2,509 research outputs found
Diet tracing in ecology: Method comparison and selection
1. Determining diet is a key prerequisite for understanding species interactions, food web structure and ecological dynamics. In recent years, there has been considerable development in both the methodology and application of novel and more traditional dietary tracing methods, yet there is no comprehensive synthesis that systematically and quantitatively compares among the different approaches. 2. Here we conceptualize diet tracing in ecology, provide recommendations for method selection, and illustrate the advantages of method integration. We summarize empirical evidence on how different methods quantify diet mixtures, by contrasting estimates of dietary proportions from multiple methods applied to the same consumer-resource datasets, or from experimental studies with known diet compositions. 3. Our data synthesis revealed an urgent need for more experiential comparisons among the dietary methods. The comparison of diet quantifications from field observations showed that different techniques aligned well in cases with less than six diet items, but diverged considerably when applied to more complex diet mixtures. 4. Efforts are ongoing to further advance dietary estimation, including how reliably compound specific stable isotope analyses and fatty acid profiles can quantify more prey items than bulk stable isotope analyses. Similarly, DNA analyses, which can depict trophic interactions at a higher resolution than any other methods, are generating new ways to better quantify diets and differentiate among life-stages of prey. Such efforts, combined with more empirical testing of each dietary method and establishment of open data repositories for dietary data, promise to greatly advance community and ecosystem ecology
Hour-glass magnetic spectrum in an insulating, hole-doped antiferromagnet
Superconductivity in layered copper-oxide compounds emerges when charge
carriers are added to antiferromagnetically-ordered CuO2 layers. The carriers
destroy the antiferromagnetic order, but strong spin fluctuations persist
throughout the superconducting phase and are intimately linked to
super-conductivity. Neutron scattering measurements of spin fluctuations in
hole-doped copper oxides have revealed an unusual `hour-glass' feature in the
momentum-resolved magnetic spectrum, present in a wide range of superconducting
and non-superconducting materials. There is no widely-accepted explanation for
this feature. One possibility is that it derives from a pattern of alternating
spin and charge stripes, an idea supported by measurements on stripe-ordered
La1.875Ba0.125CuO4. However, many copper oxides without stripe order also
exhibit an hour-glass spectrum$. Here we report the observation of an
hour-glass magnetic spectrum in a hole-doped antiferromagnet from outside the
family of superconducting copper oxides. Our system has stripe correlations and
is an insulator, which means its magnetic dynamics can conclusively be ascribed
to stripes. The results provide compelling evidence that the hour-glass
spectrum in the copper-oxide superconductors arises from fluctuating stripes.Comment: 13 pages, 4 figures, to appear in Natur
The connection between superconducting phase correlations and spin excitations in YBaCuO: A magnetic field study
One of the most striking universal properties of the
high-transition-temperature (high-) superconductors is that they are all
derived from the hole-doping of their insulating antiferromagnetic (AF) parent
compounds. From the outset, the intimate relationship between magnetism and
superconductivity in these copper-oxides has intrigued researchers. Evidence
for this link comes from neutron scattering experiments that show the
unambiguous presence of short-range AF correlations (excitations) in cuprate
superconductors. Even so, the role of such excitations in the pairing mechanism
and superconductivity is still a subject of controversy. For
YBaCuO, where controls the hole-doping level, the most
prominent feature in the magnetic excitations spectra is the ``resonance''.
Here we show that for underdoped YBaCuO, where and
are below the optimal values, modest magnetic fields suppress the resonance
significantly, much more so for fields approximately perpendicular rather than
parallel to the CuO planes. Our results indicate that the resonance
measures pairing and phase coherence, suggesting that magnetism plays an
important role in the superconductivity of cuprates. The persistence of a field
effect above favors mechanisms with preformed pairs in the normal state
of underdoped cuprates.Comment: 12 pages, 4 figures, Nature (in press
Dynamic and physical clustering of gene expression during epidermal barrier formation in differentiating keratinocytes.
The mammalian epidermis is a continually renewing structure that provides the interface between the organism and an innately hostile environment. The keratinocyte is its principal cell. Keratinocyte proteins form a physical epithelial barrier, protect against microbial damage, and prepare immune responses to danger. Epithelial immunity is disordered in many common diseases and disordered epithelial differentiation underlies many cancers. In order to identify the genes that mediate epithelial development we used a tissue model of the skin derived from primary human keratinocytes. We measured global gene expression in triplicate at five times over the ten days that the keratinocytes took to fully differentiate. We identified 1282 gene transcripts that significantly changed during differentiation (false discovery rate <0.01%). We robustly grouped these transcripts by K-means clustering into modules with distinct temporal expression patterns, shared regulatory motifs, and biological functions. We found a striking cluster of late expressed genes that form the structural and innate immune defences of the epithelial barrier. Gene Ontology analyses showed that undifferentiated keratinocytes were characterised by genes for motility and the adaptive immune response. We systematically identified calcium-binding genes, which may operate with the epidermal calcium gradient to control keratinocyte division during skin repair. The results provide multiple novel insights into keratinocyte biology, in particular providing a comprehensive list of known and previously unrecognised major components of the epidermal barrier. The findings provide a reference for subsequent understanding of how the barrier functions in health and disease
Can Antiviral Drugs Contain Pandemic Influenza Transmission?
