Multiple sources and routes of information transmission: Implications for epidemic dynamics

In a recent paper [20], we proposed and analyzed a compartmental ODE-based model describing the dynamics of an infectious disease where the presence of the pathogen also triggers the diffusion of information about the disease. In this paper, we extend this previous work by presenting results based on pairwise and simulation models that are better suited for capturing the population contact structure at a local level. We use the pairwise model to examine the potential of different information generating mechanisms and routes of information transmission to stop disease spread or to minimize the impact of an epidemic. The individual-based simulation is used to better differentiate between the networks of disease and information transmission and to investigate the impact of different basic network topologies and network overlap on epidemic dynamics. The paper concludes with an individual-based semi-analytic calculation of R₀ at the non-trivial disease free equilibrium.     

Population structure and genetic analysis of narrow-clawed crayfish (Astacus leptodactylus) populations in Turkey

The genetic differentiation among Turkish populations of the narrow-clawed crayfish was investigated using a partial sequence of cytochrome oxidase subunit I gene (585 bp) of 183 specimens from 17 different crayfish populations. Median joining network and all phylogenetic analyses disclosed a strong haplotype structure with three prominent clades diverged by a range between 20 and 50 mutations and substantial inter-group pairwise sequence divergence (5.19–6.95 %), suggesting the presence of three distinct clades within the Anatolian populations of Astacus leptodactylus. The divergence times among the three clades of Turkish A. leptodactylus are estimated to be 4.96–3.70 Mya using a molecular clock of 1.4 % sequence divergence per million years, pointing to a lower Pliocene separation. The high level of genetic variability (H _d  = 95.8 %, π = 4.17 %) and numerous private haplotypes suggest the presence of refugial populations in Anatolia unaffected by Pleistocene habitat restrictions. The pattern of genetic variation among Turkish A. leptodactylus populations, therefore, suggests that the unrevealed intraspecific genetic structure is independent of geographic tendency and congruent with the previously reported geographic distribution and number of subspecies (A. l. leptodactylus and A. l. salinus) of A. leptodactylus.     

The McClure and Weiss models of Fe–O2 bonding for oxyhemes, and the HbO2 + NO reaction

For the Fe–O₂(S = 0) linkages of oxyhemes, valence bond (VB) structures are re-presented for the McClure [Fe^II(S = 1) + O₂(S = 1)], Pauling–Coryell [Fe^II(S = 0) + O₂*(S = 0)], and Weiss [Fe^III(S = ½) + O₂ ^?(S = ½)] models of bonding. The VB structures for the McClure and Weiss models are of the increased-valence type, with more electrons participating in bonding than occur in their component Lewis structures. The Fe–O bond number and O–O bond order for the McClure structure are correlated with measured Fe–O and O–O bond lengths for oxymyoglobin. Back-bonding from O ₂ ^? to Fe^III of the Weiss structure gives a restricted form of the McClure structure. The McClure and Weiss increased-valence structures are used to provide VB formulations of mechanisms for the oxyhemoglobin + NO reaction. The products of these two formulations are Hb⁺ and NO₃ ^? (where Hb is hemoglobin) and Hb⁺ and OONO^?, respectively. Because Hb⁺ and NO₃ ^? are the observed products, they provide an experimental procedure for distinguishing the McClure and Weiss models. It is also shown that the same type of agreement between McClure-type theory and experiment occurs for oxycoboglobin + NO, cytochrome P450 monooxygenases, and related hydrogen atom transfer reactions. In the appendices, the results of density functional theory and multireference molecular orbital calculations for oxyhemes are related to one formulation of the increased-valence wavefunction for the McClure model, and theory is presented for the calculation of approximate weights for the Lewis structures that are components of the McClure increased-valence structure.     

