants, including passenger and driver alterations. Copy number variations also supported the two components were derived from a single common clone. Conclusions: These analyses strongly suggest that the two ER components of this patient’s breast cancer were derived from the same clonal origin. Our results have implications for the evolution of breast cancers with mixed histologies, and how they might be best managed for optimal therapy

From microarray to biology: an integrated experimental, statistical and in silico analysis of how the extracellular matrix modulates the phenotype of cancer cells

A statistically robust and biologically-based approach for analysis of microarray data is described that integrates independent biological knowledge and data with a global F-test for finding genes of interest that minimizes the need for replicates when used for hypothesis generation. First, each microarray is normalized to its noise level around zero. The microarray dataset is then globally adjusted by robust linear regression. Second, genes of interest that capture significant responses to experimental conditions are selected by finding those that express significantly higher variance than those expressing only technical variability. Clustering expression data and identifying expression-independent properties of genes of interest including upstream transcriptional regulatory elements (TREs), ontologies and networks or pathways organizes the data into a biologically meaningful system. We demonstrate that when the number of genes of interest is inconveniently large, identifying a subset of "beacon genes" representing the largest changes will identify pathways or networks altered by biological manipulation. The entire dataset is then used to complete the picture outlined by the "beacon genes." This allow construction of a structured model of a system that can generate biologically testable hypotheses. We illustrate this approach by comparing cells cultured on plastic or an extracellular matrix which organizes a dataset of over 2,000 genes of interest from a genome wide scan of transcription. The resulting model was confirmed by comparing the predicted pattern of TREs with experimental determination of active transcription factors

Pairing competition in a quasi-one-dimensional model of organic superconductors (TMTSF)2X_{2}X in magnetic field

We microscopically study the effect of the magnetic field (Zeeman splitting) on the superconducting state in a model for quasi-one-dimensional organic superconductors (TMTSF)$_{2}X$. We investigate the competition between spin singlet and spin triplet pairings and the Fulde-Ferrell-Larkin-Ovchinnikov(FFLO) state by random phase approximation. While we studied the competition by comparison with the eigenvalue of the gap equation at a fixed temperature in our previous study (Phys. Rev. Lett. \textbf{102} (2009) 016403), here we obtain both the $T_c$ for each pairing state and a phase diagram in the $T$(temperature)-$h_z$(field)-$V_y$(strength of the charge fluctuation) space. The phase diagram shows that consecutive transitions from singlet pairing to the FFLO state and further to $S_z=1$ triplet pairing can occur upon increasing the magnetic field when $2k_{F}$ charge fluctuations coexist with $2k_{F}$ spin fluctuations. In the FFLO state, the singlet d-wave and $S_{z}=0$ triplet $f$-wave components are strongly mixed especially when the charge fluctuations are strong.Comment: 11 pages, 9 figure

Exogenous glycosaminoglycans coat damaged bladder surfaces in experimentally damaged mouse bladder

BACKGROUND: Interstital cystitis is often treated with exogenous glycosaminoglycans such as heparin, chondroitin sulphate (Uracyst), hyaluronate (Cystistat) or the semi-synthetic pentosan polysulphate (Elmiron). The mechanism of action is presumed to be due to a coating of the bladder surface to replace the normally present chondroitin sulphate and heparan sulphate lost as a result of the disease. This study used fluorescent labelled chondroitin sulphate to track the distribution of glycosaminoglycans administered intravesically to mouse bladder that had been damaged on the surface. METHODS: The surfaces of mouse bladders were damaged by 3 mechanisms – trypsin, 10 mM HCl, and protamine sulphate. Texas Red-labeled chondroitin sulphate was instilled into the bladders of animals with damaged bladders and controls instilled only with saline. Bladders were harvested, frozen, and sectioned for examination by fluorescence. RESULTS: The normal mouse bladder bound a very thin layer of the labelled chondroitin sulphate on the luminal surface. Trypsin- and HCl-damaged bladders bound the labelled chondroitin sulphate extensively on the surface with little penetration into the bladder muscle. Protamine produced less overt damage, and much less labelling was seen, presumably due to loss of the label as it complexed with the protamine intercalated into the bladder surface. CONCLUSION: Glycosaminoglycan administered intravesically does bind to damaged bladder. Given that the changes seen following bladder damage resemble those seen naturally in interstitial cystitis, the mechanisms proposed for the action of these agents is consistent with a coating of damaged bladder

Microbial carbon use efficiency: accounting for population, community, and ecosystem-scale controls over the fate of metabolized organic matter

Microbial carbon use efficiency (CUE) is a critical regulator of soil organic matter dynamics and terrestrial carbon fluxes, with strong implications for soil biogeochemistry models. While ecologists increasingly appreciate the importance of CUE, its core concepts remain ambiguous: terminology is inconsistent and confusing, methods capture variable temporal and spatial scales, and the significance of many fundamental drivers remains inconclusive. Here we outline the processes underlying microbial efficiency and propose a conceptual framework that structures the definition of CUE according to increasingly broad temporal and spatial drivers where (1) CUEP reflects population-scale carbon use efficiency of microbes governed by species-specific metabolic and thermodynamic constraints, (2) CUEC defines community-scale microbial efficiency as gross biomass production per unit substrate taken up over short time scales, largely excluding recycling of microbial necromass and exudates, and (3) CUEE reflects the ecosystem-scale efficiency of net microbial biomass production (growth) per unit substrate taken up as iterative breakdown and recycling of microbial products occurs. CUEE integrates all internal and extracellular constraints on CUE and hence embodies an ecosystem perspective that fully captures all drivers of microbial biomass synthesis and decay. These three definitions are distinct yet complementary, capturing the capacity for carbon storage in microbial biomass across different ecological scales. By unifying the existing concepts and terminology underlying microbial efficiency, our framework enhances data interpretation and theoretical advances

Fungal and Bacterial Communities Exhibit Consistent Responses to Reversal of Soil Acidification and Phosphorus Limitation over Time

Chronic acid deposition affects many temperate hardwood forests of the northeastern United States, reduces soil pH and phosphorus (P) availability, and can alter the structure and function of soil microbial communities. The strategies that microorganisms possess for survival in acidic, low P soil come at a carbon (C) cost. Thus, how microbial communities respond to soil acidification in forests may be influenced by plant phenological stage as C allocation belowground varies; however, this remains largely unexplored. In this study, we examined microbial communities in an ecosystem level manipulative experiment where pH and/or P availability were elevated in three separate forests in Northeastern Ohio. Tag-encoded pyrosequencing was used to examine bacterial and fungal community structure at five time points across one year corresponding to plant phenological stages. We found significant effects of pH treatment and time on fungal and bacterial communities in soil. However, we found no interaction between pH treatment and time of sampling for fungal communities and only a weak interaction between pH elevation and time for bacterial communities, suggesting that microbial community responses to soil pH are largely independent of plant phenological stage. In addition, fungal communities were structured largely by site, suggesting that fungi were responding to differences between the forests, such as plant community differences