Medium Light and Medium Roast Paper-Filtered Coffee Increased Antioxidant Capacity in Healthy Volunteers: Results of a Randomized Trial

We compared the effects of medium light roast (MLR) and medium roast (MR) paper-filtered coffee on antioxidant capacity and lipid peroxidation in healthy volunteers. In a randomized crossover study, 20 volunteers consumed 482 +/- 61 ml/day of MLR or MR for four weeks. Plasma total antioxidant status (TAS), oxygen radical absorbance capacity (ORAC), oxidized LDL and 8-epi-prostaglandin F2 alpha, erythrocyte superoxide dismutase (SOD), glutathione peroxidase (GPx), and catalase (CAT) activity were measured at baseline and after the interventions. MLR had higher chlorogenic acids-(CGA; 334 mg/150 mL) and less caffeine (231 mg/150 ml) than MR had (210 and 244 mg/150 ml, respectively). MLR also had fewer Maillard reaction products (MRP) than MR had. Compared with baseline, subjects had an increase of 21 and 26 % in TAS, 13 and 13 % in CAT, 52 and 75 % in SOD, and 62 and 49 % in GPx after MLR and MR consumption (P < 0.001), respectively. ORAC increased after MLR (P = 0.004). No significant alteration in lipid peroxidation biomarkers was observed. Both coffees had antioxidant effects. Although MLR contained more CGA, there were similar antioxidant effects between the treatments. MRP may have contributed as an antioxidant. These effects may be important in protecting biological systems and reducing the risk of diseases related to oxidative stress.

Comparative Genome Analysis of Trichophyton rubrum and Related Dermatophytes Reveals Candidate Genes Involved in Infection

The major cause of athlete's foot is Trichophyton rubrum, a dermatophyte or fungal pathogen of human skin. To facilitate molecular analyses of the dermatophytes, we sequenced T. rubrum and four related species, Trichophyton tonsurans, Trichophyton equinum, Microsporum canis, and Microsporum gypseum. These species differ in host range, mating, and disease progression. The dermatophyte genomes are highly colinear yet contain gene family expansions not found in other human-associated fungi. Dermatophyte genomes are enriched for gene families containing the LysM domain, which binds chitin and potentially related carbohydrates. These LysM domains differ in sequence from those in other species in regions of the peptide that could affect substrate binding. The dermatophytes also encode novel sets of fungus-specific kinases with unknown specificity, including nonfunctional pseudokinases, which may inhibit phosphorylation by competing for kinase sites within substrates, acting as allosteric effectors, or acting as scaffolds for signaling. The dermatophytes are also enriched for a large number of enzymes that synthesize secondary metabolites, including dermatophyte-specific genes that could synthesize novel compounds. Finally, dermatophytes are enriched in several classes of proteases that are necessary for fungal growth and nutrient acquisition on keratinized tissues. Despite differences in mating ability, genes involved in mating and meiosis are conserved across species, suggesting the possibility of cryptic mating in species where it has not been previously detected. These genome analyses identify gene families that are important to our understanding of how dermatophytes cause chronic infections, how they interact with epithelial cells, and how they respond to the host immune response. IMPORTANCE Athlete's foot, jock itch, ringworm, and nail infections are common fungal infections, all caused by fungi known as dermatophytes (fungi that infect skin). This report presents the genome sequences of Trichophyton rubrum, the most frequent cause of athlete's foot, as well as four other common dermatophytes. Dermatophyte genomes are enriched for four gene classes that may contribute to the ability of these fungi to cause disease. These include (i) proteases secreted to degrade skin; (ii) kinases, including pseudokinases, that are involved in signaling necessary for adapting to skin; (iii) secondary metabolites, compounds that act as toxins or signals in the interactions between fungus and host; and (iv) a class of proteins (LysM) that appear to bind and mask cell wall components and carbohydrates, thus avoiding the host's immune response to the fungi. These genome sequences provide a strong foundation for future work in understanding how dermatophytes cause disease.

