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Find video protocols related to scientific articles indexed in Pubmed.
Sustained complete remission of primary effusion lymphoma with adjunctive ganciclovir treatment in an HIV-positive patient.
BMJ Case Rep
PUBLISHED: 10-15-2014
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Primary effusion lymphoma (PEL) is one of the least common of the AIDS-related lymphomas, accounting for less than 1-4% of cases. Clinical manifestations depend on the extent and distribution of disease and, as in the majority of patients no detectable mass lesion is found, symptoms are related to fluid accumulation, dyspnoea (pleural or pericardial effusions), abdominal distension (ascites) or joint swelling. The median survival after diagnosis, even with aggressive chemotherapy, remains poor and remissions are often of short duration. We present the case of a 31-year-old man with AIDS and diagnosis of PEL, in whom sustained and complete remission of the tumour was achieved with adjunctive ganciclovir therapy. Since the disease is so uncommon, there is a paucity of data to guide the treatment of these patients; ganciclovir might be a potential antiviral therapeutic option, as demonstrated by the 2-year remission achieved in our patient.
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Resonant electronic coupling enabled by small molecules in nanocrystal solids.
Nano Lett.
PUBLISHED: 06-03-2014
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The future exploitation of the exceptional properties of nanocrystal (NC) thin films deposited from liquid dispersions of nanoparticles relies upon our ability to produce films with improved electrical properties by simple and inexpensive means. Here, we demonstrate that the electronic conduction of solution-processed NC films can be strongly enhanced without the need of postdeposition treatments, via specific molecules adsorbed at the surfaces of adjacent NCs. This effect is demonstrated for Si NC films doped with the strong molecular oxidizing agent tetrafluoro-tetracyanoquinodimethane (F4-TCNQ). Density functional calculations were carried out with molecule-doped superlattice solid models. It is shown that, when populated by electrons, hybrid molecule/NC states edge (and may actually resonate with) the conduction-band states of the NC solid. This provides extra electronic connectivity across the NC network as the molecules effectively flatten the electronic potential barriers for electron transfer across the otherwise vacuum-filled network interstitialcies.
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Yeast metabolomics: sample preparation for a GC/MS-based analysis.
Methods Mol. Biol.
PUBLISHED: 04-19-2014
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Metabolome sample preparation is one of the key factors in metabolomics analyses. The quality of the metabolome data will depend on the suitability of the experimental procedures to the cellular system (e.g., yeast cells) and the analytical performance. Here, we summarize a protocol for metabolome analysis of yeast cells using gas chromatography-mass spectrometry (GC-MS). First, the main phases of a metabolomics analysis are identified: sample preparation, metabolite extraction, and analysis. We also provide an overview on different methods used to quench samples and extract intracellular metabolites from yeast cells. This protocol provides a detailed description of a GC-MS-based analysis of yeast metabolome, in particular for metabolites containing amino and/or carboxyl groups, which represent most of the compounds participating in the central carbon metabolism.
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Interpreting the rich behavior of ternary DNA-PEI-Fe(III) complexes.
Biomacromolecules
PUBLISHED: 01-24-2014
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This work aims to shed light on the mechanism of interaction between components of ternary DNA-PEI-Fe(III) complexes, using experimental and theoretical approaches. In the experimental part, the chelation between PEI-Fe(III) was inspected by potentiometry and electrical conductance measurements and the respective importance for the condensation of DNA analyzed. To this end, three different mixing protocols for the components were imposed using different PEIs, branched (bPEI1.2 and bPEI10) and linear (lPEI2.5 and lPEI25). A delay in DNA condensation was observed when PEI and Fe(III) were premixed and then added to DNA. The set of observations was complemented by determination of the amount of Fe(III) included in the polyplexes, which was found to be dependent on the order of mixture and on the type of PEI used, decreasing with intrinsic PEI condensation efficiency. Overall, a coherent picture in which Fe(III) compensates PEI, probably modulating the respective charge, emerges. Some points arisen from the experimental part were rationalized using Monte Carlo simulations. Different architectured polycation (PC) chains were modeled and an interaction between PC and multivalent ions, mimicking the chelation of Fe(III) by the PEI, was imposed. It was found that chelation enhances polyanion (PA) compaction, irrespective of the PC architecture and charge density. The amount of multivalent ions in each polyplex compensates the negative charge unbalanced by the PC. The charge density and the ability of chelation of each PC dictate the disposition of each condensing agent along the PA backbone, and their coexistence strengthens PA compaction. The deep understanding of these ternary mixtures is a step forward in the optimization of such systems for application in gene delivery.
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iOD907, the first genome-scale metabolic model for the milk yeast Kluyveromyces lactis.
