Three-Dimensional Fermi Surface of Overdoped La-Based Cuprates

We present a soft x-ray angle-resolved photoemission spectroscopy study of the overdoped high-temperature superconductors La$_{2-x}$Sr$_x$CuO$_4$ and La$_{1.8-x}$Eu$_{0.2}$Sr$_x$CuO$_4$. In-plane and out-of-plane components of the Fermi surface are mapped by varying the photoemission angle and the incident photon energy. No $k_z$ dispersion is observed along the nodal direction, whereas a significant antinodal $k_z$ dispersion is identified. Based on a tight-binding parametrization, we discuss the implications for the density of states near the van-Hove singularity. Our results suggest that the large electronic specific heat found in overdoped La$_{2-x}$Sr$_x$CuO$_4$ can not be assigned to the van-Hove singularity alone. We therefore propose quantum criticality induced by a collapsing pseudogap phase as a plausible explanation for observed enhancement of electronic specific heat

Neutron powder diffraction study of NaMn2_2O4_4 and Li0.92_{0.92}Mn2_2O4_4: New insights on spin-charge-orbital ordering

The high-pressure synthesized quasi-one-dimensional compounds NaMn$_2$O$_4$ and Li$_{0.92}$Mn$_2$O$_4$ are both antiferromagnetic insulators, and here their atomic and magnetic structures were investigated using neutron powder diffraction. The present crystal structural analyses of NaMn2O4 reveal that Mn3+/Mn4+ charge-ordering state exist even at low temperature (down to 1.5 K). It is evident from one of the Mn sites shows a strongly distorted Mn3+ octahedra due to the Jahn-Teller effect. Above TN = 39 K, a two-dimensional short-range correlation is observed, as indicated by an asymmetric diffuse scattering. Below TN, two antiferromagnetic transitions are observed (i) a commensurate long-range Mn3+ spin ordering below 39 K, and (ii) an incommensurate Mn4+ spin ordering below 10 K. The commensurate magnetic structure (kC = 0.5, -0.5, 0.5) follows the magnetic anisotropy of the local easy axes of Mn3+, while the incommensurate one shows a spin-density-wave order with kIC = (0,0,0.216). For Li$_{0.92}$Mn$_2$O$_4$, on the other hand, absence of a long-range spin ordered state down to 1.5 K is confirmed.Comment: 11 pages, 8 figure

Transposase-DNA complex structures reveal mechanisms for conjugative transposition of antibiotic resistance

Conjugative transposition drives the emergence of multidrug resistance in diverse bacterial pathogens, yet the mechanisms are poorly characterized. The Tn1549 conjugative transposon propagates resistance to the antibiotic vancomycin used for severe drug-resistant infections. Here, we present four high-resolution structures of the conserved Y-transposase of Tn1549 complexed with circular transposon DNA intermediates. The structures reveal individual transposition steps and explain how specific DNA distortion and cleavage mechanisms enable DNA strand exchange with an absolute minimum homology requirement. This appears to uniquely allow Tn916-like conjugative transposons to bypass DNA homology and insert into diverse genomic sites, expanding gene transfer. We further uncover a structural regulatory mechanism that prevents premature cleavage of the transposon DNA before a suitable target DNA is found and generate a peptide antagonist that interferes with the transposase-DNA structure to block transposition. Our results reveal mechanistic principles of conjugative transposition that could help control the spread of antibiotic resistance genes

Magnetism and Ion Diffusion in Honeycomb Layered Oxide K2_2Ni2_2TeO6_6: First Time Study by Muon Spin Rotation & Neutron Scattering

In the quest of finding novel and efficient batteries, a great interest has raised in K-based honeycomb layer oxide materials both for their fundamental properties and potential applications. A key issue in the realization of efficient batteries based on such compounds, is to understand the K-ion diffusion mechanism. However, investigation of potassium-ion (K$^+$) dynamics in materials using magneto-spin properties has so far been challenging, due to its inherently weak nuclear magnetic moment, in contrast to other alkali ions such as lithium and sodium. Spin-polarised muons, having a high gyromagnetic ratio, make the muon spin rotation and relaxation ($\mu$+SR) technique ideal for probing ions dynamics in weak magneto-spin moment materials. Here we report the magnetic properties and K+ dynamics in honeycomb layered oxide material of the K$_2$Ni$_2$TeO$_6$ using $\mu$+SR measurements. Our low-temperature $\mu$+SR results together with, with complementary magnetic susceptibility, find an antiferromagnetic transition at 26 K. Further $\mu$+SR studies performed at higher temperatures reveal that potassium ions (K$^+$) become mobile above 250 K and the activation energy for the diffusion process is Ea = 121(13) meV. This is the first time that K+ dynamics in potassium-based battery materials has been measured using $\mu$+SR. Finally our results also indicate an interesting possibility that K-ion self diffusion occurs predominantly at the surface of the powder particles. This opens future possibilities for improving ion diffusion and device performance using nano-structuring.Comment: 12 pages, 12 figure

