Using equilibrium frequencies in models of sequence evolution

BACKGROUND: The f factor is a new parameter for accommodating the influence of both the starting and ending states in the rate matrices of "generalized weighted frequencies" (+gwF) models for sequence evolution. In this study, we derive an expected value for f, starting from a nearly neutral model of weak selection, and then assess the biological interpretation of this factor with evolutionary simulations. RESULTS: An expected value of f = 0.5 (i.e., equal dependency on the starting and ending states) is derived for sequences that are evolving under the nearly neutral model of this study. However, this expectation is sensitive to violations of its underlying assumptions as illustrated with the evolutionary simulations. CONCLUSION: This study illustrates how selection, drift, and mutation at the population level can be linked to the rate matrices of models for sequence evolution to derive an expected value of f. However, as f is affected by a number of factors that limit its biological interpretation, this factor should normally be estimated as a free parameter rather than fixed a priori in a +gwF analysis

Nonmeromorphic operator product expansion and C_2-cofiniteness for a family of W-algebras

We prove the existence and associativity of the nonmeromorphic operator product expansion for an infinite family of vertex operator algebras, the triplet W-algebras, using results from P(z)-tensor product theory. While doing this, we also show that all these vertex operator algebras are C_2-cofinite.Comment: 21 pages, to appear in J. Phys. A: Math. Gen.; the exposition is improved and one reference is adde

A new formation model for M32: A threshed early-type spiral?

The origin of the closest compact elliptical galaxy (cE) M32 is a longstanding problem of galaxy formation in the Local Group. Our N-body/SPH simulations suggest a new scenario in which the strong tidal field of M31 can transform a spiral galaxy into a compact elliptical. As a low luminosity spiral galaxy plunges into the central region of M31, most of the outer stellar and gaseous components of its disk are dramatically stripped due to M31's tidal field The central bulge component, on the other hand, is just weakly influenced by the tidal field owing to its compact configuration, and retains its morphology. M31's strong tidal field also induces rapid gas transfer to the central region, triggers a nuclear starburst, and consequently forms the central high density and more metal-rich stellar populations with relatively young ages. Thus, in this scenario, M32 was previously the bulge of a spiral tidally interacting with M31 several Gyr ago. Furthermore, we suggest cEs like M32 are rare, the result of both the rather narrow parameter space for tidal interactions which morphologically transform spirals into cEs and the very short time scale ($<$ a few $10^9$ yr) for cEs to be swallowed.Comment: 12 pages 4 figures, 2001, accepted by ApJ

The extended tails of Palomar 5: A ten degree arc of globular cluster tidal debris

Using wide-field photometric data from the Sloan Digital Sky Survey (SDSS) we recently showed that the Galactic globular cluster Palomar 5 is in the process of being tidally disrupted. Its tidal tails were initially detected in a 2.5 degree wide band along the celestial equator. A new analysis of SDSS data for a larger field now reveals that the tails of Pal 5 have a much larger spatial extent and can be traced over an arc of 10 deg across the sky, corresponding to a projected length of 4 kpc at the distance of the cluster. The number of former cluster stars found in the tails adds up to about 1.2 times the number of stars in the cluster. The radial profile of stellar surface density in the tails follows approximately a power law r^gamma with -1.5 < gamma < -1.2. The stream of debris from Pal 5 is significantly curved, which demonstrates its acceleration by the Galactic potential. The cluster is presently near the apocenter but has repeatedly undergone disk crossings in the inner part of the Galaxy leading to strong tidal shocks. Our results suggest that the observed debris originates mostly from mass loss within the last 2 Gyrs. The cluster is likely to be destroyed after the next disk crossing, which will happen in about 100 Myr. (abridged)Comment: 44 pages, including 14 figures (Figs.1,3 & 14 with decreased resolution), accepted for publication in the Astronomical Journa

Nucleocytoplasmic transport: a thermodynamic mechanism

The nuclear pore supports molecular communication between cytoplasm and nucleus in eukaryotic cells. Selective transport of proteins is mediated by soluble receptors, whose regulation by the small GTPase Ran leads to cargo accumulation in, or depletion from the nucleus, i.e., nuclear import or nuclear export. We consider the operation of this transport system by a combined analytical and experimental approach. Provocative predictions of a simple model were tested using cell-free nuclei reconstituted in Xenopus egg extract, a system well suited to quantitative studies. We found that accumulation capacity is limited, so that introduction of one import cargo leads to egress of another. Clearly, the pore per se does not determine transport directionality. Moreover, different cargo reach a similar ratio of nuclear to cytoplasmic concentration in steady-state. The model shows that this ratio should in fact be independent of the receptor-cargo affinity, though kinetics may be strongly influenced. Numerical conservation of the system components highlights a conflict between the observations and the popular concept of transport cycles. We suggest that chemical partitioning provides a framework to understand the capacity to generate concentration gradients by equilibration of the receptor-cargo intermediary.Comment: in press at HFSP Journal, vol 3 16 text pages, 1 table, 4 figures, plus Supplementary Material include

