SimpactCyan 1.0 : an open-source simulator for individual-based models in HIV epidemiology with R and Python interfaces

SimpactCyan is an open-source simulator for individual-based models in HIV epidemiology. Its core algorithm is written in C++ for computational efficiency, while the R and Python interfaces aim to make the tool accessible to the fast-growing community of R and Python users. Transmission, treatment and prevention of HIV infections in dynamic sexual networks are simulated by discrete events. A generic “intervention” event allows model parameters to be changed over time, and can be used to model medical and behavioural HIV prevention programmes. First, we describe a more efficient variant of the modified Next Reaction Method that drives our continuous-time simulator. Next, we outline key built-in features and assumptions of individual-based models formulated in SimpactCyan, and provide code snippets for how to formulate, execute and analyse models in SimpactCyan through its R and Python interfaces. Lastly, we give two examples of applications in HIV epidemiology: the first demonstrates how the software can be used to estimate the impact of progressive changes to the eligibility criteria for HIV treatment on HIV incidence. The second example illustrates the use of SimpactCyan as a data-generating tool for assessing the performance of a phylodynamic inference framework

Exciton spin dynamics and photoluminescence polarization of CdSe/CdS dot-in-rod nanocrystals in high magnetic fields

The exciton spin dynamics and polarization properties of the related emission are investigated in colloidal CdSe/CdS dot-in-rod (DiR) and spherical core/shell nanocrystal (NC) ensembles by magneto-optical photoluminescence (PL) spectroscopy in magnetic fields up to 15 T. It is shown that the degree of circular polarization (DCP) of the exciton emission induced by the magnetic field is affected by the NC geometry as well as the exciton fine structure and can provide information on nanorod orientation. A theory to describe the circular and linear polarization properties of the NC emission in magnetic field is developed. It takes into account phonon mediated coupling between the exciton fine structure states as well as the dielectric enhancement effect resulting from the anisotropic shell of DiR NCs. This theoretical approach is used to model the experimental results and allows us to explain most of the measured features. The spin dynamics of the dark excitons is investigated in magnetic fields by time-resolved photoluminescence. The results highlight the importance of confined acoustic phonons in the spin relaxation of dark excitons. The bare core surface as well as the core/shell interface give rise to an efficient spin relaxation channel, while the surface of core/shell NCs seems to play only a minor role.Comment: 18 pages, 15 figure

Iron Deficiency Anemia, Population Health and Frailty in a Modern Portuguese Skeletal Sample

INTRODUCTION Portugal underwent significant political, demographic and epidemiological transitions during the 20th century resulting in migration to urban areas with subsequent overcrowding and issues with water sanitation. This study investigates population health during these transitions and interprets results within a framework of recent history and present-day public health information. We investigate skeletal evidence for anemia (cribra orbitalia and porotic hyperostosis) as indicators of stress and frailty-i.e., whether the lesions contribute to susceptibility for disease or increased risk of death. METHODS The presence and severity of skeletal lesions were compared against known sex and cause of death data to investigate potential heterogeneity in frailty and the relationship between lesions and risk of dying over time. Additionally, we tested for the presence of selective mortality in our data (i.e., whether or not the sample is biased for individuals with higher frailty). Our sample derives from a large, documented, modern Portuguese collection from Lisbon and is the first study of its kind using a documented collection. The collection represents primarily middle-class individuals. RESULTS AND CONCLUSIONS: Analyses indicated that porotic hyperostosis became more common and severe over time, while cribra orbitalia severity increased over time. Neither process was linked to cause of death. However, there was a significant relationship to sex; males exhibited a higher prevalence and severity of lesions and increased mortality. A Gompertz function showed decreased survivorship in early life but increased survivorship over age 60. Using comorbidities of anemia, we were unable to detect selective mortality-i.e., in our sample, lesions do not represent a sign of poor health or increased frailty and are not significantly linked with a decreased mean age-at-death. However, lesion prevalence and severity do reflect the socioeconomic processes in urban Lisbon during the 1800s and 1900s and the possibility of water-borne parasites as the contributing factor for iron deficiency anemia

Analysis of chromosome positions in the interphase nucleus of Chinese hamster cells by laser-UV-microirradiation experiments

Unsynchronized cells of an essentially diploid strain of female Chinese hamster cells derived from lung tissue (CHL) were laser-UV-microirradiated (=257 nm) in the nucleus either at its central part or at its periphery. After 7–9 h postincubation with 0.5 mM caffeine, chromosome preparations were made in situ. Twenty-one and 29 metaphase spreads, respectively, with partial chromosome shattering (PCS) obtained after micro-irradiation at these two nuclear sites, were Q-banded and analyzed in detail. A positive correlation was observed between the frequency of damage of chromosomes and both their DNA content and length at metaphase. No significant difference was observed between the frequencies of damage obtained for individual chromosomes at either site of microirradiation. The frequency of joint damage of homologous chromosomes was low as compared to nonhomologous ones. Considerable variation was noted in different cells in the combinations of jointly shattered chromosomes. Evidence which justifies an interpretation of these data in terms of an interphase arrangement of chromosome territories is discussed. Our data strongly argue against somatic pairing as a regular event, and suggest a considerable variability of chromosome positions in different nuclei. However, present data do not exclude the possibility of certain non-random chromosomal arrangements in CHL-nuclei. The interphase chromosome distribution revealed by these experiments is compared with centromere-centromere, centromere-center and angle analyses of metaphase spreads and the relationship between interphase and metaphase arrangements of chromosomes is discussed

Phonon-mediated and weakly size-dependent electron and hole cooling in CsPbBr3 nanocrystals revealed by atomistic simulations and ultrafast spectroscopy

We combine state-of-the-art ultrafast photoluminescence and absorption spectroscopy and nonadiabatic molecular dynamics simulations to investigate charge-carrier cooling in CsPbBr3 nanocrystals over a very broad size regime, from 0.8 to 12 nm. Contrary to the prevailing notion that polaron formation slows down charge-carrier cooling in lead-halide perovskites, no suppression of carrier cooling is observed in CsPbBr3 nanocrystals except for a slow cooling (over similar to 10 ps) of "warm" electrons in the vicinity (within similar to 0.1 eV) of the conduction band edge. At higher excess energies, electrons and holes cool with similar rates, on the order of 1 eV ps(-1) carrier(-1), increasing weakly with size. Our ab initio simulations suggest that cooling proceeds via fast phonon-mediated intraband transitions driven by strong and size-dependent electron-phonon coupling. The presented experimental and computational methods yield the spectrum of involved phonons and may guide the development of devices utilizing hot charge carriers

Comprehensive embryo testing. Experts opinions regarding future directions: an expert panel study on comprehensive embryo testing

What do scientists in the field of preimplantation genetic diagnosis (PGD) and preimplantation genetic screening (PGS) consider to be the future direction of comprehensive embryo testing? Although there are many biological and technical limitations, as well as uncertainties regarding the meaning of genetic variation, comprehensive embryo testing will impact the IVF/PGD practice and a timely ethical reflection is needed. Comprehensive testing using microarrays is currently being introduced in the context of PGD and PGS, and it is to be expected that whole-genome sequencing will also follow. Current ethical and empirical sociological research on embryo testing focuses on PGD as it is practiced now. However, empirical research and systematic reflection regarding the impact of comprehensive techniques for embryo testing is missing. In order to understand the potential of this technology and to be able to adequately foresee its implications, we held an expert panel with seven pioneers in PGD. We conducted an expert panel in October 2011 with seven PGD pioneers from Belgium, The Netherlands, Germany and the UK. Participants expected the use of comprehensive techniques in the context of PGD. However, the introduction of these techniques in embryo testing requires timely ethical reflection as it involves a shift from choosing an embryo without a particular genetic disease (i.e. PGD) or most likely to result in a successful pregnancy (i.e. PGS) to choosing the best embryo based on a much wider set of criteria. Such ethical reflection should take account of current technical and biological limitations and also of current uncertainties with regard to the meaning of genetic variance. However, ethicists should also not be afraid to look into the future. There was a general agreement that embryo testing will be increasingly preceded by comprehensive preconception screening, thus enabling smart combinations of genetic testing. The group was composed of seven participants from four Western Europe countries. As willingness to participate in this study may be connected with expectations regarding the pace and direction of future developments, selection bias cannot be excluded. The introduction of comprehensive screening techniques in embryo testing calls for further ethical reflection that is grounded in empirical work. Specifically, there is a need for studies querying the opinions of infertile couples undergoing IVF/PGS regarding the desirability of embryo screening beyond aneuploidy. This research was supported by the CSG, Centre for Society and Life Sciences (project number: 70.1.074). The authors declare no conflict of interest. N/A

