Nonchaotic Stagnant Motion in a Marginal Quasiperiodic Gradient System

A one-dimensional dynamical system with a marginal quasiperiodic gradient is presented as a mathematical extension of a nonuniform oscillator. The system exhibits a nonchaotic stagnant motion, which is reminiscent of intermittent chaos. In fact, the density function of residence times near stagnation points obeys an inverse-square law, due to a mechanism similar to type-I intermittency. However, unlike intermittent chaos, in which the alternation between long stagnant phases and rapid moving phases occurs in a random manner, here the alternation occurs in a quasiperiodic manner. In particular, in case of a gradient with the golden ratio, the renewal of the largest residence time occurs at positions corresponding to the Fibonacci sequence. Finally, the asymptotic long-time behavior, in the form of a nested logarithm, is theoretically derived. Compared with the Pomeau-Manneville intermittency, a significant difference in the relaxation property of the long-time average of the dynamical variable is found.Comment: 11pages, 5figure

Phenotypic analysis of heat stress in Holsteins using test-day production records and NASA POWER meteorological data.

Weather station data and test-day production records can be combined to quantify the effects of heat stress on production traits in dairy cattle. However, meteorological data sets that are retrieved from ground-based weather stations can be limited by spatial and temporal data gaps. The National Aeronautics and Space Administration Prediction of Worldwide Energy Resources (NASA POWER) database provides meteorological data over regions where surface measurements are sparse or nonexistent. The first aim of this study was to determine whether NASA POWER data are a viable alternative resource of weather data for studying heat stress in Canadian Holsteins. The results showed that average, minima, and maxima ambient temperature and dewpoint temperature as well as 4 different types of temperature-humidity index (THI) values from NASA POWER were highly correlated to the corresponding values from weather stations (regression R2 > 0.80). However, the NASA POWER values for the daily average, minima, and maxima wind speed and relative humidity were poorly correlated to the corresponding weather station values (regression R2 = 0.10 to 0.49). The second aim of this study was to quantify the influence of heat stress on Canadian dairy cattle. This was achieved by determining the THI values at which milk, protein, and fat yield started to decline due to heat stress as well as the rates of decline in these traits after the respective thresholds, using segmented polynomial regression models. This was completed for both primiparous and multiparous cows from 5 regions in Canada (Ontario, Quebec, British Columbia, the Prairies, and the Atlantic Maritime). The results showed that all production traits were negatively affected by heat stress and that the patterns of responses for milk, fat, and protein yields to increasing THI differed from each other. We found 3 THI thresholds for milk yield, 1 for fat yield, and 2 for protein yield. All thresholds marked a change in rate of decrease in production yield per unit THI, except for the first milk yield threshold, which marked a greater rate of increase. The first thresholds for milk yield ranged between 47 and 50, the second thresholds ranged between 61 and 69, and the third thresholds ranged between 72 and 76 THI units. The single THI threshold for fat yield ranged between 48 and 55 THI units. Finally, the first and second thresholds ranged between 58 and 62 THI units and 72 and 73 THI units for protein yield, respectively

Optical spectroscopy studies of Cu2ZnSnSe4 thin films

Cu2ZnSnSe4 thin films were synthesised by selenisation of magnetron sputtered metal precursors. The band gap determined from the absorption spectra increases from 1.01 eV at 300 K to 1.05 eV at 4.2 K. In lower quality films photoluminescence spectra show a broad, low intensity asymmetric band associated with a recombination of free electrons and holes localised on acceptors in the presence of spatial potential fluctuations. In high quality material the luminescence band becomes intense and narrow resolving two phonon replicas. Its shifts at changing excitation power suggest donor–acceptor pair recombination mechanisms. The proposed model involving two pairs of donors and acceptors is supported by the evolution of the band intensity and spectral position with temperature. Energy levels of the donors and acceptors are estimated using Arrhenius quenching analysis

Reflection thermal diffuse x-ray scattering for quantitative determination of phonon dispersion relations

