Variational Matrix Product Ansatz for Nonuniform Dynamics in the Thermodynamic Limit

We describe how to implement the time-dependent variational principle for matrix product states in the thermodynamic limit for nonuniform lattice systems. This is achieved by confining the nonuniformity to a (dynamically growable) finite region with fixed boundary conditions. The suppression of unphysical quasiparticle reflections from the boundary of the nonuniform region is also discussed. Using this algorithm we study the dynamics of localized excitations in infinite systems, which we illustrate in the case of the spin-1 anti-ferromagnetic Heisenberg model and the $\phi^4$ model.Comment: 8 pages, 5 figures, tensor network diagrams. Code available at http://amilsted.github.io/evoMPS

Long-term optical variability of PKS 2155-304

Aims: The optical variability of the blazar PKS 2155-304 is investigated to characterise the red noise behaviour at largely different time scales from 20 days to O(>10 yrs). Methods: The long-term optical light curve of PKS 2155-304 is assembled from archival data as well as from so-far unpublished observations mostly carried out with the ROTSE-III and the ASAS robotic telescopes. A forward folding technique is used to determine the best-fit parameters for a model of a power law with a break in the power spectral density function (PSD). The best-fit parameters are estimated using a maximum-likelihood method with simulated light curves in conjunction with the Lomb Scargle Periodogram (LSP) and the first-order Structure Function (SF). In addition, a new approach based upon the so-called Multiple Fragments Variance Function (MFVF) is introduced and compared to the other methods. Simulated light curves have been used to confirm the reliability of these methods as well as to estimate the uncertainties of the best-fit parameters. Results: The light curve is consistent with the assumed broken power-law PSD. All three methods agree within the estimated uncertainties with the MFVF providing the most accurate results. The red-noise behaviour of the PSD in frequency f follows a power law with f^-{\beta}, {\beta}=1.8 +0.1/-0.2 and a break towards f^0 at frequencies lower than f_min=(2.7 +2.2/-1.6 yrs)^-1.Comment: 10 pages, 8 figures, the ROTSE-light curve can be downloaded from http://vizier.cfa.harvard.edu/viz-bin/VizieR?-source=J/A+A/531/A12

Effects of rapid prey evolution on predator-prey cycles

We study the qualitative properties of population cycles in a predator-prey system where genetic variability allows contemporary rapid evolution of the prey. Previous numerical studies have found that prey evolution in response to changing predation risk can have major quantitative and qualitative effects on predator-prey cycles, including: (i) large increases in cycle period, (ii) changes in phase relations (so that predator and prey are cycling exactly out of phase, rather than the classical quarter-period phase lag), and (iii) "cryptic" cycles in which total prey density remains nearly constant while predator density and prey traits cycle. Here we focus on a chemostat model motivated by our experimental system [Fussmann et al. 2000,Yoshida et al. 2003] with algae (prey) and rotifers (predators), in which the prey exhibit rapid evolution in their level of defense against predation. We show that the effects of rapid prey evolution are robust and general, and furthermore that they occur in a specific but biologically relevant region of parameter space: when traits that greatly reduce predation risk are relatively cheap (in terms of reductions in other fitness components), when there is coexistence between the two prey types and the predator, and when the interaction between predators and undefended prey alone would produce cycles. Because defense has been shown to be inexpensive, even cost-free, in a number of systems [Andersson and Levin 1999, Gagneux et al. 2006,Yoshida et al. 2004], our discoveries may well be reproduced in other model systems, and in nature. Finally, some of our key results are extended to a general model in which functional forms for the predation rate and prey birth rate are not specified.Comment: 35 pages, 8 figure

Non-local effects in the mean-field disc dynamo. II. Numerical and asymptotic solutions

The thin-disc global asymptotics are discussed for axisymmetric mean-field dynamos with vacuum boundary conditions allowing for non-local terms arising from a finite radial component of the mean magnetic field at the disc surface. This leads to an integro-differential operator in the equation for the radial distribution of the mean magnetic field strength, $Q(r)$ in the disc plane at a distance $r$ from its centre; an asymptotic form of its solution at large distances from the dynamo active region is obtained. Numerical solutions of the integro-differential equation confirm that the non-local effects act similarly to an enhanced magnetic diffusion. This leads to a wider radial distribution of the eigensolution and faster propagation of magnetic fronts, compared to solutions with the radial surface field neglected. Another result of non-local effects is a slowly decaying algebraic tail of the eigenfunctions outside the dynamo active region, $Q(r)\sim r^{-4}$, which is shown to persist in nonlinear solutions where $\alpha$-quenching is included. The non-local nature of the solutions can affect the radial profile of the regular magnetic field in spiral galaxies and accretion discs at large distances from the centre.Comment: Revised version, as accepted; Geophys. Astrophys. Fluid Dyna

Toward a General Model for the Evolutionary Dynamics of Gene Duplicates

Gene duplication is an important process in the functional divergence of genes and genomes. Several processes have been described that lead to duplicate gene retention over different timescales after both smaller-scale events and whole-genome duplication, including neofunctionalization, subfunctionalization, and dosage balance. Two common modes of duplicate gene loss include nonfunctionalization and loss due to population dynamics (failed fixation). Previous work has characterized expectations of duplicate gene retention under the neofunctionalization and subfunctionalization models. Here, that work is extended to dosage balance using simulations. A general model for duplicate gene loss/retention is then presented that is capable of fitting expectations under the different models, is defined at t = 0, and decays to an orthologous asymptotic rate rather than zero, based upon a modified Weibull hazard function. The model in a maximum likelihood framework shows the property of identifiability, recovering the evolutionary mechanism and parameters of simulation. This model is also capable of recovering the evolutionary mechanism of simulation from data generated using an unrelated network population genetic model. Lastly, the general model is applied as part of a mixture model to recent gene duplicates from the Oikopleura dioica genome, suggesting that neofunctionalization may be an important process leading to duplicate gene retention in that organism

