Inhomogeneous magnetism in single crystalline Sr3_3CuIrO6+δ_{6+\delta}: Implications to phase-separation concepts

The single crystalline form of an insulator, Sr$_3$CuIrO$_{6+\delta}$, is shown to exhibit unexpectedly more than one magnetic transition (at 5 and 19 K) with spin-glass-like magnetic susceptibility behaviour. On the basis of this finding, viz., inhomogeneous magnetism in a chemically homogeneous material, we propose that the idea of "phase- separation" described for manganites [1] is more widespread in different ways. The observed experimental features enable us to make a comparison with the predictions of a recent toy model [2] on {\it magnetic} phase separation in an insulating environment.Comment: 4 pages, 4 figure

Magnetic anomalies in the spin chain system, Sr3_3Cu1−x_{1-x}Znx_xIrO6_6

We report the results of ac and dc magnetization (M) and heat-capacity (C) measurements on the solid solution, Sr$_3$Cu$_{1-x}$Zn$_x$IrO$_6$. While the Zn end member is known to form in a rhombohedral pseudo one-dimensional K$_4$CdCl$_6$ structure with an antiferromagnetic ordering temperature of (T$_N$ =) 19 K, the Cu end member has been reported to form in a monoclinically distorted form with a Curie temperature of (T$_C$ =) 19 K. The magnetism of the Zn compound is found to be robust to synthetic conditions and is broadly consistent with the behavior known in the literature. However, we find a lower magnetic ordering temperature (T$_o$) for our Cu compound (~ 13 K), thereby suggesting that T$_o$ is sensitive to synthetic conditions. The Cu sample appears to be in a spin-glass-like state at low temperatures, judged by a frequency dependence of ac magnetic susceptibility and a broadening of the C anomaly at the onset of magnetic ordering, in sharp contrast to earlier proposals. Small applications of magnetic field, however, drive this system to ferromagnetism as inferred from the M data. Small substitutions for Cu/Zn (x = 0.75 or 0.25) significantly depress magnetic ordering; in other words, T$_o$ varies non-monotonically with x (T$_o$ ~ 6, 3 and 4 K for x = 0.25, 0.5, and 0.67 respectively). The plot of inverse susceptibility versus temperature is non-linear in the paramagnetic state as if correlations within (or among) the magnetic chains continuously vary with temperature. The results establishComment: 7 pages, 7 figures, Revte

Bottom mixed layer oxygen dynamics in the Celtic Sea

The seasonally stratified continental shelf seas are highly productive, economically important environments which are under considerable pressure from human activity. Global dissolved oxygen concentrations have shown rapid reductions in response to anthropogenic forcing since at least the middle of the twentieth century. Oxygen consumption is at the same time linked to the cycling of atmospheric carbon, with oxygen being a proxy for carbon remineralisation and the release of CO2. In the seasonally stratified seas the bottom mixed layer (BML) is partially isolated from the atmosphere and is thus controlled by interplay between oxygen consumption processes, vertical and horizontal advection. Oxygen consumption rates can be both spatially and temporally dynamic, but these dynamics are often missed with incubation based techniques. Here we adopt a Bayesian approach to determining total BML oxygen consumption rates from a high resolution oxygen time-series. This incorporates both our knowledge and our uncertainty of the various processes which control the oxygen inventory. Total BML rates integrate both processes in the water column and at the sediment interface. These observations span the stratified period of the Celtic Sea and across both sandy and muddy sediment types. We show how horizontal advection, tidal forcing and vertical mixing together control the bottom mixed layer oxygen concentrations at various times over the stratified period. Our muddy-sand site shows cyclic spring-neap mediated changes in oxygen consumption driven by the frequent resuspension or ventilation of the seabed. We see evidence for prolonged periods of increased vertical mixing which provide the ventilation necessary to support the high rates of consumption observed

DAG-informed regression modelling, agent-based modelling, and microsimulation modelling: A critical comparison of methods for causal inference

The current paradigm for causal inference in epidemiology relies primarily on the evaluation of counterfactual contrasts via statistical regression models informed by graphical causal models (often in the form of directed acyclic graphs, or DAGs) and their underlying mathematical theory. However, there have been growing calls for supplementary methods, and one such method that has been proposed is agent-based modelling due to its potential for simulating counterfactuals. However, within the epidemiological literature there currently exists a general lack of clarity regarding what exactly agent-based modelling is (and is not) and, importantly, how it differs from microsimulation modelling – perhaps its closest methodological comparator. We clarify this distinction by briefly reviewing the history of each method, which provides context for their similarities and differences, and casts light on the types of research questions that they have evolved (and thus are well-suited) to answering; we do the same for DAG-informed regression methods. The distinct historical evolutions of DAG-informed regression modelling, microsimulation modelling, and agent-based modelling have given rise to distinct features of the methods themselves, and provide a foundation for critical comparison. Not only are the three methods well-suited to addressing different types of causal questions, but in doing so they place differing levels of emphasis on fixed and random effects, and also tend to operate on different timescales and in different timeframes

Development and Applications of Fluorogen/Light-Up RNA Aptamer Pairs for RNA Detection and More.

