246 research outputs found
Schematic Models for Active Nonlinear Microrheology
We analyze the nonlinear active microrheology of dense colloidal suspensions
using a schematic model of mode-coupling theory. The model describes the
strongly nonlinear behavior of the microscopic friction coefficient as a
function of applied external force in terms of a delocalization transition. To
probe this regime, we have performed Brownian dynamics simulations of a system
of quasi-hard spheres. We also analyze experimental data on hard-sphere-like
colloidal suspensions [Habdas et al., Europhys. Lett., 2004, 67, 477]. The
behavior at very large forces is addressed specifically
Bayesian shrinkage mapping of quantitative trait loci in variance component models
<p>Abstract</p> <p>Background</p> <p>In this article, I propose a model-selection-free method to map multiple quantitative trait loci (QTL) in variance component model, which is useful in outbred populations. The new method can estimate the variance of zero-effect QTL infinitely to zero, but nearly unbiased for non-zero-effect QTL. It is analogous to Xu's Bayesian shrinkage estimation method, but his method is based on allelic substitution model, while the new method is based on the variance component models.</p> <p>Results</p> <p>Extensive simulation experiments were conducted to investigate the performance of the proposed method. The results showed that the proposed method was efficient in mapping multiple QTL simultaneously, and moreover it was more competitive than the reversible jump MCMC (RJMCMC) method and may even out-perform it.</p> <p>Conclusions</p> <p>The newly developed Bayesian shrinkage method is very efficient and powerful for mapping multiple QTL in outbred populations.</p
A comprehensive review of oral glucosamine use and effects on glucose metabolism in normal and diabetic individuals
Glucosamine (GlcN) is a widely utilized dietary supplement that is used to promote joint health. Reports that oral GlcN supplementation at usual doses adversely affects glucose metabolism in subjects with impaired glucose tolerance have raised concerns that GlcN should be contraindicated in individuals with diabetes and those at risk for developing it. This review addresses its potential, when used at typical doses, to affect glucose metabolism and insulin sensitivity in healthy individuals and those with diabetes or ‘pre-diabetes’. Publicly available scientific information and data on GlcN were systematically compiled using the electronic search tool, Dialog®, and reviewed with special emphasis on human studies. In long-term clinical trials, including those containing subjects with type 2 diabetes or ‘pre-diabetes’, GlcN produced a non-significant lowering of fasting blood glucose concentrations in all groups of subjects treated for periods of up to 3 years. Owing to limitations in study design, conclusions based on studies that report adverse affects of GlcN on insulin sensitivity and glucose tolerance in pre-diabetic subjects are suspect. However, no definitive long-term studies of GlcN use for individuals with pre-diabetes are available. Nevertheless, based on available evidence, we conclude that GlcN has no effect on fasting blood glucose levels, glucose metabolism, or insulin sensitivity at any oral dose level in healthy subjects, individuals with diabetes, or those with impaired glucose tolerance
Search for short baseline nu(e) disappearance with the T2K near detector
8 pages, 6 figures, submitted to PRD rapid communication8 pages, 6 figures, submitted to PRD rapid communicationWe thank the J-PARC staff for superb accelerator performance and the CERN NA61 collaboration for providing valuable particle production data. We acknowledge the support of MEXT, Japan; NSERC, NRC and CFI, Canada; Commissariat `a l’Energie Atomique and Centre National de la Recherche Scientifique–Institut National de Physique Nucle´aire et de Physique des Particules, France; DFG, Germany; INFN, Italy; National Science Centre (NCN), Poland; Russian Science Foundation, RFBR and Ministry of Education and Science, Russia; MINECO and European Regional Development Fund, Spain; Swiss National Science Foundation and State Secretariat for Education, Research and Innovation, Switzerland; STFC, UK; and DOE, USA. We also thank CERN for the UA1/NOMAD magnet, DESY for the HERA-B magnet mover system, NII for SINET4, the WestGrid and SciNet consortia in Compute Canada, GridPP, UK. In addition participation of individual researchers and institutions has been further supported by funds from ERC (FP7), EU; JSPS, Japan; Royal Society, UK; DOE Early Career program, USA
