507 research outputs found
Segregation by thermal diffusion of an intruder in a moderately dense granular fluid
A solution of the inelastic Enskog equation that goes beyond the weak
dissipation limit and applies for moderate densities is used to determine the
thermal diffusion factor of an intruder immersed in a dense granular gas under
gravity. This factor provides a segregation criterion that shows the transition
between the Brazil-nut effect (BNE) and the reverse Brazil-nut effect (RBNE) by
varying the parameters of the system (masses, sizes, density and coefficients
of restitution). The form of the phase-diagrams for the BNE/RBNE transition
depends sensitively on the value of gravity relative to the thermal gradient,
so that it is possible to switch between both states for given values of the
parameters of the system. Two specific limits are considered with detail: (i)
absence of gravity, and (ii) homogeneous temperature. In the latter case, after
some approximations, our results are consistent with previous theoretical
results derived from the Enskog equation. Our results also indicate that the
influence of dissipation on thermal diffusion is more important in the absence
of gravity than in the opposite limit. The present analysis extends previous
theoretical results derived in the dilute limit case [V. Garz\'o, Europhys.
Lett. {\bf 75}, 521 (2006)] and is consistent with the findings of some recent
experimental results.Comment: 10 figure
Segregation of granular binary mixtures by a ratchet mechanism
We report on a segregation scheme for granular binary mixtures, where the
segregation is performed by a ratchet mechanism realized by a vertically shaken
asymmetric sawtooth-shaped base in a quasi-two-dimensional box. We have studied
this system by computer simulations and found that most binary mixtures can be
segregated using an appropriately chosen ratchet, even when the particles in
the two components have the same size, and differ only in their normal
restitution coefficient or friction coefficient. These results suggest that the
components of otherwise non-segregating granular mixtures may be separated
using our method.Comment: revtex, 4 pages, 4 figures, submitte
NMR Experiments on a Three-Dimensional Vibrofluidized Granular Medium
A three-dimensional granular system fluidized by vertical container
vibrations was studied using pulsed field gradient (PFG) NMR coupled with
one-dimensional magnetic resonance imaging (MRI). The system consisted of
mustard seeds vibrated vertically at 50 Hz, and the number of layers N_ell <= 4
was sufficiently low to achieve a nearly time-independent granular fluid. Using
NMR, the vertical profiles of density and granular temperature were directly
measured, along with the distributions of vertical and horizontal grain
velocities. The velocity distributions showed modest deviations from
Maxwell-Boltzmann statistics, except for the vertical velocity distribution
near the sample bottom which was highly skewed and non-Gaussian. Data taken for
three values of N_ell and two dimensionless accelerations Gamma=15,18 were fit
to a hydrodynamic theory, which successfully models the density and temperature
profiles including a temperature inversion near the free upper surface.Comment: 14 pages, 15 figure
The Mystery of Two Straight Lines in Bacterial Genome Statistics. Release 2007
In special coordinates (codon position--specific nucleotide frequencies)
bacterial genomes form two straight lines in 9-dimensional space: one line for
eubacterial genomes, another for archaeal genomes. All the 348 distinct
bacterial genomes available in Genbank in April 2007, belong to these lines
with high accuracy. The main challenge now is to explain the observed high
accuracy. The new phenomenon of complementary symmetry for codon
position--specific nucleotide frequencies is observed. The results of analysis
of several codon usage models are presented. We demonstrate that the
mean--field approximation, which is also known as context--free, or complete
independence model, or Segre variety, can serve as a reasonable approximation
to the real codon usage. The first two principal components of codon usage
correlate strongly with genomic G+C content and the optimal growth temperature
respectively. The variation of codon usage along the third component is related
to the curvature of the mean-field approximation. First three eigenvalues in
codon usage PCA explain 59.1%, 7.8% and 4.7% of variation. The eubacterial and
archaeal genomes codon usage is clearly distributed along two third order
curves with genomic G+C content as a parameter.Comment: Significantly extended version with new data for all the 348 distinct
bacterial genomes available in Genbank in April 200
Laser ablation loading of a radiofrequency ion trap
The production of ions via laser ablation for the loading of radiofrequency
(RF) ion traps is investigated using a nitrogen laser with a maximum pulse
energy of 0.17 mJ and a peak intensity of about 250 MW/cm^2. A time-of-flight
mass spectrometer is used to measure the ion yield and the distribution of the
charge states. Singly charged ions of elements that are presently considered
for the use in optical clocks or quantum logic applications could be produced
from metallic samples at a rate of the order of magnitude 10^5 ions per pulse.