Investigation of SARS-CoV-2 faecal shedding in the community: a prospective household cohort study (COVID-LIV) in the UK

Background SARS-CoV-2 is frequently shed in the stool of patients hospitalised with COVID-19. The extent of faecal shedding of SARS-CoV-2 among individuals in the community, and its potential to contribute to spread of disease, is unknown. Methods In this prospective, observational cohort study among households in Liverpool, UK, participants underwent weekly nasal/throat swabbing to detect SARS-CoV-2 virus, over a 12-week period from enrolment starting July 2020. Participants that tested positive for SARS-CoV-2 were asked to provide a stool sample three and 14 days later. In addition, in October and November 2020, during a period of high community transmission, stool sampling was undertaken to determine the prevalence of SARS-CoV-2 faecal shedding among all study participants. SARS-CoV-2 RNA was detected using Real-Time PCR. Results A total of 434 participants from 176 households were enrolled. Eighteen participants (4.2%: 95% confidence interval [CI] 2.5–6.5%) tested positive for SARS-CoV-2 virus on nasal/throat swabs and of these, 3/17 (18%: 95% CI 4–43%) had SARS-CoV-2 detected in stool. Two of three participants demonstrated ongoing faecal shedding of SARS-CoV-2, without gastrointestinal symptoms, after testing negative for SARS-CoV-2 in respiratory samples. Among 165/434 participants without SARS-CoV-2 infection and who took part in the prevalence study, none had SARS-CoV-2 in stool. There was no demonstrable household transmission of SARS-CoV-2 among households containing a participant with faecal shedding. Conclusions Faecal shedding of SARS-CoV-2 occurred among community participants with confirmed SARS-CoV-2 infection. However, during a period of high community transmission, faecal shedding of SARS-CoV-2 was not detected among participants without SARS-CoV-2 infection. It is unlikely that the faecal-oral route plays a significant role in household and community transmission of SARS-CoV-2

Creating and curating an archive: Bury St Edmunds and its Anglo-Saxon past

This contribution explores the mechanisms by which the Benedictine foundation of Bury St Edmunds sought to legitimise and preserve their spurious pre-Conquest privileges and holdings throughout the Middle Ages. The archive is extraordinary in terms of the large number of surviving registers and cartularies which contain copies of Anglo-Saxon charters, many of which are wholly or partly in Old English. The essay charts the changing use to which these ancient documents were put in response to threats to the foundation's continued enjoyment of its liberties. The focus throughout the essay is to demonstrate how pragmatic considerations at every stage affects the development of the archive and the ways in which these linguistically challenging texts were presented, re-presented, and represented during the Abbey’s history

Substitutions are boring: some arguments about parallel mutations and repetitive DNA

Extant genomes are largely shaped by the global transposition, copy number fluctuation, and rearrangement of DNA sequences, rather than by the substitutions of single nucleotides. Although many of these large-scale mutations have low probabilities and are unlikely to repeat, others are recurrent or predictable in their effects, leading to stereotyped genome architectures and genetic variation in both eukaryotes and prokaryotes. Such recurrent, parallel mutation modes can profoundly shape the paths taken by evolution, and directly undermine the Wright-Fisher model of evolutionary genetics. Similar patterns are also evident at the smaller scales of individual genes or short genomic sequences. The scale and extent of this ‘non-substitution’ variation has only recently come into focus through the advent of new genomic technologies; however, it still not widely included in genotype-phenotype association studies. In this review, we identify the common features of these disparate mutational phenomena and comment on the importance and interpretation of these mutational patterns

Association of health confidence with hospital length of stay and readmission

Background: Length of stay (LOS) is an important measure of hospital quality and may be impacted by patient participation. However, concepts of patient participation, like health confidence, have received little examination in hospitalized patients' LOS, especially in diverse populations. Objective: To determine if the Health Confidence Score (HCS) is associated with hospital LOS and readmission in a socioeconomically diverse population. Designs, settings and participants: We conducted a prospective cohort study in 2022 of adult general medicine patients at an academic hospital in Chicago, Illinois. Intervention: None. Main outcome and measures: Patient-reported responses to the HCS (scored 0 [lowest health confidence] to ‒12 [highest health confidence]), as well as demographic, socioeconomic, and clinical questions, were collected. Primary outcome was LOS and secondary outcomes were 30- and 90-day readmission. Results: Among 2797 socioeconomically diverse patients who completed the survey (response rate 28.5%), there was an average HCS of 9.19 (SD 2.68, range 0-12). Using linear regression, patients with high HCS (HCS ≥ 9) had a 1.53-day lower LOS (p < .01, 95% CI [-2.11, -0.95]) than patients with a low HCS (HCS < 9). This association remained when examining individual HCS questions and controlling for covariates. In logistic regression, HCS was not significantly associated with readmission, but the question "I am involved in decisions about me" (adjusted model: OR 0.83; 95% CI [0.71, 0.96]; p = .01) was associated with 90-day readmission.</p