A Computational Framework Discovers New Copy Number Variants with Functional Importance
Structural variants which cause changes in copy numbers constitute an important component of genomic variability. They account for 0.7% of genomic differences in two individual genomes, of which copy number variants (CNVs) are the largest component. A recent population-based CNV study revealed the need of better characterization of CNVs, especially the small ones (<500 bp).We propose a three step computational framework (Identification of germline Changes in Copy Number or IgC2N) to discover and genotype germline CNVs. First, we detect candidate CNV loci by combining information across multiple samples without imposing restrictions to the number of coverage markers or to the variant size. Secondly, we fine tune the detection of rare variants and infer the putative copy number classes for each locus. Last, for each variant we combine the relative distance between consecutive copy number classes with genetic information in a novel attempt to estimate the reference model bias. This computational approach is applied to genome-wide data from 1250 HapMap individuals. Novel variants were discovered and characterized in terms of size, minor allele frequency, type of polymorphism (gains, losses or both), and mechanism of formation. Using data generated for a subset of individuals by a 42 million marker platform, we validated the majority of the variants with the highest validation rate (66.7%) was for variants of size larger than 1 kb. Finally, we queried transcriptomic data from 129 individuals determined by RNA-sequencing as further validation and to assess the functional role of the new variants. We investigated the possible enrichment for variant's regulatory effect and found that smaller variants (<1 Kb) are more likely to regulate gene transcript than larger variants (p-value = 2.04e-08). Our results support the validity of the computational framework to detect novel variants relevant to disease susceptibility studies and provide evidence of the importance of genetic variants in regulatory network studies
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Localisation and origin of the bacteriochlorophyll-derived photosensitizer in the retina of the deep-sea dragon fish Malacosteus niger
Most deep-sea fish have a single visual pigment maximally sensitive at short wavelengths, approximately matching the spectrum of both downwelling sunlight and bioluminescence. However, Malcosteus niger produces far-red bioluminescence and its longwave retinal sensitivity is enhanced by red-shifted visual pigments, a longwave reflecting tapetum and, uniquely, a bacteriochlorophyllderived photosensitizer. The origin of the photosensitizer, however, remains unclear. We investigated whether the bacteriochlorophyll was produced by endosymbiotic bacteria within unusual structures adjacent to the photoreceptors that had previously been described in this species. However, microscopy, elemental analysis and SYTOX green staining provided no evidence for such localised retinal bacteria, instead the photosensitizer was shown to be distributed throughout the retina. Furthermore, comparison of mRNA from the retina of Malacosteus to that of the closely related Pachystomias microdon (which does not contain a bacterichlorophyll-derived photosensitzer) revealed no genes of bacterial origin that were specifically up-regulated in Malacosteus. Instead up-regulated Malacosteus genes were associated with photosensitivity and may relate to its unique visual ecology and the chlorophyll-based visual system. We also suggest that the unusual longwave-reflecting, astaxanthin-based, tapetum of Malacosteus may protect the retina from the potential cytotoxicity of such a system
Habitat-Mediated Facilitation and Counteracting Ecosystem Engineering Interactively Influence Ecosystem Responses to Disturbance
