Novel strategies for genomic prediction of untested single-cross maize hybrids using unbalanced historical data.

KEY MESSAGE: Weighted outperformed unweighted genomic prediction using an unbalanced dataset representative of a commercial breeding program. Moreover, the use of the two cycles preceding predictions as training set achieved optimal prediction ability. Predicting the performance of untested single-cross hybrids through genomic prediction (GP) is highly desirable to increase genetic gain. Here, we evaluate the predictive ability (PA) of novel genomic strategies to predict single-cross maize hybrids using an unbalanced historical dataset of a tropical breeding program. Field data comprised 949 single-cross hybrids evaluated from 2006 to 2013, representing eight breeding cycles. Hybrid genotypes were inferred based on their parents' genotypes (inbred lines) using single-nucleotide polymorphism markers obtained via genotyping-by-sequencing. GP analyses were fitted using genomic best linear unbiased prediction via a stage-wise approach, considering two distinct cross-validation schemes. Results highlight the importance of taking into account the uncertainty regarding the adjusted means at each step of a stage-wise analysis, due to the highly unbalanced data structure and the expected heterogeneity of variances across years and locations of a commercial breeding program. Further, an increase in the size of the training set was not always advantageous even in the same breeding program. The use of the two cycles preceding predictions achieved optimal PA of untested single-cross hybrids in a forward prediction scenario, which could be used to replace the first step of field screening. Finally, in addition to the practical and theoretical results applied to maize hybrid breeding programs, the stage-wise analysis performed in this study may be applied to any crop historical unbalanced data.

La Jument lighthouse: a real-scale laboratory for the study of giant waves and their loading on marine structures.

This paper presents results from an experiment designed to improve the understanding of the relationship between extreme breaking waves and their mechanical loading on heritage offshore lighthouses. The experiment, conducted at La Jument, an iconic French offshore lighthouse, featured several records of wave, current and structure accelerations acquired during severe storm conditions, with individual waves as high as 24 m. Data analysis focuses on a storm event marked by a strong peak in the horizontal accelerations measured inside La Jument. Thanks to stereo-video wave measurements synchronized to the acceleration record we were able to identify and describe the breaking wave responsible for this intense loading. Our observations suggest that this giant wave (19 m high) had a crest elevation high enough to directly hit the lighthouse tower, above the substructure. This paper reveals the potential for conducting ambitious field experiments from offshore lighthouses in order to collect valuable storm waves and wave loading observations. This offers a possible second service life for these heritage structures as in situ laboratories dedicated to the study of the coastal hydrodynamics and its interaction with marine structures. This article is part of the theme issue 'Environmental loading of heritage structures'.

Increased adhesion molecule levels in systemic lupus erythematosus: relationships with severity of illness, autoimmunity, metabolic syndrome and cortisol levels.

Background This study was performed to assess adhesion molecules in systemic lupus erythematosus (SLE). Methods This case-control study examined 126 SLE patients and 48 healthy individuals. Blood levels of six adhesion molecules, cortisol, nuclear autoantibody (ANA) and anti-double stranded DNA (anti-dsDNA) titers were measured, while disease activity was assessed using the SLE Disease Activity Index (SLEDAI) score. Results Platelet endothelial cell adhesion molecule 1 (PECAM-1), vascular cell adhesion molecule 1 (VCAM-1), E-selectin, P-selectin, and plasminogen activator inhibitor type-1 (PAI-1) were significantly higher in SLE patients than in controls. Binary logistic regression analysis showed that PECAM-1 and PAI-1 predicted SLE with a sensitivity of 86.5% and a specificity of 81.3%. ANA titers were significantly and positively associated with PECAM-1, VCAM-1, E-selectin, and PAI-1, whereas there were no associations between anti-dsDNA titers and adhesion molecules. Cortisol was negatively associated with PCAM-1 and ICAM-1. There were significant associations between metabolic syndrome (MetS) and E-selectin and PAI-1. 14.8% of the variance in the SLEDAI score was explained by the regression on PECAM-1 and MetS. Conclusions Our data show that adhesion molecules, especially PECAM-1, are significantly associated with SLE and disease activity, suggesting that they play a role in SLE pathophysiology. While MetS, ANA titers and cortisol levels modulate adhesion molecule levels, these associations do not explain the increased levels of adhesion molecules in SLE. Increased levels of adhesion molecules are new drug targets in SLE.