Mayaro Virus Infection in Amazonia: A Multimodel Inference Approach to Risk Factor Assessment

Background: Arboviral diseases are major global public health threats. Yet, our understanding of infection risk factors is, with a few exceptions, considerably limited. A crucial shortcoming is the widespread use of analytical methods generally not suited for observational data - particularly null hypothesis-testing (NHT) and step-wise regression (SWR). Using Mayaro virus (MAYV) as a case study, here we compare information theory-based multimodel inference (MMI) with conventional analyses for arboviral infection risk factor assessment. Methodology/Principal Findings: A cross-sectional survey of anti-MAYV antibodies revealed 44% prevalence (n = 270 subjects) in a central Amazon rural settlement. NHT suggested that residents of village-like household clusters and those using closed toilet/latrines were at higher risk, while living in non-village-like areas, using bednets, and owning fowl, pigs or dogs were protective. The "minimum adequate" SWR model retained only residence area and bednet use. Using MMI, we identified relevant covariates, quantified their relative importance, and estimated effect-sizes (beta +/- SE) on which to base inference. Residence area (beta(Village) = 2.93 +/- 0.41; beta(Upland) = -0.56 +/- 0.33, beta(Riverbanks) = -2.37 +/- 0.55) and bednet use (beta = -0.95 +/- 0.28) were the most important factors, followed by crop-plot ownership (beta = 0.39 +/- 0.22) and regular use of a closed toilet/latrine (beta = 0.19 +/- 0.13); domestic animals had insignificant protective effects and were relatively unimportant. The SWR model ranked fifth among the 128 models in the final MMI set. Conclusions/Significance: Our analyses illustrate how MMI can enhance inference on infection risk factors when compared with NHT or SWR. MMI indicates that forest crop-plot workers are likely exposed to typical MAYV cycles maintained by diurnal, forest dwelling vectors; however, MAYV might also be circulating in nocturnal, domestic-peridomestic cycles in village-like areas. This suggests either a vector shift (synanthropic mosquitoes vectoring MAYV) or a habitat/habits shift (classical MAYV vectors adapting to densely populated landscapes and nocturnal biting); any such ecological/adaptive novelty could increase the likelihood of MAYV emergence in Amazonia.

Charge dynamics in half-filled Hubbard chains with finite on-site interaction

We study the charge dynamic structure factor of the one-dimensional Hubbard model with finite on-site repulsion U at half-filling. Numerical results from the time-dependent density matrix renormalization group are analyzed by comparison with the exact spectrum of the model. The evolution of the line shape as a function of U is explained in terms of a relative transfer of spectral weight between the two-holon continuum that dominates in the limit U -> infinity and a subset of the two-holon-two-spinon continuum that reconstructs the electron-hole continuum in the limit U -> 0. Power-law singularities along boundary lines of the spectrum are described by effective impurity models that are explicitly invariant under spin and eta-spin SU(2) rotations. The Mott-Hubbard metal-insulator transition is reflected in a discontinuous change of the exponents of edge singularities at U = 0. The sharp feature observed in the spectrum for momenta near the zone boundary is attributed to a van Hove singularity that persists as a consequence of integrability.

Distribution of the CCR5delta32 allele (gene variant CCR5) in Rondonia, Western Amazonian region, Brazil

Since around 1723, on the occasion of its initial colonization by Europeans, Rondonia has received successive waves of immigrants. This has been further swelled by individuals from northeastern Brazil, who began entering at the beginning of the twentieth century. The ethnic composition varies across the state according to the various sites of settlement of each wave of immigrants. We analyzed the frequency of the CCR5 Delta 32 allele of the CCR5 chemokine receptor, which is considered a Caucasian marker, in five sample sets from the population. Four were collected in Porto Velho, the state capital and the site of several waves of migration. Of these, two, from the Hospital de Base were comprised of HB Mothers and HB Newborns presenting allele frequencies of 3.5% and 3.1%, respectively, a third from the peri-urban neighborhoods of Candelaria/Bate-Estaca (1.8%), whereas a fourth, from the Research Center on Tropical Medicine/CEPEM (0.6%), was composed of malaria patients under treament. The fifth sample (3.4%) came from the inland Quilombola village of Pedras Negras. Two homozygous individuals (CCR5 Delta 32/CCR5 Delta 32) were detected among the HB Mother samples. The frequency of this allele was heterogeneous and higher where the European inflow was more pronounced. The presence of the allele in Pedras Negras revealed European miscegenation in a community largely comprising Quilombolas.

