Testing predictability of disease outbreaks with a simple model of pathogen biogeography

Predicting disease emergence and outbreak events is a critical task for public health professionals and epidemiologists. Advances in global disease surveillance are increasingly generating datasets that are worth more than their component parts for prediction-oriented work. Here, we use a trait-free approach which leverages information on the global community of human infectious diseases to predict the biogeography of pathogens through time. Our approach takes pairwise dissimilarities between countries’ pathogen communities and pathogens’ geographical distributions and uses these to predict country–pathogen associations. We compare the success rates of our model for predicting pathogen outbreak, emergence and re-emergence potential as a function of time (e.g. number of years between training and prediction), pathogen type (e.g. virus) and transmission mode (e.g. vector-borne). With only these simple predictors, our model successfully predicts basic network structure up to a decade into the future. We find that while outbreak and re-emergence potential are especially well captured by our simple model, prediction of emergence events remains more elusive, and sudden global emergences like an influenza pandemic are beyond the predictive capacity of the model. However, these stochastic pandemic events are unlikely to be predictable from such coarse data. Together, our model is able to use the information on the existing country–pathogen network to predict pathogen outbreaks fairly well, suggesting the importance in considering information on co-occurring pathogens in a more global view even to estimate outbreak events in a single location or for a single pathogen. © 2019 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.Peer reviewe

Novel NN interaction and the spectroscopy of light nuclei

Nucleon-nucleon (NN) phase shifts and the spectroscopy of $A \le 6$ nuclei are successfully described by an inverse scattering potential that is separable with oscillator form factors.Comment: 4 pages, 1 figure, 13 table

How Low Is Too Low? Postpartum Hemorrhage Risk among Women with Thrombocytopenia

Objective To estimate the association between severity of thrombocytopenia and postpartum hemorrhage. Study Design We performed a secondary analysis of a prospective cohort of women delivering by cesarean or vaginal birth after cesarean conducted by the National Institute of Child Health and Human Development (NICHD) Maternal-Fetal Medicine Unit. Women delivering ≥ 20 weeks with platelets < 400,000/mL were included. Thrombocytopenia was defined as predelivery platelets of < 150,000/mL. Primary outcomes were (1) laboratory evidence of hemorrhage, defined as a decrease in hemoglobin ≥ 4 mg/dL and (2) clinical evidence of hemorrhage, a composite of atony, transfusion, coagulopathy, hysterectomy, laparotomy, or intensive care unit admission. Odds ratios were calculated for primary outcomes using thrombocytopenia as a dichotomous and ordinal variable. Results A total of 54,597 women were included; 5,611 (10.3%) had antepartum thrombocytopenia, 1,976 (3.6%) women had laboratory evidence of hemorrhage, and 3,862 (7.1%) had clinical evidence of hemorrhage. Thrombocytopenia was associated with both laboratory evidence of hemorrhage (adjusted odds ratio [aOR]: 1.60, 95% CI: 1.38-1.86) and clinical evidence of hemorrhage (aOR: 1.68, 95% CI: 1.52-1.83). The odds of laboratory and clinical evidence of hemorrhage increased incrementally with severity of thrombocytopenia. Conclusion Thrombocytopenia is associated with both laboratory and clinical evidence of hemorrhage; risk increases dramatically as platelet count decreases

Lattice methods and the nuclear few- and many-body problem

We begin with a brief overview of lattice calculations using chiral effective field theory and some recent applications. We then describe several methods for computing scattering on the lattice. After that we focus on the main goal, explaining the theory and algorithms relevant to lattice simulations of nuclear few- and many-body systems. We discuss the exact equivalence of four different lattice formalisms, the Grassmann path integral, transfer matrix operator, Grassmann path integral with auxiliary fields, and transfer matrix operator with auxiliary fields. Along with our analysis we include several coding examples and a number of exercises for the calculations of few- and many-body systems at leading order in chiral effective field theory.Comment: 20 pages, 3 figures, Submitted to Lect. Notes Phys., "An advanced course in computational nuclear physics: Bridging the scales from quarks to neutron stars", M. Hjorth-Jensen, M. P. Lombardo, U. van Kolck, Editor

Chaos Driven Decay of Nuclear Giant Resonances: Route to Quantum Self-Organization

The influence of background states with increasing level of complexity on the strength distribution of the isoscalar and isovector giant quadrupole resonance in $^{40}$Ca is studied. It is found that the background characteristics, typical for chaotic systems, strongly affects the fluctuation properties of the strength distribution. In particular, the small components of the wave function obey a scaling law analogous to self-organized systems at the critical state. This appears to be consistent with the Porter-Thomas distribution of the transition strength.Comment: 14 pages, 4 Figures, Illinois preprint P-93-12-106, Figures available from the author

