Pauli's Principle in Probe Microscopy

Exceptionally clear images of intramolecular structure can be attained in dynamic force microscopy through the combination of a passivated tip apex and operation in what has become known as the "Pauli exclusion regime" of the tip-sample interaction. We discuss, from an experimentalist's perspective, a number of aspects of the exclusion principle which underpin this ability to achieve submolecular resolution. Our particular focus is on the origins, history, and interpretation of Pauli's principle in the context of interatomic and intermolecular interactions.Comment: This is a chapter from "Imaging and Manipulation of Adsorbates using Dynamic Force Microscopy", a book which is part of the "Advances in Atom and Single Molecule Machines" series published by Springer [http://www.springer.com/series/10425]. To be published late 201

Spawning rings of exceptional points out of Dirac cones

The Dirac cone underlies many unique electronic properties of graphene and topological insulators, and its band structure--two conical bands touching at a single point--has also been realized for photons in waveguide arrays, atoms in optical lattices, and through accidental degeneracy. Deformations of the Dirac cone often reveal intriguing properties; an example is the quantum Hall effect, where a constant magnetic field breaks the Dirac cone into isolated Landau levels. A seemingly unrelated phenomenon is the exceptional point, also known as the parity-time symmetry breaking point, where two resonances coincide in both their positions and widths. Exceptional points lead to counter-intuitive phenomena such as loss-induced transparency, unidirectional transmission or reflection, and lasers with reversed pump dependence or single-mode operation. These two fields of research are in fact connected: here we discover the ability of a Dirac cone to evolve into a ring of exceptional points, which we call an "exceptional ring." We experimentally demonstrate this concept in a photonic crystal slab. Angle-resolved reflection measurements of the photonic crystal slab reveal that the peaks of reflectivity follow the conical band structure of a Dirac cone from accidental degeneracy, whereas the complex eigenvalues of the system are deformed into a two-dimensional flat band enclosed by an exceptional ring. This deformation arises from the dissimilar radiation rates of dipole and quadrupole resonances, which play a role analogous to the loss and gain in parity-time symmetric systems. Our results indicate that the radiation that exists in any open system can fundamentally alter its physical properties in ways previously expected only in the presence of material loss and gain

Lysine-91 of the tetraheme c-type cytochrome CymA is essential for quinone interaction and arsenate respiration in Shewanella sp. strain ANA-3

The tetraheme c-type cytochrome, CymA, is essential for arsenate respiratory reduction in Shewanella sp. ANA-3, a model arsenate reducer. CymA is predicted to mediate electron transfer from quinols to the arsenate respiratory reductase (ArrAB). Here, we present biochemical and physiological evidence that CymA interacts with menaquinol (MQH2) substrates. Fluorescence quench titration with the MQH2 analog, 2-n-heptyl-4-hydroxyquinoline-N-oxide (HOQNO), was used to demonstrate quinol binding of E. coli cytoplasmic membranes enriched with various forms of CymA. Wild-type CymA bound HOQNO with a Kd of 0.1–1 μM. It was also shown that the redox active MQH2 analog, 2,3-dimethoxy-1,4-naphthoquinone (DMNH2), could reduce CymA in cytoplasmic membrane preparations. Based on a CymA homology model made from the NrfH tetraheme cytochrome structure, it was predicted that Lys91 would be involved in CymA-quinol interactions. CymA with a K91Q substitution showed little interaction with HOQNO. In addition, DMNH2-dependent reduction of CymA-K91Q was diminished by 45% compared to wild-type CymA. A ΔcymA ANA-3 strain containing a plasmid copy of cymA-K91Q failed to grow with arsenate as an electron acceptor. These results suggest that Lys91 is physiologically important for arsenate respiration and support the hypothesis that CymA interacts with menaquinol resulting in the reduction of the cytochrome

The Impact of NOD2 Variants on Fecal Microbiota in Crohn's Disease and Controls Without Gastrointestinal Disease.

