Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome

The human pangenome, a new reference sequence, addresses many limitations of the current GRCh38 reference. The first release is based on 94 high-quality haploid assemblies from individuals with diverse backgrounds. We employed a k-mer indexing strategy for comparative analysis across multiple assemblies, including the pangenome reference, GRCh38, and CHM13, a telomere-to-telomere reference assembly. Our k-mer indexing approach enabled us to identify a valuable collection of universally conserved sequences across all assemblies, referred to as “pan-conserved segment tags” (PSTs). By examining intervals between these segments, we discerned highly conserved genomic segments and those with structurally related polymorphisms. We found 60,764 polymorphic intervals with unique geo-ethnic features in the pangenome reference. In this study, we utilized ultra-conserved sequences (PSTs) to forge a link between human pangenome assemblies and reference genomes. This methodology enables the examination of any sequence of interest within the pangenome, using the reference genome as a comparative framework

Newtonian Collapse of Scalar Field Dark Matter

In this letter, we develop a Newtonian approach to the collapse of galaxy fluctuations of scalar field dark matter under initial conditions inferred from simple assumptions. The full relativistic system, the so called Einstein-Klein-Gordon, is reduced to the Schr\"odinger-Newton one in the weak field limit. The scaling symmetries of the SN equations are exploited to track the non-linear collapse of single scalar matter fluctuations. The results can be applied to both real and complex scalar fields.Comment: 4 pages RevTex4 file, 4 eps figure

Evolution of the Schr\"odinger--Newton system for a self--gravitating scalar field

Using numerical techniques, we study the collapse of a scalar field configuration in the Newtonian limit of the spherically symmetric Einstein--Klein--Gordon (EKG) system, which results in the so called Schr\"odinger--Newton (SN) set of equations. We present the numerical code developed to evolve the SN system and topics related, like equilibrium configurations and boundary conditions. Also, we analyze the evolution of different initial configurations and the physical quantities associated to them. In particular, we readdress the issue of the gravitational cooling mechanism for Newtonian systems and find that all systems settle down onto a 0--node equilibrium configuration.Comment: RevTex file, 19 pages, 26 eps figures. Minor changes, matches version to appear in PR

Supermassive black holes in scalar field galaxy halos

Ultra-light scalar fields provide an interesting alternative to WIMPS as halo dark matter. In this paper we consider the effect of embedding a supermassive black hole within such a halo, and estimate the absorption probability and the accretion rate of dark matter onto the black hole. We show that the accretion rate would be small over the lifetime of a typical halo, and hence that supermassive central black holes can coexist with scalar field halos.Comment: 5 pages RevTex4, no figures. Updated file to match published versio

Exclusive rho^0 muoproduction on transversely polarised protons and deuterons

The transverse target spin azimuthal asymmetry A_UT in hard exclusive production of rho^0 mesons was measured at COMPASS by scattering 160 GeV/c muons off transversely polarised protons and deuterons. The measured asymmetry is sensitive to the nucleon helicity-flip generalised parton distributions E^q, which are related to the orbital angular momentum of quarks in the nucleon. The Q^2, x_B and p_t^2 dependence of A_UT is presented in a wide kinematic range. Results for deuterons are obtained for the first time. The measured asymmetry is small in the whole kinematic range for both protons and deuterons, which is consistent with the theoretical interpretation that contributions from GPDs E^u and E^d approximately cancel.Comment: 20 pages, 9 figures and 4 tables, updated author lis

Transverse spin effects in hadron-pair production from semi-inclusive deep inelastic scattering

First measurements of azimuthal asymmetries in hadron-pair production in deep-inelastic scattering of muons on transversely polarised ^6LiD (deuteron) and NH_3 (proton) targets are presented. The data were taken in the years 2002-2004 and 2007 with the COMPASS spectrometer using a muon beam of 160 GeV/c at the CERN SPS. The asymmetries provide access to the transversity distribution functions, without involving the Collins effect as in single hadron production. The sizeable asymmetries measured on the NH_ target indicate non-vanishing u-quark transversity and two-hadron interference fragmentation functions. The small asymmetries measured on the ^6LiD target can be interpreted as indication for a cancellation of u- and d-quark transversities.Comment: 13 pages, 4 figures, updated to the published versio