Biotechnol J
PUBLISHED: 01-14-2014
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We describe here the first genome-scale metabolic model of Kluyveromyces lactis, iOD907. It is partially compartmentalized (four compartments), composed of 1867 reactions and 1476 metabolites. The iOD907 model performed well when comparing the positive growth of K. lactis to Biolog experiments and to an online catalogue of strains that provides information on carbon sources in which K. lactis is able to grow. Chemostat experiments were used to adjust non-growth-associated energy requirements, and the model proved accurate when predicting the biomass, oxygen and carbon dioxide yields. When compared to published experiments, in silico knockouts accurately predicted in vivo phenotypes. The iOD907 genome-scale metabolic model complies with the MIRIAM (minimum information required for the annotation of biochemical models) standards for the annotation of enzymes, transporters, metabolites and reactions. Moreover, it contains direct links to Kyoto encyclopedia of genes and genomes (KEGG; for enzymes, metabolites and reactions) and to the Transporters Classification Database (TCDB) for transporters, allowing easy comparisons to other models. Furthermore, this model is provided in the well-established systems biology markup language (SBML) format, which means that it can be used in most metabolic engineering platforms, such as OptFlux or Cobra. The model is able to predict the behavior of K. lactis under different environmental conditions and genetic perturbations. Furthermore, by performing simulations and optimizations, it can be important in the design of minimal media and will allow insights on the milk yeast's metabolism, as well as identifying metabolic engineering targets for improving the production of products of interest.
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Evaluating the X chromosome-specific diversity of Colombian populations using insertion/deletion polymorphisms.
PLoS ONE
PUBLISHED: 01-01-2014
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The European and African contribution to the pre-existing Native American background has influenced the complex genetic pool of Colombia. Because colonisation was not homogeneous in this country, current populations are, therefore, expected to have different proportions of Native American, European and African ancestral contributions. The aim of this work was to examine 11 urban admixed populations and a Native American group, called Pastos, for 32 X chromosome indel markers to expand the current knowledge concerning the genetic background of Colombia. The results revealed a highly diverse genetic background comprising all admixed populations, harbouring important X chromosome contributions from all continental source populations. In addition, Colombia is genetically sub-structured, with different proportions of European and African influxes depending on the regions. The samples from the North Pacific and Caribbean coasts have a high African ancestry, showing the highest levels of diversity. The sample from the South Andean region showed the lowest diversity and significantly higher proportion of Native American ancestry than the other samples from the North Pacific and Caribbean coasts, Central-West and Central-East Andean regions, and the Orinoquian region. The results of admixture analysis using X-chromosomal markers suggest that the high proportion of African ancestry in the North Pacific coast was primarily male driven. These men have joined to females with higher Native American and European ancestry (likely resulting from a classic colonial asymmetric mating type: European male x Amerindian female). This high proportion of male-mediated African contributions is atypical of colonial settings, suggesting that the admixture occurred during a period when African people were no longer enslaved. In the remaining regions, the African contribution was primarily female-mediated, whereas the European counterpart was primarily male driven and the Native American ancestry contribution was not gender biased.
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Updates to BioSamples database at European Bioinformatics Institute.
Nucleic Acids Res.
PUBLISHED: 11-21-2013
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The BioSamples database at the EBI (http://www.ebi.ac.uk/biosamples) provides an integration point for BioSamples information between technology specific databases at the EBI, projects such as ENCODE and reference collections such as cell lines. The database delivers a unified query interface and API to query sample information across EBIs databases and provides links back to assay databases. Sample groups are used to manage related samples, e.g. those from an experimental submission, or a single reference collection. Infrastructural improvements include a new user interface with ontological and key word queries, a new query API, a new data submission API, complete RDF data download and a supporting SPARQL endpoint, accessioning at the point of submission to the European Nucleotide Archive and European Genotype Phenotype Archives and improved query response times.
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The interaction of long chain sodium carboxylates and sodium dodecylsulfate with lead(II) ions in aqueous solutions.
J Colloid Interface Sci
PUBLISHED: 08-24-2013
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The interaction of sodium octanoate, decanoate or dodecanoate with lead(II) has been studied in aqueous solutions using potentiometry, electrical conductivity, turbidity and ICP-OES measurements. These show an alkyl chain length dependence on the behavior. At the lead(II) concentration used (1.0 mM), relatively strong interactions are observed with the decanoate and dodecanaote, leading to formation of the lead carboxylates (soaps) as insoluble complexes. All techniques show 1:2 (metal:carboxylate) stoichiometry corresponding to charge neutralization. With sodium octanoate and lead(II), a rather weaker interaction is seen, and complexation is only observed at metal:carboxylate ratios > 0.5. However, in contrast to our previous work on octanoate and calcium(II) in aqueous solutions [1], precipitation does occur at higher concentrations. This difference between the behavior of the metal ions is probably due to the more covalent nature of the bonds of the carboxylate with Pb(2+) than with Ca(2+). Association constants of the complexes have been determined from potentiometric measurements and are consistent with data on solubility products. A comparison is made of the effect of surfactant head group on the interactions with lead(II) using two surfactants with the same chain length: dodecanoate and dodecylsulfate. Differences in their interactions with this metal ion in aqueous solutions are interpreted in terms of greater covalency of the bond between the metal and the carboxylate than with the sulfate group.
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Optimization of a pentaplex panel for MSI analysis without control DNA in a Brazilian population: correlation with ancestry markers.
Eur. J. Hum. Genet.