A linear Paul trap was loaded with Th+ ions produced by laser ablation. An
overall ion production and trapping efficiency of 10^-7 to 10^-6 was attained.
For ions injected individually, a dependence of the capture probability on the
phase of the RF field has been predicted. In the experiment this was not
observed, presumably because of collective effects within the ablation plume.Comment: submitted to Appl. Phys. B., special issue on ion trappin
JASP: Graphical Statistical Software for Common Statistical Designs
This paper introduces JASP, a free graphical software package for basic statistical procedures such as t tests, ANOVAs, linear regression models, and analyses of contingency tables. JASP is open-source and differentiates itself from existing open-source solutions in two ways. First, JASP provides several innovations in user interface design; specifically, results are provided immediately as the user makes changes to options, output is attractive, minimalist, and designed around the principle of progressive disclosure, and analyses can be peer reviewed without requiring a "syntax". Second, JASP provides some of the recent developments in Bayesian hypothesis testing and Bayesian parameter estimation. The ease with which these relatively complex Bayesian techniques are available in JASP encourages their broader adoption and furthers a more inclusive statistical reporting practice. The JASP analyses are implemented in R and a series of R packages
Transitions in the Horizontal Transport of Vertically Vibrated Granular Layers
Motivated by recent advances in the investigation of fluctuation-driven
ratchets and flows in excited granular media, we have carried out experimental
and simulational studies to explore the horizontal transport of granular
particles in a vertically vibrated system whose base has a sawtooth-shaped
profile. The resulting material flow exhibits novel collective behavior, both
as a function of the number of layers of particles and the driving frequency;
in particular, under certain conditions, increasing the layer thickness leads
to a reversal of the current, while the onset of transport as a function of
frequency occurs gradually in a manner reminiscent of a phase transition. Our
experimental findings are interpreted here with the help of extensive, event
driven Molecular Dynamics simulations. In addition to reproducing the
experimental results, the simulations revealed that the current may be reversed
as a function of the driving frequency as well. We also give details about the
simulations so that similar numerical studies can be carried out in a more
straightforward manner in the future.Comment: 12 pages, 18 figure
Enhancer trap lines with GFP driven by smad6b and frizzled1 regulatory sequences for the study of epithelial morphogenesis in the developing zebrafish inner ear
Live imaging in the zebrafish embryo using tissue-specific expression of fluorescent proteins can yield important insights into the mechanisms that drive sensory organ morphogenesis and cell differentiation. Morphogenesis of the semicircular canal ducts of the vertebrate inner ear requires a complex rearrangement of epithelial cells, including outgrowth, adhesion, fusion and perforation of epithelial projections to generate pillars of tissue that form the hubs of each canal. We report the insertion sites and expression patterns of two enhancer trap lines in the developing zebrafish embryo, each of which highlight different aspects of epithelial cell morphogenesis in the inner ear. A membrane-linked EGFP driven by smad6b regulatory sequences is expressed throughout the otic epithelium, most strongly on the lateral side of the ear and in the sensory cristae. A second enhancer trap line, with cytoplasmic EGFP driven by frizzled1 (fzd1) regulatory sequences, specifically marks cells of the ventral projection and pillar in the developing ear, and marginal cells in the sensory cristae, together with variable expression in the retina and epiphysis, and neurons elsewhere in the developing central nervous system. We have used a combination of methods to identify the insertion sites of these two transgenes, which were generated through random insertion, and show that Targeted Locus Amplification is a rapid and reliable method for the identification of insertion sites of randomly inserted transgenes
Systematic Reviews of Animal Experiments Demonstrate Poor Human Clinical and Toxicological Utility