Abrupt changes in high-latitude nutrient supply to the Atlantic during the last glacial cycle

The supply of nutrients to the low-latitude thermocline is largely controlled by intermediate-depth waters formed at the surface in the high southern latitudes. Silicic acid is an essential macronutrient for diatoms, which are responsible for a significant portion of marine carbon export production. Changes in ocean circulation, such as those observed during the last deglaciation, would influence the nutrient composition of the thermocline and, therefore, the relative abundance of diatoms in the low latitudes. Here we present the first record of the silicic acid content of the Atlantic over the last glacial cycle. Our results show that at intermediate depths of the South Atlantic, the silicic acid concentration was the same at the Last Glacial Maximum (LGM) as it is today, overprinted by high silicic acid pulses that coincided with abrupt changes in ocean and atmospheric circulation during Heinrich Stadials and the Younger Dryas. We suggest these pulses were caused by changes in intermediate water formation resulting from shifts in the subpolar hydrological cycle, with fundamental implications for the nutrient supply to the Atlantic.

RELATIONS BETWEEN SOIL SURFACE ROUGHNESS, TORTUOSITY, TILLAGE TREATMENTS, RAINFALL INTENSITY AND SOIL AND WATER LOSSES FROM A RED YELLOW LATOSOL

The soil surface roughness increases water retention and infiltration, reduces the runoff volume and speed and influences soil losses by water erosion. Similarly to other parameters, soil roughness is affected by the tillage system and rainfall volume. Based on these assumptions, the main purpose of this study was to evaluate the effect of tillage treatments on soil surface roughness (RR) and tortuosity (T) and to investigate the relationship with soil and water losses in a series of simulated rainfall events. The field study was carried out at the experimental station of EMBRAPA Southeastern Cattle Research Center in Sao Carlos (Fazenda Canchim), in Sao Paulo State, Brazil. Experimental plots of 33 m(2) were treated with two tillage practices in three replications, consisting of: untilled (no-tillage) soil (NTS) and conventionally tilled (plowing plus double disking) soil (CTS). Three successive simulated rain tests were applied in 24 h intervals. The three tests consisted of a first rain of 30 mm/h, a second of 30 mm/h and a third rain of 70 mm/h. Immediately after tilling and each rain simulation test, the surface roughness was measured, using a laser profile meter. The tillage treatments induced significant changes in soil surface roughness and tortuosity, demonstrating the importance of the tillage system for the physical surface conditions, favoring water retention and infiltration in the soil. The increase in surface roughness by the tillage treatments was considerably greater than its reduction by rain action. The surface roughness and tortuosity had more influence on the soil volume lost by surface runoff than in the conventional treatment. Possibly, other variables influenced soil and water losses from the no-tillage treatments, e. g., soil type, declivity, slope length, among others not analyzed in this study.

Unique Alterations of an Ultraconserved Non-Coding Element in the 3 ' UTR of ZIC2 in Holoprosencephaly

Coding region alterations of ZIC2 are the second most common type of mutation in holoprosencephaly (HPE). Here we use several complementary bioinformatic approaches to identify ultraconserved cis-regulatory sequences potentially driving the expression of human ZIC2. We demonstrate that an 804 bp element in the 3' untranslated region (3'UTR) is highly conserved across the evolutionary history of vertebrates from fish to humans. Furthermore, we show that while genetic variation of this element is unexpectedly common among holoprosencephaly subjects (6/528 or >1%), it is not present in control individuals. Two of six proband-unique variants are de novo, supporting their pathogenic involvement in HPE outcomes. These findings support a general recommendation that the identification and analysis of key ultraconserved elements should be incorporated into the genetic risk assessment of holoprosencephaly cases.

Physical-chemical and microbiological changes in Cerrado Soil under differing sugarcane harvest management systems

Background: Sugarcane cultivation plays an important role in Brazilian economy, and it is expanding fast, mainly due to the increasing demand for ethanol production. In order to understand the impact of sugarcane cultivation and management, we studied sugarcane under different management regimes (pre-harvest burn and mechanical, unburnt harvest, or green cane), next to a control treatment with native vegetation. The soil bacterial community structure (including an evaluation of the diversity of the ammonia oxidizing (amoA) and denitrifying (nirK) genes), greenhouse gas flow and several soil physicochemical properties were evaluated. Results: Our results indicate that sugarcane cultivation in this region resulted in changes in several soil properties. Moreover, such changes are reflected in the soil microbiota. No significant influence of soil management on greenhouse gas fluxes was found. However, we did find a relationship between the biological changes and the dynamics of soil nutrients. In particular, the burnt cane and green cane treatments had distinct modifications. There were significant differences in the structure of the total bacterial, the ammonia oxidizing and the denitrifying bacterial communities, being that these groups responded differently to the changes in the soil. A combination of physical and chemical factors was correlated to the changes in the structures of the total bacterial communities of the soil. The changes in the structures of the functional groups follow a different pattern than the physicochemical variables. The latter might indicate a strong influence of interactions among different bacterial groups in the N cycle, emphasizing the importance of biological factors in the structuring of these communities. Conclusion: Sugarcane land use significantly impacted the structure of total selected soil bacterial communities and ammonia oxidizing and denitrifier gene diversities in a Cerrado field site in Central Brazil. A high impact of land use was observed in soil under the common burnt cane management. The green cane soil also presented different profiles compared to the control soil, but to at a lesser degree.