PUBLISHED: 06-17-2013
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Microsatellite instability (MSI) testing has been advocated for all newly diagnosed colorectal cancer patients. One of the most common tests is composed by a pentaplex panel of mononucleotides markers (NR-27, NR-21, NR-24, BAT-25, and BAT-26), which allows the analysis of MSI in tumors without the need of reference DNA. For that, it is fundamental to establish a quasi-monomorphic variation range (QMVR) for each marker. Herein, we aimed to establish the QMVR in a Brazilian healthy population, to evaluate the feasibility of MSI determination of tumors, without the matching normal DNA. Furthermore, we intend to assess their ancestry using specific ancestry-informative markers (AIMs) and correlate with QMVR. The QMVR was assessed in 214 individuals, through a pentaplex PCR followed by fragment analysis. The ancestry analysis was done by 46 AIMs in a single multiplex PCR followed by capillary electrophoresis. Following QMVR establishment, we observed 23 individuals with alleles outside the QMVR. Importantly, none of them exhibited more than one marker outside the range. Therefore, individuals with instability at ?2 markers would be accurately classified as MSI. The European ancestry proportion was the most frequent (67.5%), followed by the African (19.6%). The comparison of the individuals with alleles within (n=191) and outside (n=23) the QMVR showed statistical difference in the proportions of European and African alleles, confirming the higher polymorphic nature of African ancestry. In conclusion, the present study reports an accurate methodology to assess MSI status without matched-normal DNA and independently of the ethnicity, even in the highly admixed population of Brazil.European Journal of Human Genetics advance online publication, 6 November 2013; doi:10.1038/ejhg.2013.256.
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Dual effect of platelet lysate on human articular cartilage: a maintenance of chondrogenic potential and a transient proinflammatory activity followed by an inflammation resolution.
Tissue Eng Part A
PUBLISHED: 01-31-2013
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Platelet-rich plasma (PRP), a cocktail of platelet growth factors and bioactive proteins, has been proposed as a therapeutic agent to restore damaged articular cartilage. We report the biological effect of the platelet lysate (PL), a PRP derivative, on primary human articular chondrocytes cultured under both physiological and inflammatory conditions. When added to the culture medium, PL induced a strong mitogenic response in the chondrocytes. The in vitro expanded cell population maintained a chondrogenic redifferentiation potential as revealed by micromass culture in vitro and ectopic cartilage formation in vivo. Further, in chondrocytes cultured in the presence of the proinflammatory cytokine interleukin-1? (IL-1?), the PL induced a drastic enhancement of the synthesis of the cytokines IL-6 and IL-8 and of neutrophil-gelatinase associated lipocalin, a lipocalin expressed during chondrocyte differentiation and inflammation. These events were mediated by the p38 MAP kinase and NF-?B pathways. We observed that inflammatory stimuli activated phospo-MAP kinase-activated protein kinase 2, a direct target of p38. The proinflammatory effect of the PL was a transient phenomenon; after an initial upregulation, we observed significant reduction of the NF-?B activity together with the repression of the inflammatory enzyme cyclooxygenase-2. Moreover, the medium of chondrocytes cultured in the simultaneous presence of PL and IL-1?, showed a significant enhancement of the chemoattractant activity versus untreated chondrocytes. Our findings support the concept that the platelet products have a direct beneficial effect on articular chondrocytes and could drive in sequence a transient activation and the resolution of the inflammatory process, thus providing a rational for their use as therapeutic agents in cartilage inflammation and damage.
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High dosage folic acid supplementation, oral cleft recurrence and fetal growth.
Int J Environ Res Public Health
PUBLISHED: 01-25-2013
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To evaluate the effects of folic acid supplementation on isolated oral cleft recurrence and fetal growth.
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TNA4OptFlux--a software tool for the analysis of strain optimization strategies.
BMC Res Notes
PUBLISHED: 01-07-2013
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Rational approaches for Metabolic Engineering (ME) deal with the identification of modifications that improve the microbes production capabilities of target compounds. One of the major challenges created by strain optimization algorithms used in these ME problems is the interpretation of the changes that lead to a given overproduction. Often, a single gene knockout induces changes in the fluxes of several reactions, as compared with the wild-type, and it is therefore difficult to evaluate the physiological differences of the in silico mutant. This is aggravated by the fact that genome-scale models per se are difficult to visualize, given the high number of reactions and metabolites involved.
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Revisiting the genetic ancestry of Brazilians using autosomal AIM-Indels.
PLoS ONE
PUBLISHED: 01-01-2013
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There are many different studies that contribute to the global picture of the ethnic heterogeneity in Brazilian populations. These studies use different types of genetic markers and are focused on the comparison of populations at different levels. In some of them, each geographical region is treated as a single homogeneous population, whereas other studies create different subdivisions: political (e.g., pooling populations by State), demographic (e.g., urban and rural), or ethnic (e.g., culture, self-declaration, or skin colour). In this study, we performed an enhanced reassessment of the genetic ancestry of ~ 1,300 Brazilians characterised for 46 autosomal Ancestry Informative Markers (AIMs). In addition, 798 individuals from twelve Brazilian populations representing the five geographical macro-regions of Brazil were newly genotyped, including a Native American community and a rural Amazonian community. Following an increasing North to South gradient, European ancestry was the most prevalent in all urban populations (with values up to 74%). The populations in the North consisted of a significant proportion of Native American ancestry that was about two times higher than the African contribution. Conversely, in the Northeast, Center-West and Southeast, African ancestry was the second most prevalent. At an intrapopulation level, all urban populations were highly admixed, and most of the variation in ancestry proportions was observed between individuals within each population rather than among population. Nevertheless, individuals with a high proportion of Native American ancestry are only found in the samples from Terena and Santa Isabel. Our results allowed us to further refine the genetic landscape of Brazilians while establishing the basis for the effective application of an autosomal AIM panel in forensic casework and clinical association studies within the highly admixed Brazilian populations.
