367 research outputs found
Detecting host-parasitoid interactions in an invasive Lepidopteran using nested tagging DNA metabarcoding
Determining the host-parasitoid interactions and parasitism rates for invasive species entering novel environments is an important first step in assessing potential routes for biocontrol and integrated pest management. Conventional insect rearing techniques followed by taxonomic identification are widely used to obtain such data, but this can be time consuming and prone to biases. Here we present a Next Generation Sequencing approach for use in ecological studies which allows for individual level metadata tracking of large numbers of invertebrate samples through the use of hierarchically organised molecular identification tags. We demonstrate its utility using a sample data set examining both species identity and levels of parasitism in late larval stages of the Oak Processionary Moth (Thaumetopoea processionea - Linn. 1758), an invasive species recently established in the UK. Overall we find that there are two main species exploiting the late larval stages of Oak Processionary Moth in the UK with the main parasitoid (Carcelia iliaca - Ratzeburg, 1840) parasitising 45.7% of caterpillars, while a rare secondary parasitoid (Compsilura conccinata - Meigen, 1824) was also detected in 0.4% of caterpillars. Using this approach on all life stages of the Oak Processionary Moth may demonstrate additional parasitoid diversity. We discuss the wider potential of nested tagging DNA-metabarcoding for constructing large, highly-resolved species interaction networks
Equation of state for polymer liquid crystals: theory and experiment
The first part of this paper develops a theory for the free energy of
lyotropic polymer nematic liquid crystals. We use a continuum model with
macroscopic elastic moduli for a polymer nematic phase. By evaluating the
partition function, considering only harmonic fluctuations, we derive an
expression for the free energy of the system. We find that the configurational
entropic part of the free energy enhances the effective repulsive interactions
between the chains. This configurational contribution goes as the fourth root
of the direct interactions. Enhancement originates from the coupling between
bending fluctuations and the compressibility of the nematic array normal to the
average director. In the second part of the paper we use osmotic stress to
measure the equation of state for DNA liquid crystals in 0.1M to 1M NaCl
solutions. These measurements cover 5 orders of magnitude in DNA osmotic
pressure. At high osmotic pressures the equation of state, dominated by
exponentially decaying hydration repulsion, is independent of the ionic
strength. At lower pressures the equation of state is dominated by fluctuation
enhanced electrostatic double layer repulsion. The measured equation of state
for DNA fits well with our theory for all salt concentrations. We are able to
extract the strength of the direct electrostatic double layer repulsion. This
is a new and alternative way of measuring effective charge densities along
semiflexible polyelectrolytes.Comment: text + 5 figures. Submitted to PR
Effects of external nutrient sources and extreme weather events on the nutrient budget of a Southern European coastal lagoon
The seasonal and annual nitrogen (N), phosphorus (P), and carbon (C) budgets of the mesotidal Ria Formosa lagoon, southern Portugal, were estimated to reveal the main inputs and outputs, the seasonal patterns, and how they may influence the ecological functioning of the system. The effects of extreme weather events such as long-lasting strong winds causing upwelling and strong rainfall were assessed. External nutrient inputs were quantified; ocean exchange was assessed in 24-h sampling campaigns, and final calculations were made using a hydrodynamic model of the lagoon. Rain and stream inputs were the main freshwater sources to the lagoon. However, wastewater treatment plant and groundwater discharges dominated nutrient input, together accounting for 98, 96, and 88 % of total C, N, and P input, respectively. Organic matter and nutrients were continuously exported to the ocean. This pattern was reversed following extreme events, such as strong winds in early summer that caused upwelling and after a period of heavy rainfall in late autumn. A principal component analysis (PCA) revealed that ammonium and organic N and C exchange were positively associated with temperature as opposed to pH and nitrate. These variables reflected mostly the benthic lagoon metabolism, whereas particulate P exchange was correlated to Chl a, indicating that this was more related to phytoplankton dynamics. The increase of stochastic events, as expected in climate change scenarios, may have strong effects on the ecological functioning of coastal lagoons, altering the C and nutrient budgets.Portuguese Science and Technology Foundation (FCT) [POCI/MAR/58427/2004, PPCDT/MAR/58427/2004]; Portuguese Science and Technology Foundation (FCT