The absence of birthweight paradox as a marker of disadvantages faced by low maternal education children.

Background: This study tested the hypothesis that the birthweight paradox would not be observed when assessing the effect of maternal education on neonatal mortality in the presence of socioeconomic inequality in access to health care. Methods: Non-concurrent cohort study. Passive follow-up of live-born infants using probabilistic record linkage of birth and death records for Rio de Janeiro (2004-2010; n = 1 445 367). Maternal age, birthweight and neonatal death were evaluated according to maternal educational level strata (<4, 4-11 and ≥12 years of study). We estimated the association between maternal educational level and neonatal mortality using logistical regression models adjusted for maternal age and birthweight (<2500 g and ≥2500 g). Results: Neonatal mortality was 1.8 times higher in low educational level group compared with high educational level. We did not find birthweight-specific mortality curves crossing over in the stratum under 2500 g (birthweight paradox). The odds of a low birthweight child being born in facilities without neonatal intensive care units was about 70% higher in the group of low education when compared with mothers with high education. Conclusions: The absence of crossing birthweight-specific mortality curves may be a reason for concern about the severity of the disadvantages faced by low maternal education women.

Characterization of the Dynamics of Photoluminescence Degradation in Aqueous CdTe/CdS Core-Shell Quantum Dots.

We investigate the effects of the excitation power on the photoluminescence spectra of aqueous CdTe/CdS core-shell quantum dots. We have focused our efforts on nanoparticles that are drop-cast on a silicon nitride substrate and dried out. Under such conditions, the emission intensity of these nanocrystals decreases exponentially and the emission center wavelength shifts with the time under laser excitation, displaying a behavior that depends on the excitation power. In the low-power regime a blueshift occurs, which we attribute to photo-oxidation of the quantum dot core. The blueshift can be suppressed by performing the measurements in a nitrogen atmosphere. Under high-power excitation the nanoparticles thermally expand and aggregate, and a transition to a redshift regime is then observed in the photoluminescence spectra. No spectral changes are observed for nanocrystals dispersed in the solvent. Our results show a procedure that can be used to determine the optimal conditions for the use of a given set of colloidal quantum dots as light emitters for photonic crystal optical cavities.

Synchronisation and stability in river metapopulation networks.

Spatial structure in landscapes impacts population stability. Two linked components of stability have large consequences for persistence: first, statistical stability as the lack of temporal fluctuations; second, synchronisation as an aspect of dynamic stability, which erodes metapopulation rescue effects. Here, we determine the influence of river network structure on the stability of riverine metapopulations. We introduce an approach that converts river networks to metapopulation networks, and analytically show how fluctuation magnitude is influenced by interaction structure. We show that river metapopulation complexity (in terms of branching prevalence) has nonlinear dampening effects on population fluctuations, and can also buffer against synchronisation. We conclude by showing that river transects generally increase synchronisation, while the spatial scale of interaction has nonlinear effects on synchronised dynamics. Our results indicate that this dual stability - conferred by fluctuation and synchronisation dampening - emerges from interaction structure in rivers, and this may strongly influence the persistence of river metapopulations.

Water quality concerns due to forest fires: polycyclic aromatic hydrocarbons (PAH) contamination of groundwater from mountain areas.

Water quality alterations due to forest fires may considerably affect aquatic organisms and water resources. These impacts are cumulative as a result of pollutants mobilized from fires, chemicals used to fight fire, and postfire responses. Few studies have examined postfire transport into water resources of trace elements, including the polycyclic aromatic hydrocarbons (PAH), which are organic pollutants produced during combustion and are considered carcinogenic and harmful to humans. PAH are also known to adversely affect survival, growth, and reproduction of many aquatic species. This study assessed the effects of forest wildfires on groundwater from two mountain regions located in protected areas from north and central Portugal. Two campaigns to collect water samples were performed in order to measure PAH levels. Fifteen of 16 studied PAH were found in groundwater samples collected at burned areas, most of them at concentrations significantly higher than those found in control regions, indicating aquifer contamination. The total sum of PAH in burned areas ranged from 23.1to 95.1 ng/L with a median of 62.9 ng/L, which is one- to sixfold higher than the average level measured in controls (16.2 ng/L). In addition, in control samples, the levels of light PAH with two to four rings were at higher levels than heavy PAH with five or six rings, thus showing a different profile between control and burned sites. The contribution of wildfires to groundwater contamination by PAH was demonstrated, enabling a reliable assessment of the impacts on water quality and preparation of scientifically based decision criteria for postfire forest management practices.