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Effect of metal ion hydration on the interaction between sodium carboxylates and aluminum(III) or chromium(III) ions in aqueous solution.
Langmuir
PUBLISHED: 12-13-2011
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The interaction between sodium octanoate, decanoate, and dodecanoate and aluminum(III) and chromium(III) has been studied in water at natural pH values, starting well below the surfactant critical micelle concentration, using electrical conductivity, turbidity, and potentiometric measurements. With decanoate or dodecanoate, maximum interaction occurs at 3:1 stoichiometry, corresponding to charge neutralization. Although the solutions become turbid with both metal ions, indicating phase separation, differences are observed and attributed to the fact that aluminum(III) is relatively labile to substitution and rapidly replaces its water ligands, whereas chromium(III) is substitution inert. This shows up in well-defined floc formation with Al(3+), whereas Cr(3+) suspensions do not precipitate, probably because that replacement of coordinated water by carboxylate ligands is impeded. This can be overcome by increasing temperature, and differences in the thermal behavior with Al(3+) and Cr(3+) are suggested to be due to increased involvement of substitution reactions in the latter case. The effect of octanoate on the trivalent metal ions is less clear, and with Cr(3+) interaction only occurs when the carboxylate is in excess. Hydrophobic interactions between alkyl chains play a major role in driving phase separation. At high surfactant concentrations, the solid phases do not dissolve, in contrast to what is observed with the corresponding alkylsulfates. This has implications for use of these systems in metal separation through froth flotation. The concentration of metal ions in supernatant solution has been determined for sodium dodecanoate and sodium dodecylsulfate with Al(3+) and Cr(3+) over the whole surfactant concentration range by inductively coupled plasma-mass spectrometry (ICP-MS). From this, association constants have been determined and are found to be larger for the carboxylate than the alkylsulfate, in agreement with the greater Lewis basicity of the -CO(2)(-) group.
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Encapsulation and survival of a chondrocyte cell line within xanthan gum derivative.
Macromol Biosci
PUBLISHED: 08-03-2011
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A chemical derivative of xanthan gum polysaccharide is investigated as a new artificial matrix for the encapsulation of chondrocytic cells. Toward this goal, a novel micro-droplet generator is developed to produce microcapsules. Microcapsules with an average diameter of 500 µm, smooth surface, and homogeneous size distribution are obtained. ATDC5 cells encapsulated in carboxymethyl xanthan (CMX) microcapsules remain viable and are observed to proliferate for prolonged culture periods with enhanced metabolic activity. Furthermore, retention of the chondrogenic phenotype is exhibited by the cells within CMX, suggesting the ability of this material to be applied in cell-delivery therapies.
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Semantic annotation of biological concepts interplaying microbial cellular responses.
BMC Bioinformatics
PUBLISHED: 05-18-2011
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Automated extraction systems have become a time saving necessity in Systems Biology. Considerable human effort is needed to model, analyse and simulate biological networks. Thus, one of the challenges posed to Biomedical Text Mining tools is that of learning to recognise a wide variety of biological concepts with different functional roles to assist in these processes.
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A method for the analysis of 32 X chromosome insertion deletion polymorphisms in a single PCR.
Int. J. Legal Med.
PUBLISHED: 04-22-2011
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Studies of human genetic variation predominantly use short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) but Insertion deletion polymorphisms (Indels) are being increasingly explored. They combine desirable characteristics of other genetic markers, especially the possibility of being analysed using short amplicon strategies, which increases the ease of analysis, contributing to justify their interest in population and forensic genetics. After the advent of autosomal and uniparental genomes (mtDNA and Y chromosome), these fields of research are also focusing on the X chromosome, given its special transmission pattern. The X chromosome markers brought new insights into the history of modern human populations and also proved useful in forensic kinship investigations, namely in deficient relationship cases and in cases where autosomes are uninformative. This work describes an X-Indel multiplex system amplifying 32 biallelic markers in one single PCR. The multiplex includes X-Indels shown to be polymorphic in the major human population groups and follows a short amplicon strategy. The set was applied in the genetic characterization of sub-Saharan African, European and East Asian population samples and revealed high forensic efficiency, as measured by the accumulated power of discrimination (0.9999990 was the lowest value in males and 0.999999999998 was the highest in females) and mean exclusion chance varied between 0.998 and 0.9996 in duos and between 0.99997 and 0.999998 in trios. Finally, a segregation analysis was performed using trio constellations of father-mother-daughters in order to address the transmission pattern and assess mutation rates of this type of markers.
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Encapsulation of human articular chondrocytes into 3D hydrogel: phenotype and genotype characterization.
Methods Mol. Biol.
PUBLISHED: 02-09-2011
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This chapter is intended to provide a summary of the current materials used in cell encapsulation technology as well as methods for evaluating the performance of cells encapsulated in a polymeric matrix. In particular, it describes the experimental procedure to prepare a hydrogel matrix based on natural polymers for encapsulating and culturing human articular chondrocytes with the interest in cartilage regeneration. Protocols to evaluate the viability, proliferation, differentiation, and matrix production of embedded cells are also described and include standard protocols such as the MTT and [3H] Thymidine assays, reverse transcription polymerase chain reaction (RT-PCR) technique, histology, and immunohistochemistry analysis. The assessment of cell distribution within the 3D hydrogel construct is also described using APoTome analysis.