Chlorophyll fluorescence kinetics, photosynthetic activity, and pigment composition of blue-shade and half-shade leaves as compared to sun and shade leaves of different trees

The chlorophyll (Chl) fluorescence induction kinetics, net photosynthetic CO₂ fixation rates P _N, and composition of photosynthetic pigments of differently light exposed leaves of several trees were comparatively measured to determine the differences in photosynthetic activity and pigment adaptation of leaves. The functional measurements were carried out with sun, half-shade and shade leaves of seven different trees species. These were: Acer platanoides L., Ginkgo biloba L., Fagus sylvatica L., Platanus x acerifolia Willd., Populus nigra L., Quercus robur L., Tilia cordata Mill. In three cases (beech, ginkgo, and oak), we compared the Chl fluorescence kinetics and photosynthetic rates of blue-shade leaves of the north tree crown receiving only blue sky light but no direct sunlight with that of sun leaves. In these cases, we also determined in detail the pigment composition of all four leaf types. In addition, we determined the quantum irradiance and spectral irradiance of direct sunlight, blue skylight as well as the irradiance in half shade and full shade. The results indicate that sun leaves possess significantly higher mean values for the net CO₂ fixation rates P _N (7.8–10.7 μmol CO₂ m^?2 s^?1 leaf area) and the Chl fluorescence ratio R _Fd (3.85–4.46) as compared to shade leaves (mean P _N of 2.6–3.8 μmol CO₂ m^?2 s^?1 leaf area.; mean R _Fd of 1.94–2.56). Sun leaves also exhibit higher mean values for the pigment ratio Chl a/b (3.14–3.31) and considerably lower values for the weight ratio total chlorophylls to total carotenoids, (a + b)/(x + c), (4.07–4.25) as compared to shade leaves (Chl a/b 2.62–2.72) and (a + b)/(x + c) of 5.18–5.54. Blue-shade and half-shade leaves have an intermediate position between sun and shade leaves in all investigated parameters including the ratio F _v/F _o (maximum quantum yield of PS2 photochemistry) and are significantly different from sun and shade leaves but could not be differentiated from each other. The mean values of the Chl fluorescence decrease ratio R _Fd of blue-shade and half-shade leaves fit well into the strong linear correlation with the net photosynthetic rates P _N of sun and shade leaves, thus unequivocally indicating that the determination of the Chl fluorescence decrease ratio R _Fd is a fast and indirect measurement of the photosynthetic activity of leaves. The investigations clearly demonstrate that the photosynthetic capacity and pigment composition of leaves and chloroplasts strongly depend on the amounts and quality of light received by the leaves.     

The impact of network clustering and assortativity on epidemic behaviour

Epidemic models have successfully included many aspects of the complex contact structure apparent in real-world populations. However, it is difficult to accommodate variations in the number of contacts, clustering coefficient and assortativity. Investigations of the relationship between these properties and epidemic behaviour have led to inconsistent conclusions and have not accounted for their interrelationship. In this study, simulation is used to estimate the impact of social network structure on the probability of an SIR (susceptible-infective-removed) epidemic occurring and, if it does, the final size. Increases in assortativity and clustering coefficient are associated with smaller epidemics and the impact is cumulative. Derived values of the basic reproduction ratio (R₀) over networks with the highest property values are more than 20% lower than those derived from simulations with zero values of these network properties.     

Inferring Epidemiological Dynamics with Bayesian Coalescent Inference: The Merits of Deterministic and Stochastic Models

Estimation of epidemiological and population parameters from molecular sequence data has become central to the understanding of infectious disease dynamics. Various models have been proposed to infer details of the dynamics that describe epidemic progression. These include inference approaches derived from Kingman’s coalescent theory. Here, we use recently described coalescent theory for epidemic dynamics to develop stochastic and deterministic coalescent susceptible–infected–removed (SIR) tree priors. We implement these in a Bayesian phylogenetic inference framework to permit joint estimation of SIR epidemic parameters and the sample genealogy. We assess the performance of the two coalescent models and also juxtapose results obtained with a recently published birth–death-sampling model for epidemic inference. Comparisons are made by analyzing sets of genealogies simulated under precisely known epidemiological parameters. Additionally, we analyze influenza A (H1N1) sequence data sampled in the Canterbury region of New Zealand and HIV-1 sequence data obtained from known United Kingdom infection clusters. We show that both coalescent SIR models are effective at estimating epidemiological parameters from data with large fundamental reproductive number R₀ and large population size S₀. Furthermore, we find that the stochastic variant generally outperforms its deterministic counterpart in terms of error, bias, and highest posterior density coverage, particularly for smaller R₀ and S₀. However, each of these inference models is shown to have undesirable properties in certain circumstances, especially for epidemic outbreaks with R₀ close to one or with small effective susceptible populations.     