The influence of breakfast and dairy products on dietary calcium and vitamin D intake in postpubertal adolescents and young adults

Background: Given the importance of both calcium and vitamin D for bone health and the high prevalence of vitamin D from around the world, the present study aimed to evaluate calcium and vitamin D intake in a group of healthy Brazilian adolescents and young adults and to examine the influence of breakfast and dairy products in the total intake of these nutrients. Methods: One hundred and sixty adolescents and young adults, aged 1620 years old, from a public school, participated in the present study. Three-day dietary records were used to assess calcium and vitamin D intakes. Serum 25(OH) D levels were measured using a radioimmunoassay kit. The results were expressed as the mean (SD). Results: Only 3.8% of the subjects met the daily adequate intake recommendation for calcium, and none for vitamin D [682.2 (132.2) mg day(-1) and 124.0 (28.0) IU day(-1), respectively]. 25(OH) D serum levels were insufficient in 51.5% and deficient in 9.7% of the individuals [72.5 (22.3) nmol L(-1)]. There was a significant positive correlation between dairy product intake with both calcium and vitamin D (r = 0.597 and r = 0.561, respectively; P = 0.000). Adolescents who ate breakfast had a significant higher mean calcium, vitamin D and dairy product intake than adolescents who did not report this meal. Conclusions: The majority of adolescents and young adults did not consume recommended intakes of calcium and vitamin D and also presented 25(OH) D insufficiency. The results indicate that a regular breakfast and the consumption of dairy products represent important strategies in improving calcium and vitamin D intake in the diet.

MUC1 gene polymorphism in three Nelore lines selected for growth and its association with growth and carcass traits

The objective of this study was to describe the VNTR polymorphism of the mucin 1 gene (MUC1) in three Nelore lines selected for yearling weight to determine whether allele and genotype frequencies of this polymorphism were affected by selection for growth. In addition, the effects of the polymorphism on growth and carcass traits were evaluated. Birth, weaning and yearling weights, rump height, Longissimus muscle area, backfat thickness, and rump fat thickness, were analyzed. A total of 295 Nelore heifers from the Beef Cattle Research Center, Instituto de Zootecnia de Sertozinho, were used, including 41 of the control line, 102 of the selection line and 152 of the traditional. The selection and traditional lines comprise animals selected for higher yearling weight, whereas control line animals are selected for yearling weight close to the average. Five alleles were identified, with allele 1 being the most frequent in the three lines, especially in the lines selected for higher means for yearling weight. Heterozygosity was significantly higher in the control line. Association analyses showed significant effects of allele 1 on birth weight and weaning weight while the allele 3 exert significant effects on yearling weight and back fat thickness. Despite these findings, application of this marker to marker-assisted selection requires more consistent results based on the genotyping of a larger number of animals in order to increase the accuracy of the statistical analyses.

Distribution of major elements in Atlantic surface sediments (36 degrees N-49 degrees S): Imprint of terrigenous input and continental weathering