Funerary Artifacts, Social Status, and Atherosclerosis in Ancient Peruvian Mummy Bundles

Background: Evidence of atherosclerotic plaques in ancient populations has led to the reconsideration of risk factors for heart disease and of the common belief that it is a disease of modern times. Methods: Fifty-one wrapped mummy bundles excavated from the sites of Huallamarca, Pedreros, and Rinconada La Molina from the Puruchuco Museum collection in Lima, Peru, were scanned using computed tomography to investigate the presence of atherosclerosis. Funerary artifacts contained within the undisturbed mummy bundles were analyzed as an attempt to infer the social status of the individuals to correlate social status with evidence of heart disease in this ancient Peruvian group. This work also provides an inventory of the museum mummy collection to guide and facilitate future research. Results: Statistical analysis concluded that there is little association between the types of grave goods contained within the bundles when the groups are pooled together. However, some patterns of artifact type, material, atherosclerosis, and sex emerge when the 3 excavation sites are analyzed separately. Conclusions: From the current sample, it would seem that social class is difficult to discern, but those from Huallamarca have the most markers of elite status. We had hypothesized that higher-status individuals may have had lifestyles that would place them at a higher risk for atherogenesis. There seems to be some indication of this within the site of Huallamarca, but it is inconclusive in the other 2 archeological sites. It is possible that a larger sample size in the future could reveal more statistically significant results

Simple quantitative tests to validate sampling from thermodynamic ensembles

It is often difficult to quantitatively determine if a new molecular simulation algorithm or software properly implements sampling of the desired thermodynamic ensemble. We present some simple statistical analysis procedures to allow sensitive determination of whether a de- sired thermodynamic ensemble is properly sampled. We demonstrate the utility of these tests for model systems and for molecular dynamics simulations in a range of situations, includ- ing constant volume and constant pressure simulations, and describe an implementation of the tests designed for end users.Comment: 48 pages, 4 figure

Genomic Correlates of Atherosclerosis in Ancient Humans

Paleogenetics offers a unique opportunity to study human evolution, population dynamics, and disease evolution in situ. Although histologic and computed x-ray tomographic investigations of ancient mummies have clearly shown that atherosclerosis has been present in humans for more than 5,000 years, limited data are available on the presence of genetic predisposition for cardiovascular disease in ancient human populations. In a previous whole-genome study of the Tyrolean Iceman, a 5,300-year-old glacier mummy from the Alps, an increased risk for coronary heart disease was detected. The Iceman’s genome revealed several single nucleotide polymorphisms that are linked with cardiovascular disease in genome-wide association studies. Future genetic studies of ancient humans from various geographic origins and time periods have the potential to provide more insights into the presence and possible changes of genetic risk factors in our ancestors. The study of ancient humans and a better understanding of the interaction between environmental and genetic influences on the development of heart diseases may lead to a more effective prevention and treatment of the most common cause of death in the modern world

Compression garments and fabric orthoses for rehabilitation and function: a systematic mapping review.

Background/aims: Compression garments, joint supports and dynamic movement orthoses all use elastic fibres and close-fitting designs and have been researched for their effects on movement. There is little cross-referencing between research into these interventions. This review aimed to improve inter-disciplinary understanding by analysing key characteristics of the published evidence. Methods: Systematic mapping reviews identify gaps in an evidence base and identify questions for more in-depth reviews. This review was conducted in-line with current guidance. MEDLINE, CINAHL and Sports Discuss were searched for primary research investigating compression garments and orthoses for movement and function. The following search terms were used: "elastane", "spandex", "Lycra", "elastomer*", "Theratog*", "compression", "Neoprene", "orthotic", "orthosis", "shorts", "garment*", "splint", "brace", "sock*" and "stockings". Studies were screened against predetermined criteria and key study characteristics extracted. Findings: Three hundred and fifty-one studies were selected and analysed. Compression garment research was most common (236 studies), followed by research into joint supports (64 studies) and dynamic movement orthoses (42 studies). Research largely reflects the purpose for which each intervention was originally designed. Common topics investigated include posture and movement control, proprioception and muscle activity. Pressure beneath compression garments was measured in 30% of studies. Conclusions: The review highlights a need for more robust study designs in patient populations and accurate description of interventions. There is a need for a review on the possible effects of compression and support on movement control which should be used to inform future primary research