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Blood pressure in young adults.
Rev Port Cardiol
PUBLISHED: 12-01-2010
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Hypertension (HT) is a major cardiovascular risk factor. Elevated blood pressure (BP) in childhood predisposes to HT in adulthood. Epidemiological studies in young age-groups are scarce. The aim of this study was to determine the prevalence of HT in a population of university students aged between 18 and 25 years; to analyze the profile of HT in the presence of other risk factors; and to alert patients and physicians to the need to assess and control cardiovascular risk factors in young adults.
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Genotypes and antimicrobial-resistant phenotypes of Neisseria gonorrhoeae in Portugal (2004-2009).
Sex Transm Infect
PUBLISHED: 10-14-2010
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To determine the antibiotic phenotype and MAST-genotype distribution of Neisseria gonorrhoeae isolates in Portugal between 2004 and 2009, and to evaluate specific associations between MAST-genotypes and sexual orientation, age and antibiotic resistance.
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Efficient pump beam shaping for high-power thin-disk laser systems.
Appl Opt
PUBLISHED: 09-22-2010
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We report a beam-shaping technique whereby the output power from a high-power laser-diode stack is efficiently coupled, reconfigured, and transmitted to a thin-disk laser by means of a compact optical fiber bundle. By using this technique, the power density is increased by a factor of 2 when compared to direct coupling with a octagonal fused silica rod while the numerical aperture is kept constant. Transmission efficiency of 80% was measured for the beam shaper without antireflection coating. The top-hat distribution is numerically calculated at the thin-disk laser crystal.
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A novel hemostatic delivery device for thrombin: biodegradable poly(D,L-lactide-co-glycolide) 50:50 microspheres.
J Biomed Mater Res A
PUBLISHED: 07-28-2010
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Topical thrombins are locally active hemostatic agents that can be used to minimize blood loss during any surgery. The aim of this study was to design and investigate a thrombin-containing biodegradable hemostyptic device with an optimized drug release profile to promote local blood clot formation. It is effective with ongoing systemic antithrombotic therapy and can be used in all types of bone-related surgery, for example, in dental surgery. Thrombin-loaded poly(D,L-lactide-co-glycolide) microspheres were synthesized by means of complex (w/o/w) emulsion evaporation method. The resulting enzyme activity of the serine-protease thrombin was verified by the specific chromogenic substrate S-2238. The thrombin release profile depended on four factors: (1) thrombin dosage, (2) polymer concentration in the o-phase, (3) phase quotient w1:0 in the primary emulsion, and (4) the addition of pore-introducing agents. A collagenous sponge containing thrombin-loaded microspheres by means of lyophilization was developed. The impact of several production factors of the (w1/o/w2) solvent evaporation method to optimize thrombin encapsulation, morphology of the spheres, and desired drug release profile have been investigated. The in vitro thrombin release was dependent on the polymer-to-oil phase ratio, the polymer concentration, and the type of solvent and polymer. The porosity of the spheres and release rate of the active agent were enhanced by increasing the inner aqueous w1 phase. With this study, a new biodegradable hemostyptic device could be verified and established for a potentially safe and locally controlled thrombin release to manage postsurgical hemorrhage in patients undergoing anticoagulant therapy.
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Neutrophil and monocyte activation in chronic kidney disease patients under hemodialysis and its relationship with resistance to recombinant human erythropoietin and to the hemodialysis procedure.
Hemodial Int
PUBLISHED: 07-24-2010
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The aim of the present work was to further clarify leukocyte activation due to hemodialysis (HD) procedures and to investigate its relationship with recombinant human erythropoietin resistance. Therefore, we studied the expression of CXCR1 and CD11b on neutrophils, as well as the monocyte expression of CD11b, HLA-DR, and CD14. We studied 34 chronic kidney disease (CKD) patients under HD and recombinant human erythropoietin treatment (26 responders and 8 nonresponders to recombinant human erythropoietin therapy). All CKD patients blood samples were collected before and immediately after the HD procedure. Eighteen healthy individuals (blood donors) were also studied as a control group. Hematological data, neutrophil (CD11b and CXCR1), and monocyte (CD11b, HLA-DR, and CD14) cell surface markers were measured in all patients (before and after the HD procedure) and controls. When compared with the controls, CKD patients presented a significant decrease in CXCR1 neutrophil expression, and in CD14 monocyte expression, accompanied by a significant increase in HLA-DR monocyte expression. When comparing the 2 groups of patients, we found that nonresponders showed an additional decrease in CXCR1 neutrophil expression. After the HD procedure, a statistically significant increase in CD14 and CD11b monocyte surface markers and a decrease in CXCR1 neutrophil expression and in HLA-DR monocyte expression was found. These data further strengthen our previous studies, showing that neutrophils and monocytes are activated in CKD patients, particularly in nonresponder patients. Moreover, this activation is due, at least in part, to the HD procedure, although we should not exclude that it can also be due to the enhanced inflammatory process observed in nonresponder patients.