The assumption that animal models are reasonably predictive of human outcomes provides the basis for their widespread use in toxicity testing and in biomedical research aimed at developing cures for human diseases. To investigate the validity of this assumption, the comprehensive Scopus biomedical bibliographic databases were searched for published systematic reviews of the human clinical or toxicological utility of animal experiments. In 20 reviews in which clinical utility was examined, the authors concluded that animal models were either significantly useful in contributing to the development of clinical interventions, or were substantially consistent with clinical outcomes, in only two cases, one of which was contentious. These included reviews of the clinical utility of experiments expected by ethics committees to lead to medical advances, of highly-cited experiments published in major journals, and of chimpanzee experiments — those involving the species considered most likely to be predictive of human outcomes. Seven additional reviews failed to clearly demonstrate utility in predicting human toxicological outcomes, such as carcinogenicity and teratogenicity. Consequently, animal data may not generally be assumed to be substantially useful for these purposes. Possible causes include interspecies differences, the distortion of outcomes arising from experimental environments and protocols, and the poor methodological quality of many animal experiments, which was evident in at least 11 reviews. No reviews existed in which the majority of animal experiments were of good methodological quality. Whilst the effects of some of these problems might be minimised with concerted effort (given their widespread prevalence), the limitations resulting from interspecies differences are likely to be technically and theoretically impossible to overcome. Non-animal models are generally required to pass formal scientific validation prior to their regulatory acceptance. In contrast, animal models are simply assumed to be predictive of human outcomes. These results demonstrate the invalidity of such assumptions. The consistent application of formal validation studies to all test models is clearly warranted, regardless of their animal, non-animal, historical, contemporary or possible future status. Likely benefits would include, the greater selection of models truly predictive of human outcomes, increased safety of people exposed to chemicals that have passed toxicity tests, increased efficiency during the development of human pharmaceuticals and other therapeutic interventions, and decreased wastage of animal, personnel and financial resources. The poor human clinical and toxicological utility of most animal models for which data exists, in conjunction with their generally substantial animal welfare and economic costs, justify a ban on animal models lacking scientific data clearly establishing their human predictivity or utility
Association of the gut microbiome with kidney function and damage in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL)
Background: The gut microbiome is altered in chronic kidney disease (CKD), potentially contributing to CKD progression and co-morbidities, but population-based studies of the gut microbiome across a wide range of kidney function and damage are lacking. Methods: In the Hispanic Community Health Study/Study of Latinos, gut microbiome was assessed by shotgun sequencing of stool (n = 2,438; 292 with suspected CKD). We examined cross-sectional associations of estimated glomerular filtration rate (eGFR), urinary albumin:creatinine (UAC) ratio, and CKD with gut microbiome features. Kidney trait-related microbiome features were interrogated for correlation with serum metabolites (n = 700), and associations of microbiome-related serum metabolites with kidney trait progression were examined in a prospective analysis (n = 3,635). Results: Higher eGFR was associated with overall gut microbiome composition, greater abundance of species from Prevotella, Faecalibacterium, Roseburia, and Eubacterium, and microbial functions related to synthesis of long-chain fatty acids and carbamoyl-phosphate. Higher UAC ratio and CKD were related to lower gut microbiome diversity and altered overall microbiome composition only in participants without diabetes. Microbiome features related to better kidney health were associated with many serum metabolites (e.g., higher indolepropionate, beta-cryptoxanthin; lower imidazole propionate, deoxycholic acids, p-cresol glucuronide). Imidazole propionate, deoxycholic acid metabolites, and p-cresol glucuronide were associated with prospective reductions in eGFR and/or increases in UAC ratio over ~6 y. Conclusions: Kidney function is a significant correlate of the gut microbiome, while the relationship of kidney damage with the gut microbiome depends on diabetes status. Gut microbiome metabolites may contribute to CKD progression
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