Antiviral drugs dispensed during the 2009 influenza pandemic generally failed to
contain transmission. This poses the question of whether preparedness for a
future pandemic should include plans to use antiviral drugs to mitigate
transmission
Measuring the effect of enhanced cleaning in a UK hospital : a prospective cross-over study
Increasing hospital-acquired infections have generated much attention over the last decade. There is evidence that hygienic cleaning has a role in the control of hospital-acquired infections. This study aimed to evaluate the potential impact of one additional cleaner by using microbiological standards based on aerobic colony counts and the presence of Staphylococcus aureus including meticillin-resistant S. aureus. We introduced an additional cleaner into two matched wards from Monday to Friday, with each ward receiving enhanced cleaning for six months in a cross-over design. Ten hand-touch sites on both wards were screened weekly using standardised methods and patients were monitored for meticillin-resistant S. aureus infection throughout the year-long study. Patient and environmental meticillin-resistant S. aureus isolates were characterised using molecular methods in order to investigate temporal and clonal relationships. Enhanced cleaning was associated with a 32.5% reduction in levels of microbial contamination at handtouch sites when wards received enhanced cleaning (P < 0.0001: 95% CI 20.2%, 42.9%). Near-patient sites (lockers, overbed tables and beds) were more frequently contaminated with meticillin-resistant S. aureus/S. aureus than sites further from the patient (P = 0.065). Genotyping identified indistinguishable strains from both handtouch sites and patients. There was a 26.6% reduction in new meticillin-resistant S. aureus infections on the wards receiving extra cleaning, despite higher meticillin-resistant S. aureus patient-days and bed occupancy rates during enhanced cleaning periods (P = 0.032: 95% CI 7.7%, 92.3%). Adjusting for meticillin-resistant S. aureus patient-days and based upon nine new meticillin-resistant S. aureus infections seen during routine cleaning, we expected 13 new infections during enhanced cleaning periods rather than the four that actually occurred. Clusters of new meticillin-resistant S. aureus infections were identified 2 to 4 weeks after the cleaner left both wards. Enhanced cleaning saved the hospital £30,000 to £70,000.Introducing one extra cleaner produced a measurable effect on the clinical environment, with apparent benefit to patients regarding meticillin-resistant S. aureus infection. Molecular epidemiological methods supported the possibility that patients acquired meticillin-resistant S. aureus from environmental sources. These findings suggest that additional research is warranted to further clarify the environmental, clinical and economic impact of enhanced hygienic cleaning as a component in the control of hospital-acquired infection
Measuring Black Hole Formations by Entanglement Entropy via Coarse-Graining
We argue that the entanglement entropy offers us a useful coarse-grained
entropy in time-dependent AdS/CFT. We show that the total von-Neumann entropy
remains vanishing even when a black hole is created in a gravity dual, being
consistent with the fact that its corresponding CFT is described by a
time-dependent pure state. We analytically calculate the time evolution of
entanglement entropy for a free Dirac fermion on a circle following a quantum
quench. This is interpreted as a toy holographic dual of black hole creations
and annihilations. It is manifestly free from the black hole information
problem.Comment: 25 pages, Latex, 8 figure
Could the clinical interpretability of subgroups detected using clustering methods be improved by using a novel two-stage approach?
Background: Recognition of homogeneous subgroups of patients can usefully improve prediction of their outcomes and the targeting of treatment. There are a number of research approaches that have been used to recognise homogeneity in such subgroups and to test their implications. One approach is to use statistical clustering techniques, such as Cluster Analysis or Latent Class Analysis, to detect latent relationships between patient characteristics. Influential patient characteristics can come from diverse domains of health, such as pain, activity limitation, physical impairment, social role participation, psychological factors, biomarkers and imaging. However, such 'whole person' research may result in data-driven subgroups that are complex, difficult to interpret and challenging to recognise clinically. This paper describes a novel approach to applying statistical clustering techniques that may improve the clinical interpretability of derived subgroups and reduce sample size requirements. Methods: This approach involves clustering in two sequential stages. The first stage involves clustering within health domains and therefore requires creating as many clustering models as there are health domains in the available data. This first stage produces scoring patterns within each domain. The second stage involves clustering using the scoring patterns from each health domain (from the first stage) to identify subgroups across all domains. We illustrate this using chest pain data from the baseline presentation of 580 patients. Results: The new two-stage clustering resulted in two subgroups that approximated the classic textbook descriptions of musculoskeletal chest pain and atypical angina chest pain. The traditional single-stage clustering resulted in five clusters that were also clinically recognisable but displayed less distinct differences. Conclusions: In this paper, a new approach to using clustering techniques to identify clinically useful subgroups of patients is suggested. Research designs, statistical methods and outcome metrics suitable for performing that testing are also described. This approach has potential benefits but requires broad testing, in multiple patient samples, to determine its clinical value. The usefulness of the approach is likely to be context-specific, depending on the characteristics of the available data and the research question being asked of it
Neutron Scattering and Its Application to Strongly Correlated Systems
Neutron scattering is a powerful probe of strongly correlated systems. It can
directly detect common phenomena such as magnetic order, and can be used to
determine the coupling between magnetic moments through measurements of the
spin-wave dispersions. In the absence of magnetic order, one can detect diffuse
scattering and dynamic correlations. Neutrons are also sensitive to the
arrangement of atoms in a solid (crystal structure) and lattice dynamics
(phonons). In this chapter, we provide an introduction to neutrons and neutron
sources. The neutron scattering cross section is described and formulas are
given for nuclear diffraction, phonon scattering, magnetic diffraction, and
magnon scattering. As an experimental example, we describe measurements of
antiferromagnetic order, spin dynamics, and their evolution in the
La(2-x)Ba(x)CuO(4) family of high-temperature superconductors.Comment: 31 pages, chapter for "Strongly Correlated Systems: Experimental
Techniques", edited by A. Avella and F. Mancin
Growth Factors Regulate Expression of Osteoblast‐Associated Genes
Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141995/1/jper1345.pd
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