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On the flocculation and re-dissolution of trivalent lanthanide metal ions by sodium dodecyl sulfate in aqueous solutions.
J Colloid Interface Sci
PUBLISHED: 07-07-2010
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The interaction between aqueous solutions of trivalent lanthanide ions (M(3+): La(III) and Gd(III) and Tb (III)) at fixed (1mM) concentrations and various concentrations of sodium dodecyl sulfate (SDS), ranging from pre- to post-micellar, has been investigated by ICP-AES (La(III) and Gd(III)), luminescence spectra (Gd(III)) and lifetimes (Tb(III)) and (139)La NMR spectroscopy. It has been found that at concentration ratios, r=[SDS]/[M(3+)], around the charge neutralization value (ca. 3), dodecyl sulfate (DS(-)) anion interacts with the metal ions to form insoluble aggregates. The metal ion-DS(-) complexes remain flocculated for r values below 5-6 (Gd(III) and La(III), respectively), while at higher r values, re-dissolution takes place. The flocculated aggregates have been characterized by X-ray powder diffraction, and show a lamellar structure. Job plot method indicates that a complex with a 1:3 (M(3+):DS(-)) stoichiometry is formed. From ICP-AES analysis, a model based on a three-step mechanism has been developed and association constants calculated. For all systems the interaction between DS(-) and metal ions follows an associative process with K values ranging between K(1)=10 and K(3)=10(4). These data are discussed on the basis of the physical-chemical characteristics of the metal ions. Re-dissolution with increasing surfactant concentration is attributed to formation of mixed lanthanide/sodium dodecyl sulfate aggregates, with the relative lanthanide fraction in these species decreasing with increasing SDS concentration.
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Malaria: looking for selection signatures in the human PKLR gene region.
Br. J. Haematol.
PUBLISHED: 04-04-2010
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The genetic component of susceptibility to malaria is both complex and multigenic and the better-known protective polymorphisms are those involving erythrocyte-specific structural proteins and enzymes. In vivo and in vitro data have suggested that pyruvate kinase deficiency, which causes a nonspherocytic haemolytic anaemia, could be protective against malaria severity in humans, but this hypothesis remains to be tested. In the present study, we conducted a combined analysis of Short Tandem Repeats (STRs) and Single Nucleotide Polymorphisms (SNPs) in the pyruvate kinase-encoding gene (PKLR) and adjacent regions (chromosome 1q21) to look for malaria selective signatures in two sub-Saharan African populations from Angola and Mozambique, in several groups with different malaria infection outcome. A European population from Portugal, including a control and a pyruvate kinase-deficient group, was used for comparison. Data from STR and SNP loci spread along the PKLR gene region showed a considerably higher differentiation between African and Portuguese populations than that usually found for neutral markers. In addition, a wider region showing strong linkage disequilibrium was found in an uncomplicated malaria group, and a haplotype was found to be associated with this clinical group. Altogether, this data suggests that malaria selective pressure is acting in this genomic region.
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Enhancing male sexual success in a lekking fly (Anastrepha suspensa Diptera: Tephritidae) through a juvenile hormone analog has no effect on adult mortality.
J. Insect Physiol.
PUBLISHED: 03-16-2010
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While defending lek-territories, male Anastrepha suspensa (Loew) produce chemical, acoustic and visual courtship signals. In the laboratory and under semi-natural conditions, topical application of the juvenile hormone analog methoprene doubles pheromone production and subsequently doubles sexual success. However, sexual signals and interactions are likely to be physiologically expensive and so result in higher male mortality. Comparison of males kept in isolation for 35 days, but provided daily with a potential mate or a rival male, revealed that both male- and female-interactors shortened focal-male lifespan. In addition, focal males were either treated with methoprene or not, then either provided with protein in their sucrose-based diet or not. Protein proved to similarly double sexual success and also resulted in longer male life spans in all of the interactor-categories. However, there was no evidence that methoprene induced hypersexuality resulted in higher rates of mortality, i.e., the longevity of males treated with methoprene did not significantly differ from untreated males in the same interactor/diet categories. This apparent lack of costs to a putatively sexually selected signal is unexpected but presents an opportunity to increase the sexual competence of sterile flies with few consequences to their survival following mass-release.
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Influence of a juvenile hormone analog and dietary protein on male Anastrepha suspensa (Diptera: Tephritidae) sexual success.
J. Econ. Entomol.
PUBLISHED: 03-11-2010
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Juvenile hormone levels and adult diet have important effects on the attractiveness and competitiveness of male Anastrepha suspensa (Loew) (Caribbean fruit fly). Because the success of the sterile insect technique requires the release of males that can compete in the wild, these effects are of crucial importance. Laboratory and field cage experiments were conducted to compare male sexual performance on a lifetime basis and daily basis when submitted to four different treatments: (M+P+) application of the juvenile hormone analog, methoprene (M) and sugar and hydrolyzed yeast as adult food; (M+P-) application of M and sugar as adult food; (M-P+) no application of M and sugar and hydrolyzed yeast as adult food; and (M-P-) no application of M and sugar as adult food. On a daily basis, M+P+ males always performed better sexually, and 10% of these individuals were able to mate three consecutive times in the same day. However, the copula duration decreased with the increased number of matings on same day. In addition, M caused earlier maturation. On a lifetime basis, M+P+ males had significantly greater sexual success than other flies. The substantial improvement in male sexual performance because of the hormone application, protein supply, and interaction of hormone and protein has the potential of producing more efficacious sterile males.