Synchrotron reflection x-ray thermal diffuse scattering (TDS) measurements, rather than previously reported transmission TDS, are carried out at room temperature and analyzed using a formalism based upon second-order interatomic force constants and long-range Coulomb interactions to obtain quantitative determinations of MgO phonon dispersion relations ℏω_j(q), phonon densities of states g(ℏω), and isochoric temperature-dependent vibrational heat capacities c_v(T). We use MgO as a model system for investigating reflection TDS due to its harmonic behavior as well as its mechanical and dynamic stability. Resulting phonon dispersion relations and densities of states are found to be in good agreement with independent reports from inelastic neutron and x-ray scattering experiments. Temperature-dependent isochoric heat capacities c_v(T), computed within the harmonic approximation from ℏω_j(q) values, increase with temperature from 0.4 × 10^(−4) eV/atom K at 100 K to 1.4 × 10^(−4) eV/atom K at 200 K and 1.9 × 10^(−4) eV/atom K at 300 K, in excellent agreement with isobaric heat capacity values c_p(T) between 4 and 300 K. We anticipate that the experimental approach developed here will be valuable for determining vibrational properties of heteroepitaxial thin films since the use of grazing-incidence (θ≲θ_c, where θ_c is the density-dependent critical angle) allows selective tuning of x-ray penetration depths to ≲10nm

Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification

BACKGROUND: Translating genomic technologies into healthcare applications for the malaria parasite Plasmodium falciparum has been limited by the technical and logistical difficulties of obtaining high quality clinical samples from the field. Sampling by dried blood spot (DBS) finger-pricks can be performed safely and efficiently with minimal resource and storage requirements compared with venous blood (VB). Here, the use of selective whole genome amplification (sWGA) to sequence the P. falciparum genome from clinical DBS samples was evaluated, and the results compared with current methods that use leucodepleted VB. METHODS: Parasite DNA with high (>95%) human DNA contamination was selectively amplified by Phi29 polymerase using short oligonucleotide probes of 8-12 mers as primers. These primers were selected on the basis of their differential frequency of binding the desired (P. falciparum DNA) and contaminating (human) genomes. RESULTS: Using sWGA method, clinical samples from 156 malaria patients, including 120 paired samples for head-to-head comparison of DBS and leucodepleted VB were sequenced. Greater than 18-fold enrichment of P. falciparum DNA was achieved from DBS extracts. The parasitaemia threshold to achieve >5× coverage for 50% of the genome was 0.03% (40 parasites per 200 white blood cells). Over 99% SNP concordance between VB and DBS samples was achieved after excluding missing calls. CONCLUSION: The sWGA methods described here provide a reliable and scalable way of generating P. falciparum genome sequence data from DBS samples. The current data indicate that it will be possible to get good quality sequence on most if not all drug resistance loci from the majority of symptomatic malaria patients. This technique overcomes a major limiting factor in P. falciparum genome sequencing from field samples, and paves the way for large-scale epidemiological applications

Recurrence and algorithmic information

In this paper we initiate a somewhat detailed investigation of the relationships between quantitative recurrence indicators and algorithmic complexity of orbits in weakly chaotic dynamical systems. We mainly focus on examples.Comment: 26 pages, no figure

Investigating the drivers of the spatio-temporal patterns of genetic differences between Plasmodium falciparum malaria infections in Kilifi County, Kenya

