Phylogenetic analyses of ray-finned fishes (Actinopterygii) using collagen type I protein sequences

Ray-finned fishes (Actinopterygii) are the largest and most diverse group of vertebrates, comprising over half of all living vertebrate species. Phylogenetic relationships between ray-finned fishes have historically pivoted on the study of morphology, which has notoriously failed to resolve higher order relationships, such as within the percomorphs. More recently, comprehensive genomic analyses have provided further resolution of actinopterygian phylogeny, including higher order relationships. Such analyses are rightfully regarded as the ‘gold standard’ for phylogenetics. However, DNA retrieval requires modern or well-preserved tissue and is less likely to be preserved in archaeological or fossil specimens. By contrast, some proteins, such as collagen, are phylogenetically informative and can survive into deep time. Here, we test the utility of collagen type I amino acid sequences for phylogenetic estimation of ray-finned fishes. We estimate topology using Bayesian approaches and compare the congruence of our estimated trees with published genomic phylogenies. Furthermore, we apply a Bayesian molecular clock approach and compare estimated divergence dates with previously published genomic clock analyses. Our collagen-derived trees exhibit 77% of node positions as congruent with recent genomic-derived trees, with the majority of discrepancies occurring in higher order node positions, almost exclusively within the Percomorpha. Our molecular clock trees present divergence times that are fairly comparable with genomic-based phylogenetic analyses. We estimate the mean node age of Actinopteri at ∼293 million years (Ma), the base of Teleostei at ∼211 Ma and the radiation of percomorphs beginning at ∼141 Ma (∼350 Ma, ∼250–283 Ma and ∼120–133 Ma in genomic trees, respectively). Finally, we show that the average rate of collagen (I) sequence evolution is 0.9 amino acid substitutions for every million years of divergence, with the α3 (I) sequence evolving the fastest, followed by the α2 (I) chain. This is the quickest rate known for any vertebrate group. We demonstrate that phylogenetic analyses using collagen type I amino acid sequences generate tangible signals for actinopterygians that are highly congruent with recent genomic-level studies. However, there is limited congruence within percomorphs, perhaps due to clade-specific functional constraints acting upon collagen sequences. Our results provide important insights for future phylogenetic analyses incorporating extinct actinopterygian species via collagen (I) sequencing

Factors Associated With Tyrosine Kinase Inhibitor Initiation and Adherence Among Medicare Beneficiaries With Chronic Myeloid Leukemia

There is substantial concern surrounding affordability of orally administered anticancer therapies, particularly for Medicare beneficiaries. We examined rates of initiation and adherence to tyrosine kinase inhibitors (TKIs) among Medicare beneficiaries with chronic myeloid leukemia (CML) with and without cost-sharing subsidies. We selected TKIs given their effectiveness and strong indication for use among patients diagnosed with CML

Random matrix theory, the exceptional Lie groups, and L-functions

There has recently been interest in relating properties of matrices drawn at random from the classical compact groups to statistical characteristics of number-theoretical L-functions. One example is the relationship conjectured to hold between the value distributions of the characteristic polynomials of such matrices and value distributions within families of L-functions. These connections are here extended to non-classical groups. We focus on an explicit example: the exceptional Lie group G_2. The value distributions for characteristic polynomials associated with the 7- and 14-dimensional representations of G_2, defined with respect to the uniform invariant (Haar) measure, are calculated using two of the Macdonald constant term identities. A one parameter family of L-functions over a finite field is described whose value distribution in the limit as the size of the finite field grows is related to that of the characteristic polynomials associated with the 7-dimensional representation of G_2. The random matrix calculations extend to all exceptional Lie groupsComment: 14 page

Scotland, Catalonia and the “right” to self-determination: a comment suggested by Kathryn Crameri’s “Do Catalans Have the Right to Decide?