Genetic diversity and structure of an endemic and critically endangered stream river salamander (Caudata: Ambystoma leorae) in Mexico

Small or isolated populations are highly susceptible to stochastic events. They are prone and vulnerable to random demographic or environmental fluctuations that could lead to extinction due to the loss of alleles through genetic drift and increased inbreeding. We studied Ambystoma leorae an endemic and critically threatened species. We analyzed the genetic diversity and structure, effective population size, presence of bottlenecks and inbreeding coefficient of 96 individuals based on nine microsatellite loci. We found high levels of genetic diversity expressed as heterozygosity (H_o = 0.804, H_e = 0.613, H_e* = 0.626 and H_Nei = 0.622). The population presents few alleles (4–9 per locus) and genotypes (3–14 per locus) compared with other mole salamanders species. We identified three genetically differentiated subpopulations with a significant level of genetic structure (F_ST = 0.021, R_ST = 0.044 y D_est = 0.010, 95 % CI). We also detected a reduction signal in population size and evidence of a genetic bottleneck (M = 0.367). The effective population size is small (Ne = 45.2), but similar to another mole salamanders with restricted distributions or with recently fragmented habitat. The inbreeding coefficient levels detected are low (F_IS = ?0.619–0.102) as is gene flow. Despite, high levels of genetic diversity A. leorae is critically endangered because it is a small isolated population.     

Biomass and Total Lipid Content Assessment of Microalgal Cultures Using Near and Short Wave Infrared Spectroscopy

The technique of near and short wave near-infrared spectroscopy was assessed with respect to analysis of dry matter and lipid content of microalgae with potential for biodiesel production. Microalgal culture samples were filtered through GF/C filter papers and spectral measurements of wet and oven dried (60 °C overnight) filter papers over the ranges of 300–1,100 nm and 1,100–2,500 nm were recorded. Partial least square models on culture biomass and lipid content for combined species data were poor in terms of RMSECV, R _CV and the ratio of RMSECV to SD. A single species model for C. vulgaris based on 1,100–2,500 nm spectra of dry filtrate supported a model with RMSECV, R _CV and SDR values of 0.32 g L^?1, 0.955 and 3.38 for biomass and 0.089 g L^?1, 0.874 and 2.06 with lipid, respectively. However, the dry filtrate models on biomass and lipid content performed poorly in the prediction of samples drawn from an independent series of C. vulgaris cultured under N-, P- and Fe-limited growth trial. Thus, while the near-infrared spectroscopy technique has potential for assessment of dry matter and lipid content of microalgal cultures using a dried filtrate sample, further work is required to examine the limits to model robustness.     

The beneficial effect of repaglinide on in vitro maturation and development ability of immature mouse oocytes

Repaglinide is a hypoglycemic drug, causing depolarization of the cell membrane, opening the voltage-gated calcium channels, and then increasing intracellular calcium in the pancreatic B cells by inhibition of the K-ATP-sensitive channels. Oocyte in vitro maturation (IVM) is influenced by different factors such as calcium signaling. In this study, we examined the effects of repaglinide on in vitro maturation and fertilization ability of mouse oocyte. Immature oocytes were isolated from female Naval Medical Research Institute mice which are 6–8 wk old mechanically and then cultured in 30 μl droplets of T6 medium with different concentrations of repaglinide. The control group did not receive repaglinide (R₀). Treatment groups received different concentrations (5, 10, and 100 nM and 1 and 10 μM) of repaglinide (R₁, R₂, R₃, R₄, and R₅, respectively). Oocyte in vitro maturation rate was assessed after 24 h. In vitro fertilization was performed using metaphase II oocytes obtained from R₀ and R₄ treatments. Embryo cleavage rate was calculated at 48 h post-IVF. Chi-square test was used for evaluating difference between control and treatment groups (p < 0.05). Oocyte maturation rate after 24 h in treatment groups R₂, R₃, R₄, and R₅ was significantly higher than that in the control (p < 0.05). Supplementation of medium with 1 μM of repaglinide (R₄) during IVM significantly improved outcome of embryo cleavage rate than control at 48 h post-IVF (p < 0.05). In conclusion, repaglinide can be considered as an effective agent for in vitro oocyte maturation and embryo cleavage.     