Knowledge of how malaria infections spread locally is important both for the design of targeted interventions aiming to interrupt malaria transmission and the design of trials to assess the interventions. A previous analysis of 1602 genotyped Plasmodium falciparum parasites in Kilifi, Kenya collected over 12 years found an interaction between time and geographic distance: the mean number of single nucleotide polymorphism (SNP) differences was lower for pairs of infections which were both a shorter time interval and shorter geographic distance apart. We determine whether the empiric pattern could be reproduced by a simple model, and what mean geographic distances between parent and offspring infections and hypotheses about genotype-specific immunity or a limit on the number of infections would be consistent with the data. We developed an individual-based stochastic simulation model of households, people and infections. We parameterized the model for the total number of infections, and population and household density observed in Kilifi. The acquisition of new infections, mutation, recombination, geographic location and clearance were included. We fit the model to the observed numbers of SNP differences between pairs of parasite genotypes. The patterns observed in the empiric data could be reproduced. Although we cannot rule out genotype-specific immunity or a limit on the number of infections per individual, they are not necessary to account for the observed patterns. The mean geographic distance between parent and offspring malaria infections for the base model was 0.5 km (95% CI 0.3-1.5), for a distribution with 68% of distances shorter than the mean. Very short mean distances did not fit well, but mixtures of distributions were also consistent with the data. For a pathogen which undergoes meiosis in a setting with moderate transmission and a low coverage of infections, analytic methods are limited but an individual-based model can be used with genotyping data to estimate parameter values and investigate hypotheses about underlying processes

Band-Gap Nonlinearity in Lead Chalcogenide (PbQ, Q = Te, Se, S) Alloys

Narrow band-gap lead chalcogenides have been developed for several optical and electronic applications. However, band-gap energies of the ternary and quaternary alloys have received little attention compared with the parent binary phases. Here, we have fabricated single-phase ternary (PbTe)1−x(PbSe)x and quaternary (PbTe)0.9−y(PbSe)0.1(PbS)y and (PbTe)0.65−z(PbSe)0.35(PbS)z alloys and shown that although lattice parameters follow Vegard’s law as a function of composition, the bandgap energies exhibit a substantial bowing effect. The ternary (PbTe)1−x(PbSe)x system features a smaller bowing parameter predominantly due to the difference in electronegativity between Se and Te, whereas the larger bowing parameters in quaternary alloys are generated from a larger crystal lattice mismatch and larger miscibility gap. These findings can lead to further advances in tuning the band-gap and lattice parameters for optical and electronic applications of lead chalcogenides

Method overtness, forensic autopsy, and the evidentiary suicide note: A multilevel national violent death reporting system analysis

© 2018 Rockett et al. Objective Higher prevalence of suicide notes could signify more conservatism in accounting and greater proneness to undercounting of suicide by method. We tested two hypotheses: (1) an evidentiary suicide note is more likely to accompany suicides by drug-intoxication and by other poisoning, as less violent and less forensically overt methods, than suicides by firearm and hanging/suffocation; and (2) performance of a forensic autopsy attenuates any observed association between overtness of method and the reported presence of a note. Methods This multilevel (individual/county), multivariable analysis employed a generalized linear mixed model (GLMM). Representing the 17 states participating in the United States National Violent Death Reporting System throughout 2011–2013, the study population comprised registered suicides, aged 15 years and older. Decedents totaled 32,151. The outcome measure was relative odds of an authenticated suicide note. Results An authenticated suicide note was documented in 31% of the suicide cases. Inspection of the full multivariable model showed a suicide note was more likely to manifest among drug intoxication (adjusted odds ratio [OR], 1.70; 95% CI, 1.56, 1.85) and other poisoning suicides (OR, 2.12; 1.85, 2.42) than firearm suicides, the referent. Respective excesses were larger when there was no autopsy or autopsy status was unknown (OR, 1.86; 95% CI, 1.61, 2.14) and (OR, 2.25; 95% CI, 1.86, 2.72) relative to the comparisons with a forensic autopsy (OR, 1.62, 95% CI, 1.45, 1.82 and OR, 2.01; 95% CI, 1.66, 2.43). Hanging/suffocation suicides did not differ from the firearm referent given an autopsy. Conclusions Suicide requires substantial affirmative evidence to establish manner of death, and affirmation of drug intoxication suicides appears to demand an especially high burden of proof. Findings and their implications argue for more stringent investigative standards, better training, and more resources to support comprehensive and accurate case ascertainment, as the foundation for developing evidence-based suicide prevention initiatives