3,147 research outputs found
Effective Field Theory and Finite Density Systems
This review gives an overview of effective field theory (EFT) as applied at
finite density, with a focus on nuclear many-body systems. Uniform systems with
short-range interactions illustrate the ingredients and virtues of many-body
EFT and then the varied frontiers of EFT for finite nuclei and nuclear matter
are surveyed.Comment: 27 pages, 5 figure
Little ecological divergence associated with speciation in two African rain forest tree genera
<p>Abstract</p> <p>Background</p> <p>The tropical rain forests (TRF) of Africa are the second largest block of this biome after the Amazon and exhibit high levels of plant endemism and diversity. Two main hypotheses have been advanced to explain speciation processes that have led to this high level of biodiversity: allopatric speciation linked to geographic isolation and ecological speciation linked to ecological gradients. Both these hypotheses rely on ecology: in the former conservation of ecological niches through time is implied, while in the latter adaptation via selection to alternative ecological niches would be a prerequisite. Here, we investigate the role of ecology in explaining present day species diversity in African TRF using a species level phylogeny and ecological niche modeling of two predominantly restricted TRF tree genera, <it>Isolona </it>and <it>Monodora </it>(Annonaceae). Both these genera, with 20 and 14 species, respectively, are widely distributed in African TRFs, with a few species occurring in slightly less humid regions such as in East Africa.</p> <p>Results</p> <p>A total of 11 sister species pairs were identified most of them occurring in allopatry or with little geographical overlap. Our results provide a mixed answer on the role of ecology in speciation. Although no sister species have identical niches, just under half of the tests suggest that sister species do have more similar niches than expected by chance. PCA analyses also support little ecological differences between sister species. Most speciation events within both genera predate the Pleistocene, occurring during the Late Miocene and Pliocene periods.</p> <p>Conclusions</p> <p>Ecology is almost always involved in speciation, however, it would seem to have had a little role in species generation within <it>Isolona </it>and <it>Monodora </it>at the scale analyzed here. This is consistent with the geographical speciation model for TRF diversification. These results contrast to other studies for non-TRF plant species where ecological speciation was found to be an important factor of diversification. The Pliocene period appears to be a vital time in the generation of African TRF diversity, whereas Pleistocene climatic fluctuations have had a smaller role on speciation than previously thought.</p> <p>Ecological niche modeling, species level phylogeny, ecological speciation, African tropics, <it>Isolona</it>, <it>Monodora</it>, Annonaceae</p
Nascent chains can form co-translational folding intermediates that promote post-translational folding outcomes in a disease-causing protein
During biosynthesis, proteins can begin folding co-translationally to acquire their biologically-active structures. Folding, however, is an imperfect process and in many cases misfolding results in disease. Less is understood of how misfolding begins during biosynthesis. The human protein, alpha-1-antitrypsin (AAT) folds under kinetic control via a folding intermediate; its pathological variants readily form self-associated polymers at the site of synthesis, leading to alpha-1-antitrypsin deficiency. We observe that AAT nascent polypeptides stall during their biosynthesis, resulting in full-length nascent chains that remain bound to ribosome, forming a persistent ribosome-nascent chain complex (RNC) prior to release. We analyse the structure of these RNCs, which reveals compacted, partially-folded co-translational folding intermediates possessing molten-globule characteristics. We find that the highly-polymerogenic mutant, Z AAT, forms a distinct co-translational folding intermediate relative to wild-type. Its very modest structural differences suggests that the ribosome uniquely tempers the impact of deleterious mutations during nascent chain emergence. Following nascent chain release however, these co-translational folding intermediates guide post-translational folding outcomes thus suggesting that Z’s misfolding is initiated from co-translational structure. Our findings demonstrate that co-translational folding intermediates drive how some proteins fold under kinetic control, and may thus also serve as tractable therapeutic targets for human disease
Mentoring at the University of Pennsylvania: Results of a Faculty Survey
BACKGROUND: Research suggests mentoring is related to career satisfaction and success. Most studies have focused on junior faculty. OBJECTIVE: To explore multiple aspects of mentoring at an academic medical center in relation to faculty rank, track, and gender. DESIGN: Cross-sectional mail survey in mid-2003. PARTICIPANTS: Faculty members, 1,432, at the University of Pennsylvania School of Medicine MEASUREMENTS: Self-administered survey developed from existing instruments and stakeholders. RESULTS: Response rate was 73% (n = 1,046). Most (92%) assistant and half (48%) of associate professors had a mentor. Assistant professors in the tenure track were most likely to have a mentor (98%). At both ranks, the faculty was given more types of advice than types of opportunities. Satisfaction with mentoring was correlated with the number of types of mentoring received (r = .48 and .53, P < .0001), job satisfaction (r = .44 and .31, P < .0001), meeting frequency (r = .53 and .61, P < .0001), and expectation of leaving the University within 5 years (Spearman r = −.19 and −.18, P < .0001), at the assistant and associate rank, respectively. Significant predictors of higher overall job satisfaction were associate rank [Odds ratio (OR) = 2.04, CI = 1.29–3.21], the 10-point mentoring satisfaction rating (OR = 1.27, CI = 1.17–1.35), and number of mentors (OR = 1.60, CI = 1.20–2.07). CONCLUSIONS: Having a mentor, or preferably, multiple mentors is strongly related to satisfaction with mentoring and overall job satisfaction. Surprisingly, few differences were related to gender. Mentoring of clinician–educators, research track faculty, and senior faculty, and the use of multiple mentors require specific attention of academic leadership and further study
Liver Enzymes: Interaction Analysis of Smoking with Alcohol Consumption or BMI, Comparing AST and ALT to γ-GT
A detrimental interaction between smoking and alcohol consumption with respect serum γ-glutamyltransferase (γ-GT) has recently been described. The underlying mechanisms remain unknown. The present work aimed to provide further insights by examining similar interactions pertaining to aspartate and alanine transaminase (AST, ALT), routine liver markers less prone to enzyme induction.<0.0001). The interactions all were in the same directions as for γ-GT, i.e. synergistic with alcohol and opposite with BMI.The patterns of interaction between smoking and alcohol consumption or BMI with respect to AST and ALT resembled those observed for γ-GT. This renders enzyme induction a less probable mechanism for these associations, whereas it might implicate exacerbated hepatocellular vulnerability and injury
Lorentz Violation in Warped Extra Dimensions
Higher dimensional theories which address some of the problematic issues of
the Standard Model(SM) naturally involve some form of -dimensional
Lorentz invariance violation (LIV). In such models the fundamental physics
which leads to, e.g., field localization, orbifolding, the existence of brane
terms and the compactification process all can introduce LIV in the higher
dimensional theory while still preserving 4-d Lorentz invariance. In this
paper, attempting to capture some of this physics, we extend our previous
analysis of LIV in 5-d UED-type models to those with 5-d warped extra
dimensions. To be specific, we employ the 5-d analog of the SM Extension of
Kostelecky et. al. ~which incorporates a complete set of operators arising from
spontaneous LIV. We show that while the response of the bulk scalar, fermion
and gauge fields to the addition of LIV operators in warped models is
qualitatively similar to what happens in the flat 5-d UED case, the gravity
sector of these models reacts very differently than in flat space.