The role of floods in the lives of fish-eating birds: predator loss or benefit?

Floods accompanied by high flow and high water turbidity are usually believed to cause problems to fish-eating birds and mammals searching visually for their prey. In the present study the diets of breeding kingfishers were studied during the normal river situation and during a long-lasting flood event with respect to diet composition, size of fish prey and food diversity index. During the normal situation (flow 1.75 m³ s^?1, Secchi disc depth 0.5–1 m), the diet of a kingfisher was dominated by benthic fish species (52.9% by numbers, 63.9% by weight), the average size of fish taken was 6.5 cm L _T and 3.0 g and the food diversity index reached its lowest value (1.57). In contrast, during the long-lasting flood event (flow 5–28 m³ s^?1, Secchi disc depth 0.03–0.4 m) the diet of the kingfisher was dominated by sub-surface fish species (72.4% by numbers, 76.1% by weight) and both the average size of fish taken (7.4 cm L _T and 3.7 g) and the food diversity index (1.83) increased significantly. The birds provided their nestlings with lower numbers of fish of larger sizes, which resulted in very similar weights of the young birds prior to fledging when the flood and normal situations were compared. This study provides evidence that in different foraging conditions the kingfishers adopt different foraging strategies to maintain their high breeding success.     

Modelling the Use of Wolbachia to Control Dengue Fever Transmission

Experiments and field trials have shown that the intracellular bacterium Wolbachia may be introduced into populations of the mosquito Aedes aegypti, the primary vector for dengue fever. In the absence of Wolbachia, a mosquito acquiring the dengue virus from an infected human enters an exposed (infected but not infectious) period before becoming infectious itself. A Wolbachia-infected mosquito that acquires dengue (i) may have a reduced lifespan, so that it is less likely to survive the exposed period and become infectious, and (ii) may have a reduced ability to transmit dengue, even if it has survived the exposed period. Wolbachia introduction has therefore been suggested as a potential dengue control measure. We set up a mathematical model for the system to investigate this suggestion and to evaluate the desirable properties of the Wolbachia strain to be introduced. We show that Wolbachia has excellent potential for dengue control in areas where R ₀ is not too large. However, if R ₀ is large, Wolbachia strains that reduce but do not eliminate dengue transmission have little effect on endemic steady states or epidemic sizes. Unless control measures to reduce R ₀ by reducing mosquito populations are also put in place, it may be worth the extra effort in such cases to introduce Wolbachia strains that eliminate dengue transmission completely.     

Environmental variables controlling soil respiration on diurnal, seasonal and annual time-scales in a mixed mountain forest in Switzerland

Studies on soil respiration in mountain forests are rather scarce compared to their broad distribution. Therefore, we investigated daily, seasonal and annual soil respiration rates in a mixed forest (Lägeren), located at about 700 m in the Swiss Jura mountains, during 2 years (2006 and 2007). Soil respiration (SR) was measured continuously with high temporal resolution (half-hourly) at one single point (SR_automated) and periodically with high spatial resolution (SR_manual) at 16 plots within the study site. Both, SR_automated and SR_manual showed a similar seasonal cycle. SR strongly depended on soil temperature in 2007 (R ² = 0.82–0.92), but less so in 2006 (R ² = 0.56–0.76) when SR was water limited during a summer drought. Including soil moisture improved the fit of the 2006 model significantly (R ² = 0.78–0.97). Total annual SR for the study site was estimated as 869 g C m^?2 year^?1 for 2006 and as 907 g C m^?2 year^?1 for 2007 (uncertainty <10% at the 95% confidence interval, determined by bootstrapping). Selected environmental conditions were assessed in more detail: (1) Rapid, but contrasting changes of SR were found after summer rainfall. Depending on soil moisture at pre-rain conditions, summer rain could either cause a pulse of CO₂ from the soil or an abrupt decrease of SR_automated due to water logging of soil pores. (2) Two contrasting winter seasons resulted in SR being about 60–70% (31.2–44.6 g C m^?2) higher during a mild winter (2007) compared to a harsh winter (2006). (3) Analysing SR for selected periods on a diurnal scale revealed a counter-clockwise hysteresis with soil surface temperatures. This indication of a time-lagged response of SR to temperature was further supported by a very strong relationship (R ² = 0.86–0.90) of SR to soil temperature with a time-lag of 2–4 h.     

