303 research outputs found
Formation of voids in the Universe within the Lemaitre-Tolman model
We develop models of void formation starting from a small initial fluctuation
at recombination and growing to a realistic present day density profile in
agreement with observations of voids. The model construction is an extension of
previously developed algorithms for finding a Lemaitre-Tolman metric that
evolves between two profiles of either density or velocity specified at two
times. Of the 4 profiles of concern -- those of density and velocity at
recombination and at the present day -- two can be specified and the other two
follow from the derived model. We find that, in order to reproduce the
present-day void density profiles, the initial velocity profile is more
important than the initial density profile. Extrapolation of current CMB
observations to the scales relevant to proto-voids is very uncertain. Even so,
we find that it is very difficult to make both the initial density and velocity
fluctuation amplitudes small enough, and still obtain a realistic void by
today.Comment: MN2e LaTeX style file, 17 pages, 16 figures, 22 figure files;
replecement has minor changes in reference
On the physical origin of dark matter density profiles
The radial mass distribution of dark matter haloes is investigated within the
framework of the spherical infall model. We present a new formulation of
spherical collapse including non-radial motions, and compare the analytical
profiles with a set of high-resolution N-body simulations ranging from galactic
to cluster scales. We argue that the dark matter density profile is entirely
determined by the initial conditions, which are described by only two
parameters: the height of the primordial peak and the smoothing scale. These
are physically meaningful quantities in our model, related to the mass and
formation time of the halo. Angular momentum is dominated by velocity
dispersion, and it is responsible for the shape of the density profile near the
centre. The phase-space density of our simulated haloes is well described by a
power-law profile, rho/sigma^3 = 10^{1.46\pm0.04} (rho_c/Vvir^3)
(r/Rvir)^{-1.90\pm0.05}. Setting the eccentricity of particle orbits according
to the numerical results, our model is able to reproduce the mass distribution
of individual haloes.Comment: 12 pages, 13 figures, submitted to MNRA
Recommended from our members
The ocean sampling day consortium.
Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits
Alcohol and HCV Chronic Infection Are Risk Cofactors of Type 2 Diabetes Mellitus for Hepatocellular Carcinoma in Italy
Type 2 diabetes mellitus (DM2) has been associated with hepatocellular carcinoma (HCC) development. To study this relationship, we enrolled 465 HCC patients compared with 618 Cirrhotic cases and 490 Controls. The prevalence of DM2 is significantly higher in HCC patients with an Odds Ratio of 3.12 versus Controls. In HCC cases with alcohol abuse, the frequency of DM2 is the highest. In our HCC patients, when HCV infection is associated with alcohol abuse, the liver cancer develops earlier. In addition, multivariate analysis shows that alcohol consumption is an independent risk factor for HCC more relevant than HCV infection
The ocean sampling day consortium
Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits
PubChem3D: Similar conformers
<p>Abstract</p> <p>Background</p> <p>PubChem is a free and open public resource for the biological activities of small molecules. With many tens of millions of both chemical structures and biological test results, PubChem is a sizeable system with an uneven degree of available information. Some chemical structures in PubChem include a great deal of biological annotation, while others have little to none. To help users, PubChem pre-computes "neighboring" relationships to relate similar chemical structures, which may have similar biological function. In this work, we introduce a "Similar Conformers" neighboring relationship to identify compounds with similar 3-D shape and similar 3-D orientation of functional groups typically used to define pharmacophore features.</p> <p>Results</p> <p>The first two diverse 3-D conformers of 26.1 million PubChem Compound records were compared to each other, using a shape Tanimoto (ST) of 0.8 or greater and a color Tanimoto (CT) of 0.5 or greater, yielding 8.16 billion conformer neighbor pairs and 6.62 billion compound neighbor pairs, with an average of 253 "Similar Conformers" compound neighbors per compound. Comparing the 3-D neighboring relationship to the corresponding 2-D neighboring relationship ("Similar Compounds") for molecules such as caffeine, aspirin, and morphine, one finds unique sets of related chemical structures, providing additional significant biological annotation. The PubChem 3-D neighboring relationship is also shown to be able to group a set of non-steroidal anti-inflammatory drugs (NSAIDs), despite limited PubChem 2-D similarity.</p> <p>In a study of 4,218 chemical structures of biomedical interest, consisting of many known drugs, using more diverse conformers per compound results in more 3-D compound neighbors per compound; however, the overlap of the compound neighbor lists per conformer also increasingly resemble each other, being 38% identical at three conformers and 68% at ten conformers. Perhaps surprising is that the average count of conformer neighbors per conformer increases rather slowly as a function of diverse conformers considered, with only a 70% increase for a ten times growth in conformers per compound (a 68-fold increase in the conformer pairs considered).</p> <p>Neighboring 3-D conformers on the scale performed, if implemented naively, is an intractable problem using a modest sized compute cluster. Methodology developed in this work relies on a series of filters to prevent performing 3-D superposition optimization, when it can be determined that two conformers cannot possibly be a neighbor. Most filters are based on Tanimoto equation volume constraints, avoiding incompatible conformers; however, others consider preliminary superposition between conformers using reference shapes.</p> <p>Conclusion</p> <p>The "Similar Conformers" 3-D neighboring relationship locates similar small molecules of biological interest that may go unnoticed when using traditional 2-D chemical structure graph-based methods, making it complementary to such methodologies. The computational cost of 3-D similarity methodology on a wide scale, such as PubChem contents, is a considerable issue to overcome. Using a series of efficient filters, an effective throughput rate of more than 150,000 conformers per second per processor core was achieved, more than two orders of magnitude faster than without filtering.</p
A coherent picture of water at extreme negative pressure.