Specifically, we show that LIV in this warped case leads to a non-zero bulk
mass for the 5-d graviton and so the would-be zero mode, which we identify as
the usual 4-d graviton, must necessarily become massive. The origin of this
mass term is the simultaneous existence of the constant non-zero
curvature and the loss of general co-ordinate invariance via LIV in the 5-d
theory. Thus warped 5-d models with LIV in the gravity sector are not
phenomenologically viable.Comment: 14 pages, 4 figs; discussion added, algebra repaire
Detecting the direction of a signal on high-dimensional spheres: Non-null and Le Cam optimality results
We consider one of the most important problems in directional statistics,
namely the problem of testing the null hypothesis that the spike direction
of a Fisher-von Mises-Langevin distribution on the -dimensional
unit hypersphere is equal to a given direction . After a reduction
through invariance arguments, we derive local asymptotic normality (LAN)
results in a general high-dimensional framework where the dimension goes
to infinity at an arbitrary rate with the sample size , and where the
concentration behaves in a completely free way with , which
offers a spectrum of problems ranging from arbitrarily easy to arbitrarily
challenging ones. We identify various asymptotic regimes, depending on the
convergence/divergence properties of , that yield different
contiguity rates and different limiting experiments. In each regime, we derive
Le Cam optimal tests under specified and we compute, from the Le Cam
third lemma, asymptotic powers of the classical Watson test under contiguous
alternatives. We further establish LAN results with respect to both spike
direction and concentration, which allows us to discuss optimality also under
unspecified . To investigate the non-null behavior of the Watson test
outside the parametric framework above, we derive its local asymptotic powers
through martingale CLTs in the broader, semiparametric, model of rotationally
symmetric distributions. A Monte Carlo study shows that the finite-sample
behaviors of the various tests remarkably agree with our asymptotic results.Comment: 47 pages, 4 figure
I-TRAP: A method to identify transcriptional regulator activated promoters
BACKGROUND: The differential expression of virulence genes is often used by microbial pathogens in adapting to the environment of their host. The differential expression of such sets of genes can be regulated by RNA polymerase sigma factors. Some sigma factors are differentially expressed, which can provide a means to identifying other differentially expressed genes such as those whose expression are controlled by the sigma factor. METHODS: To identify sigma factor-regulated genes, we developed a method, termed I-TRAP, for the identification of transcriptional regulator activated promoters. The I-TRAP method is based on the fact that some genes will be differentially expressed in the presence and absence of a transcriptional regulator. I-TRAP uses a DNA library in a promoter-trap vector that contains two reporter genes, one to allow the selection of active promoters in the presence of the transcriptional regulator and a second to allow screening for promoter activity in the absence of the transcriptional regulator. RESULTS: To illustrate the development and use of the I-TRAP approach, the construction of the vectors, host strains, and library necessary to identify SigmaE-regulated genes of Mycobacterium tuberculosis is described. CONCLUSION: The I-TRAP method should be a versatile and useful method for identifying and characterizing promoter activity under a variety of conditions and in response to various regulatory proteins. In our study, we isolated 360 clones that may contain plasmids carrying SigmaE-regulated promoters genes of M. tuberculosis
Transport through a strongly coupled graphene quantum dot in perpendicular magnetic field
We present transport measurements on a strongly coupled graphene quantum dot
in a perpendicular magnetic field. The device consists of an etched
single-layer graphene flake with two narrow constrictions separating a 140 nm
diameter island from source and drain graphene contacts. Lateral graphene gates
are used to electrostatically tune the device. Measurements of Coulomb
resonances, including constriction resonances and Coulomb diamonds prove the
functionality of the graphene quantum dot with a charging energy of around 4.5
meV. We show the evolution of Coulomb resonances as a function of perpendicular
magnetic field, which provides indications of the formation of the graphene
specific 0th Landau level. Finally, we demonstrate that the complex pattern
superimposing the quantum dot energy spectra is due to the formation of
additional localized states with increasing magnetic field.Comment: 6 pages, 4 figure
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