BACKGROUND/AIMS: Current models of Crohn's disease (CD) describe an inappropriate immune response to gut microbiota in genetically susceptible individuals. NOD2 variants are strongly associated with development of CD, and NOD2 is part of the innate immune response to bacteria. This study aimed to identify differences in fecal microbiota in CD patients and non-IBD controls stratified by NOD2 genotype. METHODS: Patients with CD and non-IBD controls of known NOD2 genotype were identified from patients in previous UK IBD genetics studies and the Cambridge bioresource (genotyped/phenotyped volunteers). Individuals with known CD-associated NOD2 mutations were matched to those with wild-type genotype. We obtained fecal samples from patients in clinical remission with low fecal calprotectin (<250 µg/g) and controls without gastrointestinal disease. After extracting DNA, the V1-2 region of 16S rRNA genes were polymerase chain reaction (PCR)-amplified and sequenced. Analysis was undertaken using the mothur package. Volatile organic compounds (VOC) were also measured. RESULTS: Ninety-one individuals were in the primary analysis (37 CD, 30 bioresource controls, and 24 household controls). Comparing CD with nonIBD controls, there were reductions in bacterial diversity, Ruminococcaceae, Rikenellaceae, and Christensenellaceae and an increase in Enterobacteriaceae. No significant differences could be identified in microbiota by NOD2 genotype, but fecal butanoic acid was higher in Crohn's patients carrying NOD2 mutations. CONCLUSIONS: In this well-controlled study of NOD2 genotype and fecal microbiota, we identified no significant genotype-microbiota associations. This suggests that the changes associated with NOD2 genotype might only be seen at the mucosal level, or that environmental factors and prior inflammation are the predominant determinant of the observed dysbiosis in gut microbiota.Funding was supported by CORE, the Digestive Diseases Foundation and the Wellcome Trust [grant number 097943 to NAK, 093885 to CAL and 098051 to Alan W Walker and Julian Parkhill . Dr. Walker receives core funding support from the Scottish Government Rural and Environmental Science and Analysis Service (RESAS). We also acknowledge the NIHR Biomedical Research Centre awards to Addenbrooke’s Hospital/University of Cambridge School of Clinical Medicine and acknowledge the NIHR Newcastle Biomedical Research Centre

General framework for estimating the ultimate precision limit in noisy quantum-enhanced metrology

The estimation of parameters characterizing dynamical processes is central to science and technology. The estimation error changes with the number N of resources employed in the experiment (which could quantify, for instance, the number of probes or the probing energy). Typically, it scales as 1/N^(1/2). Quantum strategies may improve the precision, for noiseless processes, by an extra factor 1/N^(1/2). For noisy processes, it is not known in general if and when this improvement can be achieved. Here we propose a general framework for obtaining attainable and useful lower bounds for the ultimate limit of precision in noisy systems. We apply this bound to lossy optical interferometry and atomic spectroscopy in the presence of dephasing, showing that it captures the main features of the transition from the 1/N to the 1/N^(1/2) behaviour as N increases, independently of the initial state of the probes, and even with use of adaptive feedback.Comment: Published in Nature Physics. This is the revised submitted version. The supplementary material can be found at http://www.nature.com/nphys/journal/v7/n5/extref/nphys1958-s1.pd

Impact of shortened crop rotation of oilseed rape on soil and rhizosphere microbial diversity in relation to yield decline

Oilseed rape (OSR) grown in monoculture shows a decline in yield relative to virgin OSR of up to 25%, but the mechanisms responsible are unknown. A long term field experiment of OSR grown in a range of rotations with wheat was used to determine whether shifts in fungal and bacterial populations of the rhizosphere and bulk soil were associated with the development of OSR yield decline. The communities of fungi and bacteria in the rhizosphere and bulk soil from the field experiment were profiled using terminal restriction fragment length polymorphism (TRFLP) and sequencing of cloned internal transcribed spacer regions and 16S rRNA genes, respectively. OSR cropping frequency had no effect on rhizosphere bacterial communities. However, the rhizosphere fungal communities from continuously grown OSR were significantly different to those from other rotations. This was due primarily to an increase in abundance of two fungi which showed 100% and 95% DNA identity to the plant pathogens Olpidium brassicae and Pyrenochaeta lycopersici, respectively. Real-time PCR confirmed that there was significantly more of these fungi in the continuously grown OSR than the other rotations. These two fungi were isolated from the field and used to inoculate OSR and Brassica oleracea grown under controlled conditions in a glasshouse to determine their effect on yield. At high doses, Olpidium brassicae reduced top growth and root biomass in seedlings and reduced branching and subsequent pod and seed production. Pyrenochaeta sp. formed lesions on the roots of seedlings, and at high doses delayed flowering and had a negative impact on seed quantity and quality

Incidence, severity, aetiology and type of neck injury in men's amateur rugby union: a prospective cohort study

<p>Abstract</p> <p>Background</p> <p>There is a paucity of epidemiological data on neck injury in amateur rugby union populations. The objective of this study was to determine the incidence, severity, aetiology and type of neck injury in Australian men's amateur rugby union.</p> <p>Methods</p> <p>Data was collected from a cohort of 262 participants from two Australian amateur men's rugby union clubs via a prospective cohort study design. A modified version of the Rugby Union Injury Report Form for Games and Training was used by the clubs physiotherapist or chiropractor in data collection.</p> <p>Results</p> <p>The participants sustained 90 (eight recurrent) neck injuries. Exposure time was calculated at 31143.8 hours of play (12863.8 hours of match time and 18280 hours of training). Incidence of neck injury was 2.9 injuries/1000 player-hours (95%CI: 2.3, 3.6). As a consequence 69.3% neck injuries were minor, 17% mild, 6.8% moderate and 6.8% severe. Neck compression was the most frequent aetiology and was weakly associated with severity. Cervical facet injury was the most frequent neck injury type.</p> <p>Conclusions</p> <p>This is the first prospective cohort study in an amateur men's rugby union population since the inception of professionalism that presents injury rate, severity, aetiology and injury type data for neck injury. Current epidemiological data should be sought when evaluating the risks associated with rugby union football.</p