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Prohypertensive Effect of Gestational Personal Exposure to Fine Particulate Matter. Prospective Cohort Study in Non-smoking and Non-obese Pregnant Women
Exposure to fine particulate matter (PM) is a recognized risk factor for elevated blood pressure (BP) and cardiovascular disease in adults, and this prospective cohort study was undertaken to evaluate whether gestational exposure to has a prohypertensive effect. We measured personal exposure to fine particulate matter () by personal air monitoring in the second trimester of pregnancy among 431 women, and BP values in the third trimester were obtained from medical records of prenatal care clinics. In the general estimating equation model, the effect of on BP was adjusted for relevant covariates such as maternal age, education, parity, gestational weight gain (GWG), prepregnancy BMI, environmental tobacco smoke (ETS), and blood lead level. Systolic blood pressure (SBP) increased in a linear fashion across a dosage of and on average augmented by 6.1 mm Hg (95% CI, 0.6–11.6) with log unit of concentration. Effects of age, maternal education, prepregnancy BMI, blood lead level, and ETS were insignificant. Women with excessive gestational weight gain (>18 kg) had higher mean SBP parameters by 5.5 mmHg (95% CI, 2.7–8.3). In contrast, multiparous women had significantly lower SBP values (coeff. = −4.2 mm Hg; 95% CI, −6.8 to −1.6). Similar analysis performed for diastolic blood pressure (DBP) has demonstrated that PM2.5 also affected DBP parameters (coeff. = 4.1; 95% CI, −0.02 to 8.2), but at the border significance level. DBP values were positively associated with the excessive GWG (coeff. = 2.3; 95% CI, 0.3–4.4) but were inversely related to parity (coeff. = −2.7; 95% CI, −4.6 to −0.73). In the observed cohort, the exposure to fine particulate matter during pregnancy was associated with increased maternal blood pressure
Counterion adsorption on flexible polyelectrolytes: comparison of theories
Counterion adsorption on a flexible polyelectrolyte chain in a spherical
cavity is considered by taking a "permuted" charge distribution on the chain so
that the "adsorbed" counterions are allowed to move along the backbone. We
compute the degree of ionization by using self-consistent field theory (SCFT)
and compare with the previously developed variational theory. Analysis of
various contributions to the free energy in both theories reveals that the
equilibrium degree of ionization is attained mainly as an interplay of the
adsorption energy of counterions on the backbone, the translational entropy of
the small ions, and their correlated density fluctuations. Degree of ionization
computed from SCFT is significantly lower than that from the variational
formalism. The difference is entirely due to the density fluctuations of the
small ions in the system, which are accounted for in the variational procedure.
When these fluctuations are deliberately suppressed in the truncated
variational procedure, there emerges a remarkable quantitative agreement in the
various contributing factors to the equilibrium degree of ionization, in spite
of the fundamental differences in the approximations and computational
procedures used in these two schemes. Nevertheless, since the significant
effects from density fluctuations of small ions are not captured by the SCFT,
and due to the close agreement between SCFT and the other contributing factors
in the more transparent variational procedure, the latter is a better
computational tool for obtaining the degree of ionization
Qualitative Evaluation of Common Quantitative Metrics for Clinical Acceptance of Automatic Segmentation:a Case Study on Heart Contouring from CT Images by Deep Learning Algorithms
Organs-at-risk contouring is time consuming and labour intensive. Automation by deep learning algorithms would decrease the workload of radiotherapists and technicians considerably. However, the variety of metrics used for the evaluation of deep learning algorithms make the results of many papers difficult to interpret and compare. In this paper, a qualitative evaluation is done on five established metrics to assess whether their values correlate with clinical usability. A total of 377 CT volumes with heart delineations were randomly selected for training and evaluation. A deep learning algorithm was used to predict the contours of the heart. A total of 101 CT slices from the validation set with the predicted contours were shown to three experienced radiologists. They examined each slice independently whether they would accept or adjust the prediction and if there were (small) mistakes. For each slice, the scores of this qualitative evaluation were then compared with the Sørensen-Dice coefficient (DC), the Hausdorff distance (HD), pixel-wise accuracy, sensitivity and precision. The statistical analysis of the qualitative evaluation and metrics showed a significant correlation. Of the slices with a DC over 0.96 (N = 20) or a 95% HD under 5 voxels (N = 25), no slices were rejected by the readers. Contours with lower DC or higher HD were seen in both rejected and accepted contours. Qualitative evaluation shows that it is difficult to use common quantification metrics as indicator for use in clinic. We might need to change the reporting of quantitative metrics to better reflect clinical acceptance
