Exchange interactions and magnetic phases of transition metal oxides: benchmarking advanced ab initio methods

The magnetic properties of the transition metal monoxides MnO and NiO are investigated at equilibrium and under pressure via several advanced first-principles methods coupled with Heisenberg Hamiltonian MonteCarlo. The comparative first-principles analysis involves two promising beyond-local density functionals approaches, namely the hybrid density functional theory and the recently developed variational pseudo-self-interaction correction method, implemented with both plane-wave and atomic-orbital basis sets. The advanced functionals deliver a very satisfying rendition, curing the main drawbacks of the local functionals and improving over many other previous theoretical predictions. Furthermore, and most importantly, they convincingly demonstrate a degree of internal consistency, despite differences emerging due to methodological details (e.g. plane waves vs. atomic orbitals

Topology of SO(5)-monopoles and three-dimensional, stable Dirac semimetals

The band-touching points of stable, three-dimensional, Kramers-degenerate, Dirac semimetals are singularities of a five-component, unit vector field and non-Abelian, $SO(5)$-Berry's connections, whose topological classification is an important, open problem. We solve this problem by performing second homotopy classification of Berry's connections. Using Abelian projected connections, the generic planes, orthogonal to the direction of nodal separation, and lying between two Dirac points are shown to be higher-order topological insulators, which support quantized, chromo-magnetic flux or relative Chern number, and gapped, edge states. The Dirac points are identified as a pair of unit-strength, $SO(5)$- monopole and anti-monopole, where the relative Chern number jumps by $\pm 1$. Using these bulk invariants, we determine the topological universality class of different types of Dirac semimetals. We also describe a universal recipe for computing quantized, non-Abelian flux for Dirac materials from the windings of spectra of planar Wilson loops, displaying $SO(5)$-gauge invariance. With non-perturbative, analytical solutions of surface-states, we show the absence of helical Fermi arcs, and predict the fermiology and the spin-orbital textures. We also discuss the similarities and important topological distinction between the surface-states Hamiltonian and the generator of Polyakov loop of Berry's connections.Comment: 19 pages, 8 figure

Fermi-surface pockets in magnetic underdoped cuprates from first principles

Using an innovative first-principles band theory enabling the exploration of Mott-insulating magnetic cuprates, we study the Fermi surface of underdoped Y$_{1-x}$Ca$_x$Ba$_2$Cu$_3$O$_6$ in a selection of magnetically ordered and polaronic states. All phases exhibit qualitatively similar, hole-like nodal-point small pockets. Their properties (area, masses, mass sign) only partially match those extracted from recent quantum-oscillation experiments. Ab initio calculations, therefore, do not straightforwardly support a magnetic origin of quantum oscillations.Comment: 4 pages, 4 figure

Diazotroph Activity in Surface Narragansett Bay Sediments in Summer is Stimulated by Hypoxia and Organic Matter Delivery

Bacteria that carry out many processes of the nitrogen cycle inhabit estuarine sediments. Denitrification is known to be a dominant process causing estuarine sediments to behave as net nitrogen sinks. However, measurements of nitrogen fluxes in the sediments of Narragansett Bay, Rhode Island, USA, have at times revealed high rates of net nitrogen (N2) fixation. Whereas changes in primary production, in magnitude and phenology, within Narragansett Bay have been identified as possible causes for these changes in nitrogen cycling within the benthos, a factor that has not been examined thus far is seasonal hypoxia. Since anaerobic diazotrophs figure so prominently within the sediments of Narragansett Bay, we hypothesized that dissolved oxygen concentrations in the bottom waters affect their activity. In order to explore this relationship, we measured the activity of diazotrophs in the surface sediments of 3 study areas during the summers of 2013 and 2014 using the acetylene reduction assay. We explored the effects of several water quality parameters on nitrogenase activity including, among others, dissolved oxygen and chlorophyll concentrations. Our measurements of nitrogenase activity were generally low, ranging between 2 and 5 nmol ethylene g-1 d-1 but spiked to 16 nmol ethylene g-1 d-1 at an area experiencing severe hypoxia in July 2013. Our data suggest that diazotrophy in estuarine sediments is enhanced when the benthos experiences very low dissolved oxygen in conjunction with recent influxes of autochthonous organic matter. Experiments with sediment core incubations conducted in the laboratory support our hypothesis that low dissolved oxygen and organic matter additions promote N2 fixation

Milk cathelicidin and somatic cell counts in dairy goats along the course of lactation