No abstract available

The Intrinsic Dimensionality of Attractiveness: A Study in Face Profiles

The study of human attractiveness with pattern analysis techniques is an emerging research field. One still largely unresolved problem is which are the facial features relevant to attractiveness, how they combine together, and the number of independent parameters required for describing and identifying harmonious faces. In this paper, we present a first study about this problem, applied to face profiles. First, according to several empirical results, we hypothesize the existence of two well separated manifolds of attractive and unattractive face profiles. Then, we analyze with manifold learning techniques their intrinsic dimensionality. Finally, we show that the profile data can be reduced, with various techniques, to the intrinsic dimensions, largely without loosing their ability to discriminate between attractive and unattractive face

Imprints of Relic Gravitational Waves in Cosmic Microwave Background Radiation

A strong variable gravitational field of the very early Universe inevitably generates relic gravitational waves by amplifying their zero-point quantum oscillations. We begin our discussion by contrasting the concepts of relic gravitational waves and inflationary `tensor modes'. We explain and summarize the properties of relic gravitational waves that are needed to derive their effects on CMB temperature and polarization anisotropies. The radiation field is characterized by four invariants I, V, E, B. We reduce the radiative transfer equations to a single integral equation of Voltairre type and solve it analytically and numerically. We formulate the correlation functions C^{XX'}_{\ell} for X, X'= T, E, B and derive their amplitudes, shapes and oscillatory features. Although all of our main conclusions are supported by exact numerical calculations, we obtain them, in effect, analytically by developing and using accurate approximations. We show that the TE correlation at lower \ell's must be negative (i.e. an anticorrelation), if it is caused by gravitational waves, and positive if it is caused by density perturbations. This difference in TE correlation may be a signature more valuable observationally than the lack or presence of the BB correlation, since the TE signal is about 100 times stronger than the expected BB signal. We discuss the detection by WMAP of the TE anticorrelation at \ell \approx 30 and show that such an anticorrelation is possible only in the presence of a significant amount of relic gravitational waves (within the framework of all other common assumptions). We propose models containing considerable amounts of relic gravitational waves that are consistent with the measured TT, TE and EE correlations.Comment: 61 pages including 15 figures, v.2: additional references and clarifications, to be published in Phys. Rev.

Applications and generalizations of Fisher-Hartwig asymptotics

Fisher-Hartwig asymptotics refers to the large $n$ form of a class of Toeplitz determinants with singular generating functions. This class of Toeplitz determinants occurs in the study of the spin-spin correlations for the two-dimensional Ising model, and the ground state density matrix of the impenetrable Bose gas, amongst other problems in mathematical physics. We give a new application of the original Fisher-Hartwig formula to the asymptotic decay of the Ising correlations above $T_c$, while the study of the Bose gas density matrix leads us to generalize the Fisher-Hartwig formula to the asymptotic form of random matrix averages over the classical groups and the Gaussian and Laguerre unitary matrix ensembles. Another viewpoint of our generalizations is that they extend to Hankel determinants the Fisher-Hartwig asymptotic form known for Toeplitz determinants.Comment: 25 page

Stein's Method and Characters of Compact Lie Groups

Stein's method is used to study the trace of a random element from a compact Lie group or symmetric space. Central limit theorems are proved using very little information: character values on a single element and the decomposition of the square of the trace into irreducible components. This is illustrated for Lie groups of classical type and Dyson's circular ensembles. The approach in this paper will be useful for the study of higher dimensional characters, where normal approximations need not hold.Comment: 22 pages; same results, but more efficient exposition in Section 3.

For Uninsured Cancer Patients, Outpatient Charges Can Be Costly, Putting Treatments Out Of Reach

Reimbursement information for public and private payers has long been available. However, information about charges—the amounts that providers request before payments are negotiated—has been scarce, particularly for outpatient care. Using the new Medicare Provider Utilization and Payment Data Public Use File and other sources, we evaluated physician charges, reimbursements by Medicare and large private health plans, and expected patient cost sharing for outpatient oncology care. In 2012 the average Medicare reimbursement for chemotherapy was 39.6 percent of charges; for private insurance, the share was 55.7 percent. Uninsured patients faced potential prices for chemotherapy that were 2–43 times as much as the total Medicare allowed amount and 2–5 times as much as the private insurance allowed amount. Charges for outpatient chemotherapy and office visits were substantially higher than insurer-reimbursed amounts, which is consistent with previous evidence about hospital charges. The charges for outpatient services underscore the pressure that the current system places on people who are least able to pay. Encouraging rational pricing for health care services will be an important step toward ensuring access to care for everyone