Experimental investigation of transverse spin asymmetries in muon-p SIDIS processes: Collins asymmetries

The COMPASS Collaboration at CERN has measured the transverse spin azimuthal asymmetry of charged hadrons produced in semi-inclusive deep inelastic scattering using a 160 GeV positive muon beam and a transversely polarised NH_3 target. The Collins asymmetry of the proton was extracted in the Bjorken x range 0.003<x<0.7. These new measurements confirm with higher accuracy previous measurements from the COMPASS and HERMES collaborations, which exhibit a definite effect in the valence quark region. The asymmetries for negative and positive hadrons are similar in magnitude and opposite in sign. They are compatible with model calculations in which the u-quark transversity is opposite in sign and somewhat larger than the d-quark transversity distribution function. The asymmetry is extracted as a function of Bjorken $x$, the relative hadron energy $z$ and the hadron transverse momentum p_T^h. The high statistics and quality of the data also allow for more detailed investigations of the dependence on the kinematic variables. These studies confirm the leading-twist nature of the Collins asymmetry.Comment: 11 pages, 5 figure

Global Retinoblastoma Presentation and Analysis by National Income Level

Importance: Early diagnosis of retinoblastoma, the most common intraocular cancer, can save both a child's life and vision. However, anecdotal evidence suggests that many children across the world are diagnosed late. To our knowledge, the clinical presentation of retinoblastoma has never been assessed on a global scale. Objectives: To report the retinoblastoma stage at diagnosis in patients across the world during a single year, to investigate associations between clinical variables and national income level, and to investigate risk factors for advanced disease at diagnosis. Design, Setting, and Participants: A total of 278 retinoblastoma treatment centers were recruited from June 2017 through December 2018 to participate in a cross-sectional analysis of treatment-naive patients with retinoblastoma who were diagnosed in 2017. Main Outcomes and Measures: Age at presentation, proportion of familial history of retinoblastoma, and tumor stage and metastasis. Results: The cohort included 4351 new patients from 153 countries; the median age at diagnosis was 30.5 (interquartile range, 18.3-45.9) months, and 1976 patients (45.4) were female. Most patients (n = 3685 84.7%) were from low-and middle-income countries (LMICs). Globally, the most common indication for referral was leukocoria (n = 2638 62.8%), followed by strabismus (n = 429 10.2%) and proptosis (n = 309 7.4%). Patients from high-income countries (HICs) were diagnosed at a median age of 14.1 months, with 656 of 666 (98.5%) patients having intraocular retinoblastoma and 2 (0.3%) having metastasis. Patients from low-income countries were diagnosed at a median age of 30.5 months, with 256 of 521 (49.1%) having extraocular retinoblastoma and 94 of 498 (18.9%) having metastasis. Lower national income level was associated with older presentation age, higher proportion of locally advanced disease and distant metastasis, and smaller proportion of familial history of retinoblastoma. Advanced disease at diagnosis was more common in LMICs even after adjusting for age (odds ratio for low-income countries vs upper-middle-income countries and HICs, 17.92 95% CI, 12.94-24.80, and for lower-middle-income countries vs upper-middle-income countries and HICs, 5.74 95% CI, 4.30-7.68). Conclusions and Relevance: This study is estimated to have included more than half of all new retinoblastoma cases worldwide in 2017. Children from LMICs, where the main global retinoblastoma burden lies, presented at an older age with more advanced disease and demonstrated a smaller proportion of familial history of retinoblastoma, likely because many do not reach a childbearing age. Given that retinoblastoma is curable, these data are concerning and mandate intervention at national and international levels. Further studies are needed to investigate factors, other than age at presentation, that may be associated with advanced disease in LMICs. © 2020 American Medical Association. All rights reserved

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