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A new multiplex for human identification using insertion/deletion polymorphisms.
Electrophoresis
PUBLISHED: 10-29-2009
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Human identification is usually based on the study of STRs or SNPs depending on the particular characteristics of the investigation. However, other types of genetic variation such as insertion/deletion polymorphisms (indels) have considerable potential in the field of identification, since they can combine the desirable characteristics of both STRs and SNPs. In this study, a set of 38 non-coding bi-allelic autosomal indels reported to be polymorphic in African, European, and Asian populations were selected. We developed a sensitive genotyping assay, which is able to characterize all 38 bi-allelic markers using a single multiplex PCR and detected with standard CE analyzers. Amplicon length was designed to be shorter than 160 bp. Complete profiles were obtained using 0.3 ng of DNA, and full genotyping of degraded samples was possible in cases where standard STR typing had partially failed. A total of 306 individuals from Angola, Mozambique, Portugal, Macau, and Taiwan were studied and population data are presented. All indels were polymorphic in the three population groups studied and the random match probabilities of the set ranged in orders of magnitude from 10(-14) to 10(-15). Therefore, the indel-plex represents a valuable approach in human identification studies, especially in challenging DNA cases, as a more straightforward and efficient alternative to SNP typing.
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Patterns of pharmacogenetic diversity in African populations: role of ancient and recent history.
Pharmacogenomics
PUBLISHED: 09-19-2009
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The knowledge that genetic variation influencing drug response is clearly structured among human populations has prompted many studies aimed at obtaining pharmacogenetic profiles in specific populations. While large amounts of data are being produced for populations from developed countries, the African continent still remains very poorly studied. To help to fill this gap, this work characterized three previously uncharacterized African populations for a set of pharmacogenetically relevant polymorphisms.
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Assessing interethnic admixture using an X-linked insertion-deletion multiplex.
Am. J. Hum. Biol.
PUBLISHED: 06-18-2009
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In this study, a PCR multiplex was optimized, allowing the simultaneous analysis of 13 X-chromosome Insertion/deletion polymorphisms (INDELs). Genetic variation observed in Africans, Europeans, and Native Americans reveals high inter-population variability. The estimated proportions of X-chromosomes in an admixed population from the Brazilian Amazon region show a predominant Amerindian contribution (approximately 41%), followed by European (approximately 32%) and African (approximately 27%) contributions. The proportion of Amerindian contribution based on X-linked data is similar to the expected value based on mtDNA and Y-chromosome information. The accuracy for assessing interethnic admixture, and the high differentiation between African, European, and Native American populations, demonstrates the suitability of this INDEL set to measure ancestry proportions in three-hybrid populations, as it is the case of Latin American populations.
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X-chromosome STR sequence variation, repeat structure, and nomenclature in humans and chimpanzees.
Int. J. Legal Med.
PUBLISHED: 06-17-2009
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Qualitative information on the sequence composition of the allele and locus structure of the X-STRs DXS8378, DXS9898, DXS6789, GATA31E08, and GATA172D05 was generated in this study. Sequence data were obtained from chimpanzees (Pan troglodytes) and diverse human population groups including Africans, Caucasians, Asians, African-Americans, and Hispanics. Results revealed DXS8378 as the most stable locus. On the other hand, DXS9898 and GATA172D05 showed unstable regions identified through chimpanzee-human sequence comparison. At DXS6789, intra-allelic variation was found in all human populations, i.e., alleles with same fragment sizes showed structural differences only detected by sequencing. At the GATA31E08 locus, a previously unreported variation between humans and chimpanzees was identified in an adjacent region upstream from the repeat. This resulted in the addition of two repeat units and the proposal of a new allele nomenclature at this locus. Also, the sequence analyses did not detect ethnic differences between the studied population samples that would justify the use of these markers to help identify ethnic origin in an anthropological context.
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Chitosan scaffolds incorporating lysozyme into CaP coatings produced by a biomimetic route: a novel concept for tissue engineering combining a self-regulated degradation system with in situ pore formation.
Acta Biomater
PUBLISHED: 03-25-2009
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This study describes an innovative self-regulated degrading material with gradual in situ pore formation ability for bone tissue engineering applications. This approach is based on the incorporation of the lysozyme enzyme into calcium phosphate (CaP) coatings, prepared on the surface of chitosan scaffolds by means of a biomimetic coating technique with the aim of controlling their degradation rate and subsequent formation of pores. However, because lysozyme has antibacterial properties, these coatings may act as a carrier for its sustained release, preventing infection upon implantation. In order to prove the concept of in situ pore formation, the coated scaffolds (with and without lysozyme) were incubated in two different solutions at different pH to simulate normal physiological conditions (pH 7.4) and inflammatory response (pH 5). The weight loss and morphology of the scaffolds was monitored over time. At pH 7.4, the scaffolds remained more stable than at pH 5. The scaffolds incubated at pH 5 showed a rapid decrease in their initial weight, and scanning electron microscopy imaging revealed the formation of a highly porous structure. Furthermore, evaluation of the activity of the incorporated lysozyme revealed that the enzyme was able to hydrolyse the peptidoglycan of the bacteria cell walls (as detected by the decrease in optical density with time), indicating that the enzyme remained active after being incorporated into the CaP coating.
