Neighborhoods of trees in circular orderings

In phylogenetics, a common strategy used to construct an evolutionary tree for a set of species X is to search in the space of all such trees for one that optimizes some given score function (such as the minimum evolution, parsimony or likelihood score). As this can be computationally intensive, it was recently proposed to restrict such searches to the set of all those trees that are compatible with some circular ordering of the set X. To inform the design of efficient algorithms to perform such searches, it is therefore of interest to find bounds for the number of trees compatible with a fixed ordering in the neighborhood of a tree that is determined by certain tree operations commonly used to search for trees: the nearest neighbor interchange (nni), the subtree prune and regraft (spr) and the tree bisection and reconnection (tbr) operations. We show that the size of such a neighborhood of a binary tree associated with the nni operation is independent of the tree’s topology, but that this is not the case for the spr and tbr operations. We also give tight upper and lower bounds for the size of the neighborhood of a binary tree for the spr and tbr operations and characterize those trees for which these bounds are attained

Orientational phase transitions in the hexagonal phase of a diblock copolymer melt under shear flow

We generalize the earlier theory by Fredrickson [J. Rheol. v.38, 1045 (1994)] to study the orientational behaviour of the hexagonal phase of diblock copolymer melt subjected to steady shear flow. We use symmetry arguments to show that the orientational ordering in the hexagonal phase is a much weaker effect than in the lamellae. We predict the parallel orientation to be stable at low and the perpendicular orientation at high shear rates. Our analysis reproduces the experimental results by Tepe et al. [Macromolecules v.28, 3008 (1995)] and explains the difficulties in experimental observation of the different orientations in the hexagonal phase.Comment: 21 pages, 6 eps figures, submitted to Physical Review

Turner syndrome and associated problems in turkish children: A multicenter study

Objective: Turner syndrome (TS) is a chromosomal disorder caused by complete or partial X chromosome monosomy that manifests various clinical features depending on the karyotype and on the genetic background of affected girls. This study aimed to systematically investigate the key clinical features of TS in relationship to karyotype in a large pediatric Turkish patient population. Methods: Our retrospective study included 842 karyotype-proven TS patients aged 0-18 years who were evaluated in 35 different centers in Turkey in the years 2013-2014. Results: The most common karyotype was 45,X (50.7%), followed by 45,X/46,XX (10.8%), 46,X,i(Xq) (10.1%) and 45,X/46,X,i(Xq) (9.5%). Mean age at diagnosis was 10.2±4.4 years. The most common presenting complaints were short stature and delayed puberty. Among patients diagnosed before age one year, the ratio of karyotype 45,X was significantly higher than that of other karyotype groups. Cardiac defects (bicuspid aortic valve, coarctation of the aorta and aortic stenosi) were the most common congenital anomalies, occurring in 25% of the TS cases. This was followed by urinary system anomalies (horseshoe kidney, double collector duct system and renal rotation) detected in 16.3%. Hashimoto’s thyroiditis was found in 11.1% of patients, gastrointestinal abnormalities in 8.9%, ear nose and throat problems in 22.6%, dermatologic problems in 21.8% and osteoporosis in 15.3%. Learning difficulties and/or psychosocial problems were encountered in 39.1%. Insulin resistance and impaired fasting glucose were detected in 3.4% and 2.2%, respectively. Dyslipidemia prevalence was 11.4%. Conclusion: This comprehensive study systematically evaluated the largest group of karyotype-proven TS girls to date. The karyotype distribution, congenital anomaly and comorbidity profile closely parallel that from other countries and support the need for close medical surveillance of these complex patients throughout their lifespan. © Journal of Clinical Research in Pediatric Endocrinology

Observation of High-Energy Astrophysical Neutrinos in Three Years of IceCube Data

A search for high-energy neutrinos interacting within the IceCube detector between 2010 and 2012 provided the first evidence for a high-energy neutrino flux of extraterrestrial origin. Results from an analysis using the same methods with a third year (2012-2013) of data from the complete IceCube detector are consistent with the previously reported astrophysical flux in the 100 TeV - PeV range at the level of $10^{-8}\, \mathrm{GeV}\, \mathrm{cm}^{-2}\, \mathrm{s}^{-1}\, \mathrm{sr}^{-1}$ per flavor and reject a purely atmospheric explanation for the combined 3-year data at $5.7 \sigma$. The data are consistent with expectations for equal fluxes of all three neutrino flavors and with isotropic arrival directions, suggesting either numerous or spatially extended sources. The three-year dataset, with a livetime of 988 days, contains a total of 37 neutrino candidate events with deposited energies ranging from 30 to 2000 TeV. The 2000 TeV event is the highest-energy neutrino interaction ever observed.Comment: 8 pages, 5 figures. Accepted by PRL. The event catalog, event displays, and other data tables are included after the final page of the article. Changed from the initial submission to reflect referee comments, expanding the section on atmospheric backgrounds, and fixes offsets of up to 0.9 seconds in reported event times. Address correspondence to: J. Feintzeig, C. Kopper, N. Whitehor

Search for Prompt Neutrino Emission from Gamma-Ray Bursts with IceCube

We present constraints derived from a search of four years of IceCube data for a prompt neutrino flux from gamma-ray bursts (GRBs). A single low-significance neutrino, compatible with the atmospheric neutrino background, was found in coincidence with one of the 506 observed bursts. Although GRBs have been proposed as candidate sources for ultra-high energy cosmic rays, our limits on the neutrino flux disfavor much of the parameter space for the latest models. We also find that no more than $\sim1\%$ of the recently observed astrophysical neutrino flux consists of prompt emission from GRBs that are potentially observable by existing satellites.Comment: 15 pages, 3 figure