The semi-classical expansion and resurgence in gauge theories: new perturbative, instanton, bion, and renormalon effects

We study the dynamics of four dimensional gauge theories with adjoint fermions for all gauge groups, both in perturbation theory and non-perturbatively, by using circle compactification with periodic boundary conditions for the fermions. There are new gauge phenomena. We show that, to all orders in perturbation theory, many gauge groups are Higgsed by the gauge holonomy around the circle to a product of both abelian and nonabelian gauge group factors. Non-perturbatively there are monopole-instantons with fermion zero modes and two types of monopole-anti-monopole molecules, called bions. One type are "magnetic bions" which carry net magnetic charge and induce a mass gap for gauge fluctuations. Another type are "neutral bions" which are magnetically neutral, and their understanding requires a generalization of multi-instanton techniques in quantum mechanics - which we refer to as the Bogomolny-Zinn-Justin (BZJ) prescription - to compactified field theory. The BZJ prescription applied to bion-anti-bion topological molecules predicts a singularity on the positive real axis of the Borel plane (i.e., a divergence from summing large orders in peturbation theory) which is of order N times closer to the origin than the leading 4-d BPST instanton-anti-instanton singularity, where N is the rank of the gauge group. The position of the bion--anti-bion singularity is thus qualitatively similar to that of the 4-d IR renormalon singularity, and we conjecture that they are continuously related as the compactification radius is changed. By making use of transseries and Ecalle's resurgence theory we argue that a non-perturbative continuum definition of a class of field theories which admit semi-classical expansions may be possible.Comment: 112 pages, 7 figures; v2: typos corrected, discussion of supersymmetric models added at the end of section 8.1, reference adde

Climatic regions as an indicator of forest coarse and fine woody debris carbon stocks in the United States

<p>Abstract</p> <p>Background</p> <p>Coarse and fine woody debris are substantial forest ecosystem carbon stocks; however, there is a lack of understanding how these detrital carbon stocks vary across forested landscapes. Because forest woody detritus production and decay rates may partially depend on climatic conditions, the accumulation of coarse and fine woody debris carbon stocks in forests may be correlated with climate. This study used a nationwide inventory of coarse and fine woody debris in the United States to examine how these carbon stocks vary by climatic regions and variables.</p> <p>Results</p> <p>Mean coarse and fine woody debris forest carbon stocks vary by Köppen's climatic regions across the United States. The highest carbon stocks were found in regions with cool summers while the lowest carbon stocks were found in arid desert/steppes or temperate humid regions. Coarse and fine woody debris carbon stocks were found to be positively correlated with available moisture and negatively correlated with maximum temperature.</p> <p>Conclusion</p> <p>It was concluded with only medium confidence that coarse and fine woody debris carbon stocks may be at risk of becoming net emitter of carbon under a global climate warming scenario as increases in coarse or fine woody debris production (sinks) may be more than offset by increases in forest woody detritus decay rates (emission). Given the preliminary results of this study and the rather tenuous status of coarse and fine woody debris carbon stocks as either a source or sink of CO₂, further research is suggested in the areas of forest detritus decay and production.</p

Dietary soy and meat proteins induce distinct physiological and gene expression changes in rats

This study reports on a comprehensive comparison of the effects of soy and meat proteins given at the recommended level on physiological markers of metabolic syndrome and the hepatic transcriptome. Male rats were fed semi-synthetic diets for 1 wk that differed only regarding protein source, with casein serving as reference. Body weight gain and adipose tissue mass were significantly reduced by soy but not meat proteins. The insulin resistance index was improved by soy, and to a lesser extent by meat proteins. Liver triacylglycerol contents were reduced by both protein sources, which coincided with increased plasma triacylglycerol concentrations. Both soy and meat proteins changed plasma amino acid patterns. The expression of 1571 and 1369 genes were altered by soy and meat proteins respectively. Functional classification revealed that lipid, energy and amino acid metabolic pathways, as well as insulin signaling pathways were regulated differently by soy and meat proteins. Several transcriptional regulators, including NFE2L2, ATF4, Srebf1 and Rictor were identified as potential key upstream regulators. These results suggest that soy and meat proteins induce distinct physiological and gene expression responses in rats and provide novel evidence and suggestions for the health effects of different protein sources in human diets