This research communication reports the evaluation of cathelicidin in dairy goat milk for its relationship with the somatic cell count (SCC) and microbial culture results. Considering the limited performances of SCC for mastitis monitoring in goats, there is interest in evaluating alternative diagnostic tools. Cathelicidin is an antimicrobial protein involved in innate immunity of the mammary gland. In this work, half-udder milk was sampled bimonthly from a herd of 37 Alpine goats along an entire lactation and tested with the cathelicidin ELISA together with SCC and bacterial culture. Cathelicidin and SCC showed a strong correlation (r = 0.72; n = 360 milk samples). This was highest in mid-lactation (r = 0.83) and lowest in late lactation (r = 0.61), and was higher in primiparous (0.80, n = 130) than in multiparous goats (0.71, n = 230). Both markers increased with stage of lactation, but cathelicidin increased significantly less than SCC. Inaddition, peak level in late lactation was lower for cathelicidin (5.05-fold increase) than for SCC (7.64-fold increase). Twenty-one (5.8%) samples were positive to bacteriological culture, 20 for coagulase-negative staphylococci and one for Streptococcus spp.; 18 of them were positive to the cathelicidin ELISA (85.71% sensitivity). Sensitivity of SCC >500 000 and of SCC >1 000 000 cells/ml was lower (71.43 and 23.81%, respectively). Therefore, the high correlation of cathelicidin with SCC during the entire lactation, along with its lower increase in late lactation and good sensitivity indetecting intramammary infection (IMI), indicate a potential for monitoring subclinical mastitis in dairy goats. However, based on this preliminary assessment, specificity should be improved (40.41% for cathelicidin vs. 54.57 and 67.85% for SCC >500 000 and >1 000 000 cells/ml, respectively). Therefore, the application of cathelicidin for detecting goat IMI will require further investigation and optimization, especially concerning the definition of diagnostic thresholds

Proteomic changes in the milk of water buffaloes (Bubalus bubalis) with subclinical mastitis due to intramammary infection by Staphylococcus aureus and by non-aureus staphylococci

Subclinical mastitis by Staphylococcus aureus (SAU) and by non-aureus staphylococci (NAS) is a major issue in the water buffalo. To understand its impact on milk, 6 quarter samples with >3,000,000 cells/ mL (3 SAU-positive and 3 NAS-positive) and 6 culture-negative quarter samples with <50,000 cells/ mL were investigated by shotgun proteomics and label-free quantitation. A total of 1530 proteins were identified, of which 152 were significantly changed. SAU was more impacting, with 162 vs 127 differential proteins and higher abundance changes (P < 0.0005). The 119 increased proteins had mostly structural (n = 43, 28.29%) or innate immune defence functions (n = 39, 25.66%) and included vimentin, cathelicidins, histones, S100 and neutrophil granule proteins, haptoglobin, and lysozyme. The 33 decreased proteins were mainly involved in lipid metabolism (n = 13, 59.10%) and included butyrophilin, xanthine dehydrogenase/oxidase, and lipid biosynthetic enzymes. The same biological processes were significantly affected also upon STRING analysis. Cathelicidins were the most increased family, as confirmed by western immunoblotting, with a stronger reactivity in SAU mastitis. S100A8 and haptoglobin were also validated by western immunoblotting. In conclusion, we generated a detailed buffalo milk protein dataset and defined the changes occurring in SAU and NAS mastitis, with potential for improving detection (ProteomeXchange identifier PXD012355)

A variational pseudo-self-interaction correction approach: ab-initio description of correlated oxides and molecules

We present a fully variational generalization of the pseudo self-interaction correction (VPSIC) approach previously presented in two implementations based on plane-waves and atomic orbital basis set, known as PSIC and ASIC, respectively. The new method is essentially equivalent to the previous version for what concern the electronic properties, but it can be exploited to calculate total-energy derived properties as well, such as forces and structural optimization. We apply the method to a variety of test cases including both non-magnetic and magnetic correlated oxides and molecules, showing a generally good accuracy in the description of both structural and electronic properties.Comment: 23 pages, 9 tables, 16 figure

Relationship of Late Lactation Milk Somatic Cell Count and Cathelicidin with Intramammary Infection in Small Ruminants

Late lactation is a critical moment for making mastitis management decisions, but in small ruminants the reliability of diagnostic tests is typically lower at this stage. We evaluated somatic cell counts (SCC) and cathelicidins (CATH) in late lactation sheep and goat milk for their relationship with intramammary infections (IMI), as diagnosed by bacteriological culture (BC). A total of 315 sheep and 223 goat half-udder milk samples collected in the last month of lactation were included in the study. IMI prevalence was 10.79% and 15.25%, respectively, and non-aureus staphylococci were the most common finding. Taking BC as a reference, the diagnostic performance of SCC and CATH was quite different in the two species. In sheep, receiver operating characteristic (ROC) analysis produced a higher area under the curve (AUC) value for CATH than SCC (0.9041 versus 0.8829, respectively). Accordingly, CATH demonstrated a higher specificity than SCC (82.92% versus 73.67%, respectively) at comparable sensitivity (91.18%). Therefore, CATH showed a markedly superior diagnostic performance than SCC in late lactation sheep milk. In goats, AUC was <0.67 for both parameters, and CATH was less specific than SCC (61.90% versus 65.08%) at comparable sensitivity (64.71%). Therefore, both CATH and SCC performed poorly in late lactation goats. In conclusion, sheep can be screened for mastitis at the end of lactation, while goats should preferably be tested at peak lactation. In late lactation sheep, CATH should be preferred over SCC for its higher specificity, but careful cost/benefit evaluations will have to be made