Atmospheric and Astrophysical Neutrinos above 1 TeV Interacting in IceCube

The IceCube Neutrino Observatory was designed primarily to search for high-energy (TeV--PeV) neutrinos produced in distant astrophysical objects. A search for $\gtrsim 100$~TeV neutrinos interacting inside the instrumented volume has recently provided evidence for an isotropic flux of such neutrinos. At lower energies, IceCube collects large numbers of neutrinos from the weak decays of mesons in cosmic-ray air showers. Here we present the results of a search for neutrino interactions inside IceCube's instrumented volume between 1~TeV and 1~PeV in 641 days of data taken from 2010--2012, lowering the energy threshold for neutrinos from the southern sky below 10 TeV for the first time, far below the threshold of the previous high-energy analysis. Astrophysical neutrinos remain the dominant component in the southern sky down to 10 TeV. From these data we derive new constraints on the diffuse astrophysical neutrino spectrum, $\Phi_{\nu} = 2.06^{+0.4}_{-0.3} \times 10^{-18} \left({E_{\nu}}/{10^5 \,\, \rm{GeV}} \right)^{-2.46 \pm 0.12} {\rm {GeV^{-1} \, cm^{-2} \, sr^{-1} \, s^{-1}} }$, as well as the strongest upper limit yet on the flux of neutrinos from charmed-meson decay in the atmosphere, 1.52 times the benchmark theoretical prediction used in previous IceCube results at 90\% confidence.Comment: 18 pages, 12 figure

Search for a diffuse flux of astrophysical muon neutrinos with the IceCube 59-string configuration

A search for high-energy neutrinos was performed using data collected by the IceCube Neutrino Observatory from May 2009 to May 2010, when the array was running in its 59-string configuration. The data sample was optimized to contain muon neutrino induced events with a background contamination of atmospheric muons of less than 1%. These data, which are dominated by atmospheric neutrinos, are analyzed with a global likelihood fit to search for possible contributions of prompt atmospheric and astrophysical neutrinos, neither of which have yet been identified. Such signals are expected to follow a harder energy spectrum than conventional atmospheric neutrinos. In addition, the zenith angle distribution differs for astrophysical and atmospheric signals. A global fit of the reconstructed energies and directions of observed events is performed, including possible neutrino flux contributions for an astrophysical signal and atmospheric backgrounds as well as systematic uncertainties of the experiment and theoretical predictions. The best fit yields an astrophysical signal flux for nu(mu) + (nu) over bar (mu) of E-2. Phi(E) = 0.25 x 10(-8) GeV cm(-2) s(-1) sr(-1), and a zero prompt component. Although the sensitivity of this analysis for astrophysical neutrinos surpasses the Waxman and Bahcall upper bound, the experimental limit at 90% confidence level is a factor of 1.5 above at a flux of E-2 . Phi(E) = 1.44 x 10(-8) GeV cm(-2) s(-1) sr(-1)

Limits on the high-energy gamma and neutrino fluxes from the SGR 1806-20 giant flare of December 27th, 2004 with the AMANDA-II detector

On December 27th 2004, a giant gamma flare from the Soft Gamma-ray Repeater 1806-20 saturated many satellite gamma-ray detectors. This event was by more than two orders of magnitude the brightest cosmic transient ever observed. If the gamma emission extends up to TeV energies with a hard power law energy spectrum, photo-produced muons could be observed in surface and underground arrays. Moreover, high-energy neutrinos could have been produced during the SGR giant flare if there were substantial baryonic outflow from the magnetar. These high-energy neutrinos would have also produced muons in an underground array. AMANDA-II was used to search for downgoing muons indicative of high-energy gammas and/or neutrinos. The data revealed no significant signal. The upper limit on the gamma flux at 90% CL is dN/dE < 0.05 (0.5) TeV^-1 m^-2 s^-1 for gamma=-1.47 (-2). Similarly, we set limits on the normalization constant of the high-energy neutrino emission of 0.4 (6.1) TeV^-1 m^-2 s^-1 for gamma=-1.47 (-2).Comment: 14 pages, 3 figure

Mid-Rapidity Direct-Photon Production in p+p Collisions at sqrt(s) = 200 GeV

A measurement of direct photons in p+p collisions at sqrt(s)=200 GeV is presented. A photon excess above background from pi^0 --> gamma+gamma, eta --> gamma+gamma, and other decays is observed in the transverse momentum range 5.5 < p_T < 7 GeV/c. The result is compared to a next-to-leading-order perturbative QCD calculation. Within errors, good agreement is found between the QCD calculation and the measured result.Comment: 330 authors, 7 pages text, RevTeX, 2 figures, 2 tables. Submitted to Physical Review D. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

Suppressed pi^0 Production at Large Transverse Momentum in Central Au+Au Collisions at sqrt(s_NN) = 200 GeV

Transverse momentum spectra of neutral pions in the range 1 < p_T < 10 GeV/c have been measured at mid-rapidity by the PHENIX experiment at RHIC in Au+Au collisions at sqrt(s_NN) = 200 GeV. The pi^0 multiplicity in central reactions is significantly below the yields measured at the same sqrt(s_NN) in peripheral Au+Au and p+p reactions scaled by the number of nucleon-nucleon collisions. For the most central bin, the suppression factor is ~2.5 at p_T = 2 GeV/c and increases to ~4-5 at p_T ~= 4 GeV/c. At larger p_T, the suppression remains constant within errors. The deficit is already apparent in semi-peripheral reactions and increases smoothly with centrality.Comment: 326 authors, 6 pages text, RevTeX, 3 figures, 2 tables. Submitted to PRL. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm