DM-PhyClus: A Bayesian phylogenetic algorithm for infectious disease transmission cluster inference

Background. Conventional phylogenetic clustering approaches rely on arbitrary cutpoints applied a posteriori to phylogenetic estimates. Although in practice, Bayesian and bootstrap-based clustering tend to lead to similar estimates, they often produce conflicting measures of confidence in clusters. The current study proposes a new Bayesian phylogenetic clustering algorithm, which we refer to as DM-PhyClus, that identifies sets of sequences resulting from quick transmission chains, thus yielding easily-interpretable clusters, without using any ad hoc distance or confidence requirement. Results. Simulations reveal that DM-PhyClus can outperform conventional clustering methods, as well as the Gap procedure, a pure distance-based algorithm, in terms of mean cluster recovery. We apply DM-PhyClus to a sample of real HIV-1 sequences, producing a set of clusters whose inference is in line with the conclusions of a previous thorough analysis. Conclusions. DM-PhyClus, by eliminating the need for cutpoints and producing sensible inference for cluster configurations, can facilitate transmission cluster detection. Future efforts to reduce incidence of infectious diseases, like HIV-1, will need reliable estimates of transmission clusters. It follows that algorithms like DM-PhyClus could serve to better inform public health strategies

Pressure-induced hole doping of the Hg-based cuprate superconductors

We investigate the electronic structure and the hole content in the copper-oxygen planes of Hg based high Tc cuprates for one to four CuO2 layers and hydrostatic pressures up to 15 GPa. We find that with the pressure-induced additional number of holes of the order of 0.05e the density of states at the Fermi level changes approximately by a factor of 2. At the same time the saddle point is moved to the Fermi level accompanied by an enhanced k_z dispersion. This finding explains the pressure behavior of Tc and leads to the conclusion that the applicability of the van Hove scenario is restricted. By comparison with experiment, we estimate the coupling constant to be of the order of 1, ruling out the weak coupling limit.Comment: 4 pages, 4 figure

Two components for one resistivity in LaVO3/SrTiO3 heterostructures

A series of 100 nm LaVO3 thin films have been synthesized on (001)-oriented SrTiO3 substrates using the pulsed laser deposition technique, and the effects of growth temperature are analyzed. Transport properties reveal a large electronic mobility and a non-linear Hall effect at low temperature. In addition, a cross-over from a semiconducting state at high-temperature to a metallic state at low-temperature is observed, with a clear enhancement of the metallic character as the growth temperature increases. Optical absorption measurements combined with the two-bands analysis of the Hall effect show that the metallicity is induced by the diffusion of oxygen vacancies in the SrTiO3 substrate. These results allow to understand that the film/substrate heterostructure behaves as an original semiconducting-metallic parallel resistor, and electronic transport properties are consistently explained.Comment: Improved version as accepted in Journ Phys: Cond Mat. Additional Optical measurements are presente

EVALUATING THE EFFECT OF A PERCEPTUAL-COGNITIVE TASK ON LANDING BIOMECHANICS OF THE LOWER LIMB

The majority of anterior cruciate ligament (ACL) injuries occur without player contact following a movement such as a landing or change of direction. Much attention has been focused on muscle strengthening to delay the biomechanical effects of muscle fatigue reduce the risk of injury. However, recent studies have indicated there may be a link between cognitive factors and non-contact ACL injuries. In this study, kinematic data was acquired from seven athletes who performed jumping and landing trials. Half of the trials performed while tracking multiple virtual objects in a 3D volume, meant to simulate a game-situation cognitive load. For all participants, significant differences were observed for several angles. Increased knee abduction, which is known to increase strain on the ACL, was observed in 4 of 7 participants

SiNx:Tb3+--Yb3+, an efficient down-conversion layer compatible with a silicon solar cell process

SiN x : Tb 3+-Yb 3+, an efficient down-conversion layer compatible with silicon solar cell process Abstract Tb 3+-Yb 3+ co-doped SiN x down-conversion layers compatible with silicon Photovoltaic Technology were prepared by reactive magnetron co-sputtering. Efficient sensitization of Tb 3+ ions through a SiN x host matrix and cooperative energy transfer between Tb 3+ and Yb 3+ ions were evidenced as driving mechanisms of the down-conversion process. In this paper, the film composition and microstructure are investigated alongside their optical properties, with the aim of maximizing the rare earth ions incorporation and emission efficiency. An optimized layer achieving the highest Yb 3+ emission intensity was obtained by reactive magnetron co-sputtering in a nitride rich atmosphere for 1.2 W/cm${}^2$ and 0.15 W/cm${}^2$ power density applied on the Tb and Yb targets, respectively. It was determined that depositing at 200 {\textdegree}C and annealing at 850 {\textdegree}C leads to comparable Yb 3+ emission intensity than depositing at 500 {\textdegree}C and annealing at 600 {\textdegree}C, which is promising for applications toward silicon solar cells.Comment: Solar Energy Materials and Solar Cells, Elsevier, 201

Influence of BMI and dietary restraint on self-selected portions of prepared meals in US women

The rise of obesity prevalence has been attributed in part to an increase in food and beverage portion sizes selected and consumed among overweight and obese consumers. Nevertheless, evidence from observations of adults is mixed and contradictory findings might reflect the use of small or unrepresentative samples. The objective of this study was i) to determine the extent to which BMI and dietary restraint predict self-selected portion sizes for a range of commercially available prepared savoury meals and ii) to consider the importance of these variables relative to two previously established predictors of portion selection, expected satiation and expected liking. A representative sample of female consumers (N = 300, range 18–55 years) evaluated 15 frozen savoury prepared meals. For each meal, participants rated their expected satiation and expected liking, and selected their ideal portion using a previously validated computer-based task. Dietary restraint was quantified using the Dutch Eating Behaviour Questionnaire (DEBQ-R). Hierarchical multiple regression was performed on self-selected portions with age, hunger level, and meal familiarity entered as control variables in the first step of the model, expected satiation and expected liking as predictor variables in the second step, and DEBQ-R and BMI as exploratory predictor variables in the third step. The second and third steps significantly explained variance in portion size selection (18% and 4%, respectively). Larger portion selections were significantly associated with lower dietary restraint and with lower expected satiation. There was a positive relationship between BMI and portion size selection (p = 0.06) and between expected liking and portion size selection (p = 0.06). Our discussion considers future research directions, the limited variance explained by our model, and the potential for portion size underreporting by overweight participants

Consumer Understanding, Perception and Interpretation of Serving Size Information on Food Labels: A Scoping Review

Theincreaseinpackagedfoodandbeverageportionsizeshasbeenidentifiedasapotential factorimplicatedintheriseoftheprevalenceofobesity. Inthiscontext,theobjectiveofthissystematic scopingreviewwastoinvestigatehowhealthyadultsperceiveandinterpretservingsizeinformation on food packages and how this influences product perception and consumption. Such knowledge is needed to improve food labelling understanding and guide consumers toward healthier portion size choices. A search of seven databases (2010 to April 2019) provided the records for title and abstract screening, with relevant articles assessed for eligibility in the full-text. Fourteen articles met the inclusion criteria, with relevant data extracted by one reviewer and checked for consistency by a second reviewer. Twelve studies were conducted in North America, where the government regulates serving size information. Several studies reported a poor understanding of serving size labelling. Indeed, consumers interpreted the labelled serving size as a recommended serving for dietary guidelines for healthy eating rather than a typical consumption unit, which is set by the manufacturer or regulated in some countries such as in the U.S. and Canada. Not all studies assessed consumption; however, larger labelled serving sizes resulted in larger self-selected portion sizes in three studies. However, another study performed on confectionary reported the opposite effect, with largerlabelledservingsizesleadingtoreducedconsumption. Thelimitednumberofincludedstudies showedthatlabelledservingsizeaffectsportionsizeselectionandconsumption,andthatanylabelled serving size format changes may result in increased portion size selection, energy intake and thus contribute to the rise of the prevalence of overweight and obesity. Research to test cross-continentally labelled serving size format changes within experimental and natural settings (e.g., at home) are needed. In addition, tailored, comprehensive and serving-size-specific food literacy initiatives need to be evaluated to provide recommendations for effective serving size labelling. This is required to ensure the correct understanding of nutritional content, as well as informing food choices and consumption, for both core foods and discretionary foods. Keywords: serving size; portion size; food labeling; nutrition facts label; back of pack; front of pack; health framin

ZFIRE: Using Hα\alpha equivalent widths to investigate the in situ initial mass function at z~2

We use the ZFIRE survey (http://zfire.swinburne.edu.au) to investigate the high mass slope of the initial mass function (IMF) for a mass-complete (log10(M$_*$/M$_\odot$)~9.3) sample of 102 star-forming galaxies at z~2 using their H$\alpha$ equivalent widths (H$\alpha$-EW) and rest-frame optical colours. We compare dust-corrected H$\alpha$-EW distributions with predictions of star-formation histories (SFH) from PEGASE.2 and Starburst99 synthetic stellar population models. We find an excess of high H$\alpha$-EW galaxies that are up to 0.3--0.5 dex above the model-predicted Salpeter IMF locus and the H$\alpha$-EW distribution is much broader (10--500 \AA) than can easily be explained by a simple monotonic SFH with a standard Salpeter-slope IMF. Though this discrepancy is somewhat alleviated when it is assumed that there is no relative attenuation difference between stars and nebular lines, the result is robust against observational biases, and no single IMF (i.e. non-Salpeter slope) can reproduce the data. We show using both spectral stacking and Monte Carlo simulations that starbursts cannot explain the EW distribution. We investigate other physical mechanisms including models with variations in stellar rotation, binary star evolution, metallicity, and the IMF upper-mass cutoff. IMF variations and/or highly rotating extreme metal poor stars (Z~0.1Z$_\odot$) with binary interactions are the most plausible explanations for our data. If the IMF varies, then the highest H$\alpha$-EWs would require very shallow slopes ($\Gamma$>-1.0) with no one slope able to reproduce the data. Thus, the IMF would have to vary stochastically. We conclude that the stellar populations at z~2 show distinct differences from local populations and there is no simple physical model to explain the large variation in H$\alpha$-EWs at z~2.Comment: Accepted to MNRAS. 43 pages, 27 Figures. Survey website: http://zfire.swinburne.edu.au

ZFIRE: A KECK/MOSFIRE Spectroscopic Survey of Galaxies in Rich Environments at z~2

We present an overview and the first data release of ZFIRE, a spectroscopic redshift survey of star-forming galaxies that utilizes the MOSFIRE instrument on Keck-I to study galaxy properties in rich environments at $1.5<z<2.5$. ZFIRE measures accurate spectroscopic redshifts and basic galaxy properties derived from multiple emission lines. The galaxies are selected from a stellar mass limited sample based on deep near infra-red imaging ($\mathrm{K_{AB}<25}$) and precise photometric redshifts from the ZFOURGE and UKIDSS surveys as well as grism redshifts from 3DHST. Between 2013--2015 ZFIRE has observed the COSMOS and UDS legacy fields over 13 nights and has obtained 211 galaxy redshifts over $1.57<z<2.66$ from a combination of nebular emission lines (such as \Halpha, \NII, \Hbeta, \OII, \OIII, \SII) observed at 1--2\micron. Based on our medium-band NIR photometry, we are able to spectrophotometrically flux calibrate our spectra to \around10\% accuracy. ZFIRE reaches $5\sigma$ emission line flux limits of \around$\mathrm{3\times10^{-18}~erg/s/cm^2}$ with a resolving power of $R=3500$ and reaches masses down to \around10$^{9}$\msol. We confirm that the primary input survey, ZFOURGE, has produced photometric redshifts for star-forming galaxies (including highly attenuated ones) accurate to $\Delta z/(1+z\mathrm{_{spec})}=0.015$ with $0.7\%$ outliers. We measure a slight redshift bias of $<0.001$, and we note that the redshift bias tends to be larger at higher masses. We also examine the role of redshift on the derivation of rest-frame colours and stellar population parameters from SED fitting techniques. The ZFIRE survey extends spectroscopically-confirmed $z\sim 2$ samples across a richer range of environments, here we make available the first public release of the data for use by the community.\footnote{\url{http://zfire.swinburne.edu.au}}Comment: Published in ApJ. Data available at http://zfire.swinburne.edu.au, Code for figures at https://github.com/themiyan/zfire_survey, 31 pages, 24 figure