Modeling of Fano resonances in the reflectivity of photonic crystal cavities with finite spot size excitation.

We study the reflectivity spectra of photonic crystal slab cavities using an extension of the scattering matrix method that allows treating finite sizes of the spot of the excitation beam. The details of the implementation of the method are presented and then we show that Fano resonances arise as a consequence of the electromagnetic interference between the discrete contribution of the fundamental cavity mode and the continuum contribution of the light scattered by the photonic crystal pattern. We control the asymmetry lineshape of the Fano resonance through the polarization of the incident field, which determines the relative phase between the two electromagnetic contributions to the interference. We analyse the electric field profile inside and outside of the crystal to help in the understanding of the dependence on polarization of the reflectivity lineshape. We also study with our implementation the dependence of the Fano resonances on the size of the incident radiation spot.

Potential of marine compounds in the treatment of neurodegenerative diseases: a review.

Neurodegenerative diseases (ND) are characterized, especially, by the progressive loss of neurons, resulting in neuropsychomotor dysfunctions. Even with a high prevalence, NDs are treated with drugs that alleviate the symptoms of patients, but which develop adverse events and still do not inhibit the progression of the disease. Thus, within a new pharmacological perspective, this review aimed to verify the therapeutic potential of natural compounds of marine origin against ND. For this, an integrative review was carried out, according to the PRISMA methodology, which included steps such as: search, pre-selection and inclusion of articles. The results described revealed species such as Acaudina malpodioides, Holothuria scabra and Xylaria sp., which presented important evidence in relation to Alzheimer's, reducing the generation of ROS, presenting neuroprotective effects and reducing the concentration of Aß peptide. Regarding Parkinson's disease (PD), another example of ND, the bioactive compounds from Holothuria scabra and Xylaria sp., showed to be able to reduce the degeneration of dopaminergic neurons, reduce the deposition of alpha synuclein and reduce the formation of Mutant Huntingtin protein (Mhtt). The other marine compounds and bioactive substances are also described in this review. In conclusion, the evaluated studies indicate that compounds of marine origin emerge as a promising source of bioactive compounds, revealing an important therapeutic potential for the treatment of ND.

The nested assembly of individual-resource networks.

1. Much of the current understanding of ecological systems is based on theory that does not explicitly take into account individual variation within natural populations. However, individuals may show substantial variation in resource use. This variation in turn may be translated into topological properties of networks that depict interactions among individuals and the food resources they consume (individual-resource networks). 2. Different models derived from optimal diet theory (ODT) predict highly distinct patterns of trophic interactions at the individual level that should translate into distinct network topologies. As a consequence, individual-resource networks can be useful tools in revealing the incidence of different patterns of resource use by individuals and suggesting their mechanistic basis. 3. In the present study, using data from several dietary studies, we assembled individual-resource networks of 10 vertebrate species, previously reported to show interindividual diet variation, and used a network-based approach to investigate their structure. 4. We found significant nestedness, but no modularity, in all empirical networks, indicating that (i) these populations are composed of both opportunistic and selective individuals and (ii) the diets of the latter are ordered as predictable subsets of the diets of the more opportunistic individuals. 5. Nested patterns are a common feature of species networks, and our results extend its generality to trophic interactions at the individual level. This pattern is consistent with a recently proposed ODT model, in which individuals show similar rank preferences but differ in their acceptance rate for alternative resources. Our findings therefore suggest a common mechanism underlying interindividual variation in resource use in disparate taxa.

Quantum dot dipole orientation and excitation efficiency of micropillar modes.