Spectral Characteristics of Near-Infrared Surface Plasmon Resonance

Intrinsic properties of surface plasmons (SPs) excited with Kretschmann configuration were analyzed as a function of wavelength, including the propagation length, the penetration depth, the Goos–Hänchen (GH) shift, and the field enhancement. The calculated results indicate that there exists a critical thickness (t _cr) of the gold layer and that the maximum GH shift occurring exactly at the SP resonance wavelength (λ _R) rapidly varies from positive to negative with changing of the gold layer thickness from t?<?t _cr to t?>?t _cr. The maximum field enhancement happens not at λ _R but at a wavelength smaller than λ _R due to the phase retardation between the transmitted and reflected light. Simulations also reveal that a broadband collimated near-infrared beam can simultaneously excite two SPs with different responses to a refractive index (RI) change: the shorter-wavelength SP able to make a small redshift and the longer-wavelength SP capable of yielding a large blueshift. Only the shorter-wavelength SP was experimentally observed and its RI sensitivity was measured to increase from 3,539 nm/RIU at λ _R?=?707.6 nm to 57,143 nm/RIU at λ _R?=?1,398 nm. The SP at λ _R?=?1,013 nm moved to λ _R?=?1,029 nm in response to the saturation adsorption of bovine serum albumin, and the corresponding surface coverage was determined to be Γ?=?1.565 ng/mm² based on a quasilinear dependence of Γ on the resonance wavelength shift (?λ _R) deduced theoretically. Butyrylcholinesterase adsorption from a dilute solution of 10 nM protein in phosphate buffer solution leads to a redshift of ?λ _R?=?10 nm, corresponding to Γ?≈?0.97 ng/mm².     

Composite interval mapping and mixed models reveal QTL associated with performance and carcass traits on chicken chromosomes 1, 3, and 4

Interval mapping (IM) implemented in QTL Express or GridQTL is widely used, but presents some limitations, such as restriction to a fixed model, risk of mapping two QTL when there may be only one and no discrimination of two or more QTL using both cofactors located on the same and other chromosomes. These limitations were overcome with composite interval mapping (CIM). We reported QTL associated with performance and carcass traits on chicken chromosomes 1, 3, and 4 through implementation of CIM and analysis of phenotypic data using mixed models. Thirty-four microsatellite markers were used to genotype 360 F₂ chickens from crosses between males from a layer line and females from a broiler line. Sixteen QTL were mapped using CIM and 14 QTL with IM. Furthermore, of those 30 QTL, six were mapped only when CIM was used: for body weight at 35 days (first and third peaks on GGA4), body weight at 41 days (GGA1B and second peak on GGA4), and weights of back and legs (both on GGA4). Three new regions had evidence for QTL presence: one on GGA1B associated with feed intake 35–41 d at 404 cM (LEI0107-ADL0183) and two on GGA4 associated with weight of back at 163 cM (LEI0076-MCW0240) and weight gain 35–41 d, feed efficiency 35–41 d and weight of legs at 241 cM (LEI0085-MCW0174). We dissected one more linked QTL on GGA4, where three QTL for BW35 and two QTL for BW41 were mapped. Therefore, these new regions mapped here need further investigations using high-density SNP to confirm these QTL and identify candidate genes associated with those traits.