Management of pregnancy and survival of infants with trisomy 13 or trisomy 18

Objective The objective of this study was to describe antenatal/intrapartum management and survival of liveborn infants with known trisomy 13 (T13) or trisomy 18 (T18) based on planned neonatal care. Study Design This is a retrospective cohort study of singleton pregnancies complicated by T13/T18 at a tertiary center from 2004 to 2015. We included pregnancies with antenatal or neonatal cytogenetic T13/T18 diagnosis and excluded those which were terminated or had a fetal demise < 20 weeks. We compared antenatal/intrapartum management and neonatal survival by planned neonatal care, defined as either neonatal intervention (INT), including neonatal cardiopulmonary resuscitative measures or comfort care (CC) without resuscitative measures. Results In this study, 32 women (10 with T13 and 22 with T18) met study criteria; 12 (38%) elected INT and 20 (62%) CC. Compared with those who elected INT, women who elected CC were more likely to undergo elective induction (40 vs. 0%, p = 0.01), have an intrapartum stillbirth (0 vs. 32%, p = 0.14), and deliver vaginally (25 vs. 63%, p < 0.01). In neonatal survival analysis (n = 26), median survival was longer in the INT group compared with CC group (64 days [interquartile range, IQR: 2, 155) vs. 3 days [IQR]: 0.3, 42), p = 0.28), but survival to hospital discharge was similar (53 vs. 57%, p = 0.95). Conclusion Regardless of desired level of neonatal INT, many women who continue pregnancies complicated by T13/18 have infants who survive beyond hospital discharge

Excited Baryons in Lattice QCD

We present first results for the masses of positive and negative parity excited baryons calculated in lattice QCD using an O(a^2)-improved gluon action and a fat-link irrelevant clover (FLIC) fermion action in which only the irrelevant operators are constructed with APE-smeared links. The results are in agreement with earlier calculations of N^* resonances using improved actions and exhibit a clear mass splitting between the nucleon and its chiral partner. An correlation matrix analysis reveals two low-lying J^P=(1/2)^- states with a small mass splitting. The study of different Lambda interpolating fields suggests a similar splitting between the lowest two Lambda1/2^- octet states. However, the empirical mass suppression of the Lambda^*(1405) is not evident in these quenched QCD simulations, suggesting a potentially important role for the meson cloud of the Lambda^*(1405) and/or a need for more exotic interpolating fields.Comment: Correlation matrix analysis performed. Increased to 400 configurations. 22 pages, 13 figures, 15 table

A Region of Violent Star Formation in the Irr Galaxy IC 10: Structure and Kinematics of Ionized and Neutral Gas

We have used observations of the galaxy IC 10 at the 6-m telescope of the Special Astrophysical Observatory with the SCORPIO focal reducer in the Fabry-Perot interferometer mode and with the MPFS spectrograph to study the structure and kinematics of ionized gas in the central region of current intense star formation. Archive VLA 21-cm observations are used to analyze the structure and kinematics of neutral gas in this region. High-velocity wings of the H-alpha and [SII] emission lines were revealed in the inner cavity of the nebula HL 111 and in other parts of the complex of violent star formation. We have discovered local expanding neutral-gas shells around the nebulae HL 111 and HL 106.Comment: 22 pages, 10 figures; accepted in Astronomy Report

Exact spectra, spin susceptibilities and order parameter of the quantum Heisenberg antiferromagnet on the triangular lattice

Exact spectra of periodic samples are computed up to $N=36$. Evidence of an extensive set of low lying levels, lower than the softest magnons, is exhibited. These low lying quantum states are degenerated in the thermodynamic limit; their symmetries and dynamics as well as their finite-size scaling are strong arguments in favor of N\'eel order. It is shown that the N\'eel order parameter agrees with first-order spin-wave calculations. A simple explanation of the low energy dynamics is given as well as the numerical determinations of the energies, order parameter and spin susceptibilities of the studied samples. It is shown how suitable boundary conditions, which do not frustrate N\'eel order, allow the study of samples with $N=3p+1$ spins. A thorough study of these situations is done in parallel with the more conventional case $N=3p$.Comment: 36 pages, REVTeX 3.0, 13 figures available upon request, LPTL preprin

Weaker HLA footprints on HIV in the unique and highly genetically admixed host population of Mexico

HIV circumvents HLA class I-restricted CD8+ T-cell responses through selection of escape mutations that leave characteristic mutational “footprints,” also known as HLA-associated polymorphisms (HAPs), on HIV sequences at the population level. While many HLA footprints are universal across HIV subtypes and human populations, others can be region specific as a result of the unique immunogenetic background of each host population. Using a published probabilistic phylogenetically informed model, we compared HAPs in HIV Gag and Pol (PR-RT) in 1,612 subtype B-infected, antiretroviral treatment-naive individuals from Mexico and 1,641 individuals from Canada/United States. A total of 252 HLA class I allele subtypes were represented, including 140 observed in both cohorts, 67 unique to Mexico, and 45 unique to Canada/United States. At the predefined statistical threshold of a q value of <0.2, 358 HAPs (201 in Gag, 157 in PR-RT) were identified in Mexico, while 905 (534 in Gag and 371 in PR-RT) were identified in Canada/United States. HAPs identified in Mexico included both canonical HLA-associated escape pathways and novel associations, in particular with HLA alleles enriched in Amerindian and mestizo populations. Remarkably, HLA footprints on HIV in Mexico were not only fewer but also, on average, significantly weaker than those in Canada/United States, although some exceptions were noted. Moreover, exploratory analyses suggested that the weaker HLA footprint on HIV in Mexico may be due, at least in part, to weaker and/or less reproducible HLA-mediated immune pressures on HIV in this population. The implications of these differences for natural and vaccine-induced anti-HIV immunity merit further investigation