Recovery of an ecosystem following disturbance can be severely hampered or even shift altogether when a point disturbance exceeds a certain spatial threshold. Such scale-dependent dynamics may be caused by preemptive competition, but may also result from diminished self-facilitation due to weakened ecosystem engineering. Moreover, disturbance can facilitate colonization by engineering species that alter abiotic conditions in ways that exacerbate stress on the original species. Consequently, establishment of such counteracting engineers might reduce the spatial threshold for the disturbance, by effectively slowing recovery and increasing the risk for ecosystem shifts to alternative states. We tested these predictions in an intertidal mudflat characterized by a two-state mosaic of hummocks (humps exposed during low tide) dominated by the sediment-stabilizing seagrass Zostera noltii) and hollows (low-tide waterlogged depressions dominated by the bioturbating lugworm Arenicola marina). In contrast to expectations, seagrass recolonized both natural and experimental clearings via lateral expansion and seemed unaffected by both clearing size and lugworm addition. Near the end of the growth season, however, an additional disturbance (most likely waterfowl grazing and/or strong hydrodynamics) selectively impacted recolonizing seagrass in the largest (1 m2) clearings (regardless of lugworm addition), and in those medium (0.25 m2) clearings where lugworms had been added nearly five months earlier. Further analyses showed that the risk for the disturbance increased with hollow size, with a threshold of 0.24 m2. Hollows of that size were caused by seagrass removal alone in the largest clearings, and by a weaker seagrass removal effect exacerbated by lugworm bioturbation in the medium clearings. Consequently, a sufficiently large disturbance increased the vulnerability of recolonizing seagrass to additional disturbance by weakening seagrass engineering effects (sediment stabilization). Meanwhile, the counteracting ecosystem engineering (lugworm bioturbation) reduced that threshold size. Therefore, scale-dependent interactions between habitat-mediated facilitation, competition and disturbance seem to maintain the spatial two-state mosaic in this ecosystem
The Circadian Response of Intrinsically Photosensitive Retinal Ganglion Cells
Intrinsically photosensitive retinal ganglion cells (ipRGC) signal environmental
light level to the central circadian clock and contribute to the pupil light
reflex. It is unknown if ipRGC activity is subject to extrinsic (central) or
intrinsic (retinal) network-mediated circadian modulation during light
entrainment and phase shifting. Eleven younger persons (18–30 years) with
no ophthalmological, medical or sleep disorders participated. The activity of
the inner (ipRGC) and outer retina (cone photoreceptors) was assessed hourly
using the pupil light reflex during a 24 h period of constant environmental
illumination (10 lux). Exogenous circadian cues of activity, sleep, posture,
caffeine, ambient temperature, caloric intake and ambient illumination were
controlled. Dim-light melatonin onset (DLMO) was determined from salivary
melatonin assay at hourly intervals, and participant melatonin onset values were
set to 14 h to adjust clock time to circadian time. Here we demonstrate in
humans that the ipRGC controlled post-illumination pupil response has a
circadian rhythm independent of external light cues. This circadian variation
precedes melatonin onset and the minimum ipRGC driven pupil response occurs post
melatonin onset. Outer retinal photoreceptor contributions to the inner retinal
ipRGC driven post-illumination pupil response also show circadian variation
whereas direct outer retinal cone inputs to the pupil light reflex do not,
indicating that intrinsically photosensitive (melanopsin) retinal ganglion cells
mediate this circadian variation
Phosphatidylserine Increases IKBKAP Levels in Familial Dysautonomia Cells
Familial Dysautonomia (FD) is an autosomal recessive congenital neuropathy that results from abnormal development and progressive degeneration of the sensory and autonomic nervous system. The mutation observed in almost all FD patients is a point mutation at position 6 of intron 20 of the IKBKAP gene; this gene encodes the IκB kinase complex-associated protein (IKAP). The mutation results in a tissue-specific splicing defect: Exon 20 is skipped, leading to reduced IKAP protein expression. Here we show that phosphatidylserine (PS), an FDA-approved food supplement, increased IKAP mRNA levels in cells derived from FD patients. Long-term treatment with PS led to a significant increase in IKAP protein levels in these cells. A conjugate of PS and an omega-3 fatty acid also increased IKAP mRNA levels. Furthermore, PS treatment released FD cells from cell cycle arrest and up-regulated a significant number of genes involved in cell cycle regulation. Our results suggest that PS has potential for use as a therapeutic agent for FD. Understanding its mechanism of action may reveal the mechanism underlying the FD disease
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