Non-monotonic variation with salt concentration of the second virial coefficient in protein solutions
The osmotic virial coefficient of globular protein solutions is
calculated as a function of added salt concentration at fixed pH by computer
simulations of the ``primitive model''. The salt and counter-ions as well as a
discrete charge pattern on the protein surface are explicitly incorporated. For
parameters roughly corresponding to lysozyme, we find that first
decreases with added salt concentration up to a threshold concentration, then
increases to a maximum, and then decreases again upon further raising the ionic
strength. Our studies demonstrate that the existence of a discrete charge
pattern on the protein surface profoundly influences the effective interactions
and that non-linear Poisson Boltzmann and Derjaguin-Landau-Verwey-Overbeek
(DLVO) theory fail for large ionic strength. The observed non-monotonicity of
is compared to experiments. Implications for protein crystallization are
discussed.Comment: 43 pages, including 17 figure
Temporal variations in the stable isotopic composition of Hg in sediments of the Central Portuguese Margin
Metalloporphyrin intercalation in liposome membranes: ESR study
Liposomes characterized by membranes featuring diverse fluidity (liquid-crystalline and/or gel phase), prepared from egg yolk lecithin (EYL) and dipalmitoylphosphatidylcholine (DPPC), were doped with selected metalloporphyrins and the time-related structural and dynamic changes within the lipid double layer were investigated. Porphyrin complexes of Mg(II), Mn(III), Fe(III), Co(II), Ni(II), Cu(II), Zn(II), and the metal-free base were embedded into the particular liposome systems and tested for 350 h at 24°C using the electron spin resonance (ESR) spin probe technique. 5-DOXYL, 12-DOXYL, and 16-DOXYL stearic acid methyl ester spin labels were applied to explore the interior of the lipid bilayer. Only the 16-DOXYL spin probe detected evident structural changes inside the lipid system due to porphyrin intercalation. Fluidity of the lipid system and the type of the porphyrin complex introduced significantly affected the intermolecular interactions, which in certain cases may result in self-assembly of metalloporphyrin molecules within the liposome membrane, reflected in the presence of new lines in the relevant ESR spectra. The most pronounced time-related effects were demonstrated by the EYL liposomes (liquid-crystalline phase) when doped with Mg and Co porphyrins, whereas practically no spectral changes were revealed for the metal-free base and both the Ni and Zn dopants. ESR spectra of the porphyrin-doped gel phase of DPPC liposomes did not show any extra lines; however, they indicated the formation of a more rigid lipid medium. Electronic configuration of the porphyrin’s metal center appeared crucial to the degree of molecular reorganization within the phospholipid bilayer system
Adsorption of mono- and multivalent cat- and anions on DNA molecules
Adsorption of monovalent and multivalent cat- and anions on a deoxyribose
nucleic acid (DNA) molecule from a salt solution is investigated by computer
simulation. The ions are modelled as charged hard spheres, the DNA molecule as
a point charge pattern following the double-helical phosphate strands. The
geometrical shape of the DNA molecules is modelled on different levels ranging
from a simple cylindrical shape to structured models which include the major
and minor grooves between the phosphate strands. The densities of the ions
adsorbed on the phosphate strands, in the major and in the minor grooves are
calculated. First, we find that the adsorption pattern on the DNA surface
depends strongly on its geometrical shape: counterions adsorb preferentially
along the phosphate strands for a cylindrical model shape, but in the minor
groove for a geometrically structured model. Second, we find that an addition
of monovalent salt ions results in an increase of the charge density in the
minor groove while the total charge density of ions adsorbed in the major
groove stays unchanged. The adsorbed ion densities are highly structured along
the minor groove while they are almost smeared along the major groove.
Furthermore, for a fixed amount of added salt, the major groove cationic charge
is independent on the counterion valency. For increasing salt concentration the
major groove is neutralized while the total charge adsorbed in the minor groove
is constant. DNA overcharging is detected for multivalent salt. Simulations for
a larger ion radii, which mimic the effect of the ion hydration, indicate an
increased adsorbtion of cations in the major groove.Comment: 34 pages with 14 figure
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