The central role of RNA in living systems made it highly desirable to have noninvasive and sensitive technologies allowing for imaging the synthesis and the location of these molecules in living cells. This need motivated the development of small pro-fluorescent molecules called "fluorogens" that become fluorescent upon binding to genetically encodable RNAs called "light-up aptamers." Yet, the development of these fluorogen/light-up RNA pairs is a long and thorough process starting with the careful design of the fluorogen and pursued by the selection of a specific and efficient synthetic aptamer. This chapter summarizes the main design and the selection strategies used up to now prior to introducing the main pairs. Then, the vast application potential of these molecules for live-cell RNA imaging and other applications is presented and discussed.journal article2020importe

Oxygen dynamics in shelf seas sediments incorporating seasonal variability

Shelf sediments play a vital role in global biogeochemical cycling and are particularly important areas of oxygen consumption and carbon mineralisation. Total benthic oxygen uptake, the sum of diffusive and faunal mediated uptake, is a robust proxy to quantify carbon mineralisation. However, oxygen uptake rates are dynamic, due to the diagenetic processes within the sediment, and can be spatially and temporally variable. Four benthic sites in the Celtic Sea, encompassing gradients of cohesive to permeable sediments, were sampled over four cruises to capture seasonal and spatial changes in oxygen dynamics. Total oxygen uptake (TOU) rates were measured through a suite of incubation experiments and oxygen microelectrode profiles were taken across all four benthic sites to provide the oxygen penetration depth and diffusive oxygen uptake (DOU) rates. The difference between TOU and DOU allowed for quantification of the fauna mediated oxygen uptake and diffusive uptake. High resolution measurements showed clear seasonal and spatial trends, with higher oxygen uptake rates measured in cohesive sediments compared to the permeable sediment. The significant differences in oxygen dynamics between the sediment types were consistent between seasons, with increasing oxygen consumption during and after the phytoplankton bloom. Carbon mineralisation in shelf sediments is strongly influenced by sediment type and seasonality

Protein-RNA interactions: structural characteristics and hotspot amino acids

Structural information about protein-RNA complexes supports the understanding of crucial recognition processes in the cell, and it can allow the development of high affinity ligands to interfere with these processes. In this respect, the identification of amino acid hotspots is particularly important. In contrast to protein-protein interactions, in silico approaches for protein-RNA interactions lag behind in their development. Herein, we report an analysis of available protein-RNA structures. We assembled a data set of 322 crystal and NMR structures and analyzed them regarding interface properties. In addition, we describe a computational alanine-scanning approach which provides interaction scores for interface amino acids, allowing the identification of potential hotspots in protein-RNA interfaces. We have made the computational approach available as an online tool, which allows interaction scores to be calculated for any structure of a protein-RNA complex by uploading atomic coordinates to the PRI HotScore web server (https://pri-hotscore.labs.vu.nl)

Synergistic DNA- and Protein-Based Recognition Promote an RNA-Templated Bio-orthogonal Reaction

Biomolecular assemblies composed of proteins and oligonucleotides play a central role in biological processes. While in nature, oligonucleotides and proteins usually assemble via non-covalent interactions, synthetic conjugates have been developed which covalently link both modalities. The resulting peptide-oligonucleotide conjugates have facilitated novel biological applications as well as the design of functional supramolecular systems and materials. However, despite the importance of concerted protein/oligonucleotide recognition in nature, conjugation approaches have barely utilized the synergistic recognition abilities of such complexes. Herein, the structure-based design of peptide-DNA conjugates that bind RNA through Watson-Crick base pairing combined with peptide-mediated major groove recognition is reported. Two distinct conjugate families with tunable binding characteristics have been designed to adjacently bind a particular RNA sequence. In the resulting ternary complex, their peptide elements are located in proximity, a feature that was used to enable an RNA-templated click reaction. The introduced structure-based design approach opens the door to novel functional biomolecular assemblies

Potential contribution of haemoconcentration to changes in lipid parameters with empagliflozin in patients with type 2 diabetes mellitus – a post hoc analysis of pooled data from four phase III randomized clinical trials

Aims: The selective sodium-glucose cotransporter 2 inhibitor empagliflozin increases urinary glucose, sodium excretion, and urinary volume, and reduces plasma glucose in type 2 diabetes mellitus (T2DM) patients. Changes in lipids with empagliflozin have also been observed. We examined the association between changes in lipids and markers of haemoconcentration (haematocrit and serum albumin) with empagliflozin, using pooled data from four phase-3 randomized trials. Materials and Methods: T2DM patients received placebo (n = 825), empagliflozin 10 mg (n = 830) or 25 mg (n = 822) for 24 weeks. In post hoc mediation analyses, we assessed total changes in LDL-cholesterol, HDL-cholesterol, triglycerides, apolipoprotein (Apo) B, and Apo A-I, and changes in these parameters associated with, and independent of, changes in haematocrit and serum albumin at week 24 using ANCOVA models. Results: Empagliflozin versus placebo increased serum LDL-cholesterol, HDL-cholesterol, and Apo A-I, decreased triglycerides (empagliflozin 10 mg only), and (non-significantly) increased Apo B. Empagliflozin modestly increased haematocrit and serum albumin. In mediation analyses, haematocrit changes (increases) with empagliflozin were associated with significant changes (increases) in all lipid parameters, including Apo B. Except for triglycerides (non-significant), similar lipid parameter associations were observed with serum albumin changes. Haematocrit- and serum albumin-independent changes in lipids with empagliflozin were significant for HDL-cholesterol (increases), mostly significant for triglycerides (decreases), and less so for other lipid fractions. Conclusion: Haematocrit and serum albumin increases were associated with increases in lipid fractions with empagliflozin. Empagliflozin-associated changes in serum lipids, particularly LDL-cholesterol increases, may be partly due to haemoconcentration resulting from increased urinary volume and subsequent volume contraction