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

The InParanoid project gathers proteomes of completely sequenced eukaryotic species plus Escherichia coli and calculates pairwise ortholog relationships among them. The new release 7.0 of the database has grown by an order of magnitude over the previous version and now includes 100 species and their collective 1.3 million proteins organized into 42.7 million pairwise ortholog groups. The InParanoid algorithm itself has been revised and is now both more specific and sensitive. Based on results from our recent benchmarking of low-complexity filters in homology assignment, a two-pass BLAST approach was developed that makes use of high-precision compositional score matrix adjustment, but avoids the alignment truncation that sometimes follows. We have also updated the InParanoid web site (http://InParanoid.sbc.su.se). Several features have been added, the response times have been improved and the site now sports a new, clearer look. As the number of ortholog databases has grown, it has become difficult to compare among these resources due to a lack of standardized source data and incompatible representations of ortholog relationships. To facilitate data exchange and comparisons among ortholog databases, we have developed and are making available two XML schemas: SeqXML for the input sequences and OrthoXML for the output ortholog clusters

Integrated population models poorly estimate the demographic contribution of immigration

Estimating the contribution of demographic parameters to changes in population growth is essential for understanding why populations fluctuate. Integrated population models (IPMs) offer a possibility to estimate the contributions of additional demographic parameters, for which no data have been explicitly collected—typically immigration. Such parameters are often subsequently highlighted as important drivers of population growth. Yet, accuracy in estimating their temporal variation, and consequently their contribution to changes in population growth rate, has not been investigated. To quantify the magnitude and cause of potential biases when estimating the contribution of immigration using IPMs, we simulated data (using northern wheatear Oenanthe oenanthe population estimates) from controlled scenarios to examine potential biases and how they depend on IPM parameterization, formulation of priors, the level of temporal variation in immigration and sample size. We also used empirical data on populations with known rates of immigration: Soay sheep Ovis aries and Mauritius kestrel Falco punctatus with zero immigration and grey wolf Canis lupus in Scandinavia with near-zero immigration. IPMs strongly overestimated the contribution of immigration to changes in population growth in scenarios when immigration was simulated with zero temporal variation (proportion of variance attributed to immigration = 63% for the more constrained formulation and real sample size) and in the wild populations, where the true number of immigrants was zero or near-zero (kestrel 19.1%–98.2%, sheep 4.2%–36.1% and wolf 84.0%–99.2%). Although the estimation of the contribution of immigration in the simulation study became more accurate with increasing temporal variation and sample size, it was often not possible to distinguish between an accurate estimation from data with high temporal variation versus an overestimation from data with low temporal variation. Unrealistically, large sample sizes may be required to estimate the contribution of immigration well. To minimize the risk of overestimating the contribution of immigration (or any additional parameter) in IPMs, we recommend to: (a) look for evidence of variation in immigration before investigating its contribution to population growth, (b) simulate and model data for comparison to the real data and (c) use explicit data on immigration when possible

Evaluating the role of human papillomaviruses in conjunctival neoplasia

Mucosal, cutaneous and Epidermodysplasia verruciformis (EV)-related human papillomaviruses (HPVs) were searched by broad-spectrum PCR in 86 conjunctival neoplasia biopsies and 63 conjunctival non-neoplastic control tissue from Ugandan subjects. Seven different EV-related HPV types, including a putative new HPV, and two mucosal HPVs were detected in 25% (14 out of 56) of HIV-positive, in 10% (three out of 30) of HIV-negative conjunctival neoplasia samples, and rarely (0–1.6%) in control subjects. The absence of high-risk HPVs and the low detection frequency of EV-related HPV types in more advanced tumour stages (10%) raise doubts about their role in conjunctival carcinomas