Numerous studies use major element concentrations measured on continental margin sediments to reconstruct terrestrial climate variations. The choice and interpretation of climate proxies however differ from site to site. Here we map the concentrations of major elements (Ca, Fe, Al, Si, Ti, K) in Atlantic surface sediments (36 degrees N-49 degrees S) to assess the factors influencing the geochemistry of Atlantic hemipelagic sediments and the potential of elemental ratios to reconstruct different terrestrial climate regimes. High concentrations of terrigenous elements and low Ca concentrations along the African and South American margins reflect the dominance of terrigenous input in these regions. Single element concentrations and elemental ratios including Ca (e. g., Fe/Ca) are too sensitive to dilution effects (enhanced biological productivity, carbonate dissolution) to allow reliable reconstructions of terrestrial climate. Other elemental ratios reflect the composition of terrigenous material and mirror the climatic conditions within the continental catchment areas. The Atlantic distribution of Ti/Al supports its use as a proxy for eolian versus fluvial input in regions of dust deposition that are not affected by the input of mafic rock material. The spatial distributions of Al/Si and Fe/K reflect the relative input of intensively weathered material from humid regions versus slightly weathered particles from drier areas. High biogenic opal input however influences the Al/Si ratio. Fe/K is sensitive to the input of mafic material and the topography of Andean river drainage basins. Both ratios are suitable to reconstruct African and South American climatic zones characterized by different intensities of chemical weathering in well-understood environmental settings.

STOCHASTIC MODEL FOR SIMULATING MAIZE YIELD

Maize is one of the most important crops in the world. The products generated from this crop are largely used in the starch industry, the animal and human nutrition sector, and biomass energy production and refineries. For these reasons, there is much interest in figuring the potential grain yield of maize genotypes in relation to the environment in which they will be grown, as the productivity directly affects agribusiness or farm profitability. Questions like these can be investigated with ecophysiological crop models, which can be organized according to different philosophies and structures. The main objective of this work is to conceptualize a stochastic model for predicting maize grain yield and productivity under different conditions of water supply while considering the uncertainties of daily climate data. Therefore, one focus is to explain the model construction in detail, and the other is to present some results in light of the philosophy adopted. A deterministic model was built as the basis for the stochastic model. The former performed well in terms of the curve shape of the above-ground dry matter over time as well as the grain yield under full and moderate water deficit conditions. Through the use of a triangular distribution for the harvest index and a bivariate normal distribution of the averaged daily solar radiation and air temperature, the stochastic model satisfactorily simulated grain productivity, i.e., it was found that 10,604 kg ha(-1) is the most likely grain productivity, very similar to the productivity simulated by the deterministic model and for the real conditions based on a field experiment.

Searching for the first stars with the Gaia mission

Aims. We construct a theoretical model to predict the number of orphan afterglows (OA) from gamma-ray bursts (GRBs) triggered by primordial metal-free (Pop III) stars expected to be observed by the Gaia mission. In particular, we consider primordial metal-free stars that were affected by radiation from other stars (Pop III. 2) as a possible target. Methods. We use a semi-analytical approach that includes all relevant feedback effects to construct cosmic star formation history and its connection with the cumulative number of GRBs. The OA events are generated using the Monte Carlo method, and realistic simulations of Gaia's scanning law are performed to derive the observation probability expectation. Results. We show that Gaia can observe up to 2.28 +/- 0.88 off-axis afterglows and 2.78 +/- 1.41 on-axis during the five-year nominal mission. This implies that a nonnegligible percentage of afterglows that may be observed by Gaia (similar to 10%) could have Pop III stars as progenitors.

Antigenotoxic Effects of Piquia (Caryocar villosum) in Multiple Rat Organs

This study investigated the in vivo genotoxicity of piquia pulp (Caryocar villosum) and its potential antigenotoxicity on doxorubicin (DXR)-induced DNA damage by comet assay and micronucleus test. In addition, the phytochemicals present in piquia pulp were determined. Piquia fruit pulp (75, 150 or 300 mg/kg b.w.) was administered by gavage to Wistar rats for 14 days, and the animals received an injection of saline or DXR (15 mg/kg b.w., i.p.) 24 h before they were euthanized. The phytochemical analysis revealed the presence of carotenoids; phenolic compounds, including flavonoids; tannins and alpha-tocopherol in piquia pulp. No statistically significant differences were observed in the evaluated parameters, demonstrating the absence of cytotoxic and genotoxic effects of piquia pulp at all tested doses. In liver, kidney, cardiac and bone marrow cells, piquia significantly reduced the DNA damage induced by DXR. Our results showed that the lowest piquia dose caused the largest decrease in DNA damage and the highest dose caused the smallest decrease, demonstrating an inverse dose-response of piquia pulp. Furthermore, we observed a difference in the potential antigenotoxic effects in several tissues. In conclusion, our results demonstrated that piquia pulp was not genotoxic and inhibited the genotoxicity induced by DXR, but some of the protective effects that were observed depended on the doses and experimental conditions. Therefore, further investigations are needed to clarify how piquia pulp positively affects human health.