The relative intensity of photonic modes in microcavity pillars with embedded self-assembled quantum dots is shown to be a sensitive function of quantum dot dipole orientation and position. This is deduced from a comparison of experiment and calculated intensities of light emission for many nominally identical pillars. We are able to obtain the overall degree of in-plane polarization of the quantum dot ensemble and also to obtain information on the degree of polarization along the growth axis.

Development and use of single nucleotide polymorphism markers for candidate resistance genes in wild peanuts (Arachis spp).

The cultivated peanut (Arachis hypogaea L.) is an allotetraploid of recent origin, with an AABB genome and low genetic diversity. Perhaps because of its limited genetic diversity, this species lacks resistance to a number of important pests and diseases. In contrast, wild species of Arachis are genetically diverse and are rich sources of disease resistance genes. Consequently, a study of wild peanut relatives is attractive from two points of view: to help understand peanut genetics and to characterize wild alleles that could confer disease resistance. With this in mind, a diploid population from a cross between two wild peanut relatives was developed, in order to make a dense genetic map that could serve as a reference for peanut genetics and in order to characterize the regions of the Arachis genome that code for disease resistance. We tested two methods for developing and genotyping single nucleotide polymorphisms in candidate genes for disease resistance; one is based on single-base primer extension methods and the other is based on amplification refractory mutation system-polymerase chain reaction. We found single-base pair extension to be an efficient method, suitable for high-throughput, single-nucleotide polymorphism mapping; it allowed us to locate five candidate genes for resistance on our genetic map.

WITHDRAWN: Association between polymorphisms in genes of inflammatory response and axonal repair with spinal cord injury.

Ahead of Print article withdrawn by publisher. Please see re-submitted article 'DNA polymorphisms as tools for spinal cord injury research' Spinal Cord advance online publication, 20 May 2008; doi:10.1038/sc.2008.67.

Dynamics of the transverse Ising model with next-nearest-neighbor interactions.

We study the effects of next-nearest-neighbor (NNN) interactions on the dynamics of the one-dimensional spin-1/2 transverse Ising model in the high-temperature limit. We use exact diagonalization to obtain the time-dependent transverse correlation function and the corresponding spectral density for a tagged spin. Our results for chains of 13 spins with periodic boundary conditions produce results which are valid in the infinite-size limit. In general we find that the NNN coupling produces slower dynamics accompanied by an enhancement of the central mode behavior. Even in the case of a strong transverse field, if the NNN coupling is sufficiently large, then there is a crossover from collective mode to central mode behavior. We also obtain several recurrants for the continued fraction representation of the relaxation function.

Molecular cloning of cDNAs encoding insecticidal neurotoxic peptides from the spider Phoneutria nigriventer.

From a Phoneutria nigriventer venom gland cDNA library several clones coding for the insect specific neurotoxin Tx4(6-1) were isolated. cDNA analysis showed that the encoded protein contained three distinct segments, comprising a signal sequence of 16 amino acids, followed by a glutamate-rich sequence of 18 amino acids and, finally, the coding region for the mature toxin. The deduced amino acid sequence for the mature polypeptide was identical to the protein sequence determined chemically. In addition, two new putative toxins called Pn4A and Pn4B were characterized and their predicted complete amino acid sequence revealed approximately 78% similarity to Tx4(6-1).

Cloning of cDNAS encoding neurotoxic peptides from the spider Phoneutria nigriventer.

A cDNA library made from venom glands of the spider Phoneutria nigriventer was constructed and used to clone neurotoxic peptides. A cDNA of about 360 nucleotides encoding the precursor for the toxin Tx2-1 active on mammals has been isolated. The deduced amino acid sequence for the mature polypeptide confirms the polypeptide sequence previously published. In addition, two new putative toxins called Pn2-1A and Pn2-5A have been characterized and their complete amino acid sequence show 92% similarity to Tx2-1 and 94% similarity to Tx2-5 respectively. The cDNAs revealed that the precursors contain signal peptides characterized by a very hydrophobic core and a propeptide interposed between the signal sequence and the peptide toxin.

Quality protein maize: a biochemical study of enzymes involved in lysine metabolism.