International audienceLiquid water at atmospheric pressure can be supercooled to 41 C (ref. 1) and superheated to C302 C (ref. 2). Experiments involving fluid inclusions of water in quartz suggest that water is capable of sustaining pressures as low as 140 MPa before it breaks by cavitation3. Other techniques, for which cavitation occurs consistently at around 30MPa (ref. 4), produce results that cast doubt on this claim. Here we reproduce the fluid-inclusion experiment, performing repeated measurements on a single sample--a method used in meteorology5, bioprotection6 and protein crystallization7, but not yet in liquid water under large mechanical tension. The resulting cavitation statistics are characteristic of a thermally activated process, and both the free energy and the volume of the critical bubble are well described by classical nucleation theory when the surface tension is reduced by less than 10%, consistent with homogeneous cavitation. The line of density maxima of water at negative pressure is found to reach 922:8 kgm3 at around 300 K, which further constrains its contested phase diagram
Recommended from our members
Effect of rehabilitation worker input on visual function outcomes in individuals with low vision: study protocol for a randomised controlled trial
BACKGROUND: Visual Rehabilitation Officers help people with a visual impairment maintain their independence. This intervention adopts a flexible, goal-centred approach, which may include training in mobility, use of optical and non-optical aids, and performance of activities of daily living. Although Visual Rehabilitation Officers are an integral part of the low vision service in the United Kingdom, evidence that they are effective is lacking. The purpose of this exploratory trial is to estimate the impact of a Visual Rehabilitation Officer on self-reported visual function, psychosocial and quality-of-life outcomes in individuals with low vision.
METHODS/DESIGN: In this exploratory, assessor-masked, parallel group, randomised controlled trial, participants will be allocated either to receive home visits from a Visual Rehabilitation Officer (n = 30) or to a waiting list control group (n = 30) in a 1:1 ratio. Adult volunteers with a visual impairment, who have been identified as needing rehabilitation officer input by a social worker, will take part. Those with an urgent need for a Visual Rehabilitation Officer or who have a cognitive impairment will be excluded. The primary outcome measure will be self-reported visual function (48-item Veterans Affairs Low Vision Visual Functioning Questionnaire). Secondary outcome measures will include psychological and quality-of-life metrics: the Patient Health Questionnaire (PHQ-9), the Warwick-Edinburgh Mental Well-being Scale (WEMWBS), the Adjustment to Age-related Visual Loss Scale (AVL-12), the Standardised Health-related Quality of Life Questionnaire (EQ-5D) and the UCLA Loneliness Scale. The interviewer collecting the outcomes will be masked to the group allocations. The analysis will be undertaken on a complete case and intention-to-treat basis. Analysis of covariance (ANCOVA) will be applied to follow-up questionnaire scores, with the baseline score as a covariate.
DISCUSSION: This trial is expected to provide robust effect size estimates of the intervention effect. The data will be used to design a large-scale randomised controlled trial to evaluate fully the Visual Rehabilitation Officer intervention. A rigorous evaluation of Rehabilitation Officer input is vital to direct a future low vision rehabilitation strategy and to help direct government resources.
TRIAL REGISTRATION: The trial was registered with ( ISRCTN44807874 ) on 9 March 2015
Physics of Neutron Star Crusts
The physics of neutron star crusts is vast, involving many different research
fields, from nuclear and condensed matter physics to general relativity. This
review summarizes the progress, which has been achieved over the last few
years, in modeling neutron star crusts, both at the microscopic and macroscopic
levels. The confrontation of these theoretical models with observations is also
briefly discussed.Comment: 182 pages, published version available at
<http://www.livingreviews.org/lrr-2008-10
A Linear Framework for Time-Scale Separation in Nonlinear Biochemical Systems
Cellular physiology is implemented by formidably complex biochemical systems with highly nonlinear dynamics, presenting a challenge for both experiment and theory. Time-scale separation has been one of the few theoretical methods for distilling general principles from such complexity. It has provided essential insights in areas such as enzyme kinetics, allosteric enzymes, G-protein coupled receptors, ion channels, gene regulation and post-translational modification. In each case, internal molecular complexity has been eliminated, leading to rational algebraic expressions among the remaining components. This has yielded familiar formulas such as those of Michaelis-Menten in enzyme kinetics, Monod-Wyman-Changeux in allostery and Ackers-Johnson-Shea in gene regulation. Here we show that these calculations are all instances of a single graph-theoretic framework. Despite the biochemical nonlinearity to which it is applied, this framework is entirely linear, yet requires no approximation. We show that elimination of internal complexity is feasible when the relevant graph is strongly connected. The framework provides a new methodology with the potential to subdue combinatorial explosion at the molecular level
- …