Sex chromosome positions in human interphase nuclei as studied by in situ hybridization with chromosome specific DNA probes

Two cloned repetitive DNA probes, pXBR and CY1, which bind preferentially to specific regions of the human X and Y chromosome, respectively, were used to study the distribution of the sex chromosomes in human lymphocyte nuclei by in situ hybridization experiments. Our data indicate a large variability of the distances between the sex chromosomes in male and female interphase nuclei. However, the mean distance observed between the X and Y chromosome was significantly smaller than the mean distance observed between the two X-chromosomes. The distribution of distances determined experimentally is compared with three model distributions of distances, and the question of a non-random distribution of sex chromosomes is discussed. Mathematical details of these model distributions are provided in an Appendix to this paper. In the case of a human translocation chromosome (XqterXp22.2::Yq11Y qter) contained in the Chinese hamster x human hybrid cell line 445 x 393, the binding sites of pXBR and CY1 were found close to each other in most interphase nuclei. These data demonstrate the potential use of chromosome-specific repetitive DNA probes to study the problem of interphase chromosome topography

Quantum Rod Emission Coupled to Plasmonic Lattice Resonances: A Collective Directional Source of Polarized Light

We demonstrate that an array of optical antennas may render a thin layer of randomly oriented semiconductor nanocrystals into an enhanced and highly directional source of polarized light. The array sustains collective plasmonic lattice resonances which are in spectral overlap with the emission of the nanocrystals over narrow angular regions. Consequently, different photon energies of visible light are enhanced and beamed into definite directions.Comment: 4 pages, 3 figure

The social contact hypothesis under the assumption of endemic equilibrium: Elucidating the transmission potential of VZV in Europe.

The basic reproduction number R0 and the effective reproduction number R are pivotal parameters in infectious disease epidemiology, quantifying the transmission potential of an infection in a population. We estimate both parameters from 13 pre-vaccination serological data sets on varicella zoster virus (VZV) in 12 European countries and from population-based social contact surveys under the commonly made assumptions of endemic and demographic equilibrium. The fit to the serology is evaluated using the inferred effective reproduction number R as a model eligibility criterion combined with AIC as a model selection criterion. For only 2 out of 12 countries, the common choice of a constant proportionality factor is sufficient to provide a good fit to the seroprevalence data. For the other countries, an age-specific proportionality factor provides a better fit, assuming physical contacts lasting longer than 15 min are a good proxy for potential varicella transmission events. In all countries, primary infection with VZV most often occurs in early childhood, but there is substantial variation in transmission potential with R0 ranging from 2.8 in England and Wales to 7.6 in The Netherlands. Two non-parametric methods, the maximal information coefficient (MIC) and a random forest approach, are used to explain these differences in R0 in terms of relevant country-specific characteristics. Our results suggest an association with three general factors: inequality in wealth, infant vaccination coverage and child care attendance. This illustrates the need to consider fundamental differences between European countries when formulating and parameterizing infectious disease models