Quality protein maize (QPM) varieties have been produced by the introduction of opaque-2 modifier genes. Two QPM varieties, BR451 and BR473, a wild type and an opaque-2 variety, have been used to study key enzymes controlling lysine metabolism in the endosperm during development. Aspartate kinase and homoserine dehydrogenase enzymes, which are involved in lysine and threonine biosynthesis, respectively, exhibited identical activity patterns during endosperm development, with a maximum specific activity at 16 days after pollination. The QPM varieties exhibited higher levels of aspartate kinase activity in the endosperm, suggesting an increased rate of lysine biosynthesis when compared to the opaque-2 and wild-type genotypes. Similar results were observed for the lysine ketoglutarate reductase and saccharopine dehydrogenase enzymes, which form a single bifunctional polypetide involved in endosperm lysine degradation. Both enzyme activities were strongly reduced in the opaque-2 maize variety when compared to the wild-type maize, whereas the QPM varieties exhibited even lower levels of lysine ketoglutarate reductase-saccharopine dehydrogenase activities when compared to the opaque-2 variety. The developmental pattern of enzyme activity showed a different profile when compared to the enzymes involved in lysine biosynthesis, with activity being detected only 12-16 days after pollination (DAP) and maximum activities approximately 24 DAP. These results also suggest that the modifier genes have intensified the effect of the opaque-2 mutation on lysine ketoglutarate reductase-saccharopine dehydrogenase. These alterations lead to an increase in soluble lysine in the endosperm of the QPM varieties when compared to the opaque-2 and wild type.

Quantitative analysis of modes of invasion and lymph node metastases in oral squamous cell carcinoma.

The mode of tumor invasion has been suggested to have a relationship to the occurrence of cervical metastasis and to prognosis in oral squamous cell carcinoma (OSCC). However, a tumor usually does not have a single mode of invasion, and the importance, if any, of the relative proportions of different modes for metastatic potential has not been studied. Forty two cases of OSCC resected with cervical lymph nodes were selected, 20 of which had nodal metastases and 22 which had not. The mode of invasion in the tumor-host interface was classified as: I - pushing borders, II - bands, III - thin cords, IV - single cells and analyzed in 20 consecutive medium power fields. Also studied were other morphological parameters: perineural and angiolymphatic invasion, tissue eosinophilia, mitosis and intensity of inflammatory infiltrate at the tumor-host interface. The majority of the cases (95.2%) showed two or more modes of invasion. Modes I, II and III occurred with similar frequency in cases with and without metastases. Mode II was the commonest and most extensive in both groups. No mode of invasion was significantly associated with metastases, independent of its extension. The other morphological parameters were neither significantly associated with cervical metastasis. In conclusion, OSCC usually shows two or more modes of tumor invasion if a large extension of tumor-host interface is analyzed. However, the relative proportions of the modes have no correlation with the metastatic potential.

Eggplant (Solanum melongena) infusion has a modest and transitory effect on hypercholesterolemic subjects.

Eggplant (Solanum melongena) is consumed extensively in Brazil. It has been believed that infusion of a powdered preparation of the fruit may reduce serum cholesterol. However, there are few documented reports on its effects on cholesterol metabolism and its possible hypocholesterolemic effect has not been proved by well-controlled studies. The aim of the present study was to observe the effects of S. melongena on the serum cholesterol and triglycerides of 38 hypercholesterolemic human volunteers ingesting S. melongena infusion for five weeks. Thirty-eight hypercholesterolemic subjects receiving either S. melongena infusion (N = 19) or placebo (N = 19) participated in two clinical experiments in which the effect of S. melongena infusion was studied with (N = 16) or without (N = 38) dietary orientation. Total cholesterol and its fractions, triglycerides, and apolipoproteins A and B were measured in blood at the beginning of the experiment and three and five weeks thereafter. No differences were observed compared to control. Intraindividual analysis showed that S. melongena infusion significantly reduced the blood levels of total and LDL cholesterol and of apolipoprotein B. After dietary orientation, no intra- or intergroup differences were seen for any of the parameters analyzed. The results suggest that S. melongena infusion had a modest and transitory effect, which was not different from that obtained with standard orientation for dyslipidemia patients (diet and physical activities).