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Pancytopenia in a cat with visceral leishmaniasis.
Vet Clin Pathol
PUBLISHED: 03-12-2009
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A 4-year-old, domestic shorthair, female spayed cat was presented for decreased appetite and depression. Severe pancytopenia with erythrocyte autoagglutination was found. The cat was seronegative for feline immunodeficiency and leukemia viruses. Immune-mediated hemolytic anemia was suspected but no response to treatment with a blood transfusion, enrofloxacin, and prednisone was observed. Blood and bone marrow smears obtained 11 days later contained Leishmania amastigotes in the cytoplasm of neutrophils and macrophages, respectively. Serologic and PCR testing of peripheral blood confirmed infection with Leishmania infantum. Despite treatment, the cat worsened clinically and was euthanized. At necropsy, visceral dissemination of the parasite was confirmed. The findings in this case indicate that visceral leishmaniasis should be considered as a differential diagnoses in cats with pancytopenia in areas endemic for Leishmania. In addition, amastigotes may be observed in peripheral blood neutrophils.
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Evaluation of DXS9902, DXS7132, DXS6809, DXS7133, and DXS7423 in humans and chimpanzees: sequence variation, repeat structure, and nomenclature.
Int. J. Legal Med.
PUBLISHED: 03-10-2009
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Sequencing data obtained in this study provide information on the short tandem repeat allele structures of DXS9902, DXS7132, DXS6809, DXS7133, and DXS7423. Data were obtained from the three human major population groups, namely Africans, Caucasians, and Asians as well as from chimpanzees (Pan troglodytes). DXS7133 was found to be the most stable locus and DXS6809 seemed to have evolved from a simple array of CTAT units but currently reveals a highly complex and compound structure within and between humans and chimpanzees. DXS9902 results support a TAGA allele nomenclature, which increases in one repeat unit previously reported allele distributions at this locus. For DXS7132, human/chimpanzee comparisons performed in this study provided important evidence that the CTAT allele structure should be considered for allele nomenclature purposes. Also, possible population-specific intermediate type alleles (with Native American origin) were detected at this locus that could be useful for ethnic group differentiation. DXS7423 results revealed two different sequence structures and one of these structures seems to be restricted to a single allele class in just one population group (Africans).
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Quantification of epigenetic and genetic 2nd hits in CDH1 during hereditary diffuse gastric cancer syndrome progression.
Gastroenterology
PUBLISHED: 02-16-2009
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Hereditary diffuse gastric cancer (HDGC) families carry CDH1 heterozygous germline mutations; their tumors acquire complete CDH1 inactivation through "2nd-hit" mechanisms. Most frequently, this occurs via promoter hypermethylation (epigenetic modification), and less frequently via CDH1 mutations and loss of heterozygosity (LOH). We quantified the different 2nd hits in CDH1 occurring in neoplastic lesions from HDGC patients.
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Influence of methoprene and dietary protein on male Anastrepha suspensa (Diptera:Tephritidae) mating aggregations.
J. Insect Physiol.
PUBLISHED: 01-29-2009
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The Caribbean fruit fly, Anastrepha suspensa (Loew), like many polyphagous tephritids, exhibits a lek polygyny mating system, and juvenile hormone levels and adult diet are known to have important positive effects on male sexual success. Among the potential components of this success are male lek tenure and female response to the sexual signals of lekking males. Male A. suspensa where submitted to four different treatments: (M(+)P(+)) application of juvenile hormone analog, methoprene (M) and sugar and hydrolyzed yeast as adult food; (M(+)P(-)) application of M and sugar as adult food; (M(-)P(+)) no application of M and sugar and hydrolyzed yeast as adult food; and (M(-)P(-)) no application of M and sugar as adult food. M(+)P(+) males initiated and participated more in aggregations, mated more frequently, and occupied the lek centers more often. They also had fewer unsuccessful mounting attempts than males in all the other treatments. M(+)P(+) males also emitted pheromones and acoustically signaled more often and attracted more females than males in other treatments. Male sexual performance was improved due to methoprene, protein supply, and the interaction of methoprene and protein for most of the parameters. Since the success of the sterile insect technique (SIT), a commonly employed technique to control pest tephritids, requires the release of males that can form leks, engage in agonistic sexual interactions, and attract females, these positive effects of protein and methoprene may substantially improve SIT programs.
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ArrayExpress update--trends in database growth and links to data analysis tools.
Nucleic Acids Res.
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The ArrayExpress Archive of Functional Genomics Data (http://www.ebi.ac.uk/arrayexpress) is one of three international functional genomics public data repositories, alongside the Gene Expression Omnibus at NCBI and the DDBJ Omics Archive, supporting peer-reviewed publications. It accepts data generated by sequencing or array-based technologies and currently contains data from almost a million assays, from over 30 000 experiments. The proportion of sequencing-based submissions has grown significantly over the last 2 years and has reached, in 2012, 15% of all new data. All data are available from ArrayExpress in MAGE-TAB format, which allows robust linking to data analysis and visualization tools, including Bioconductor and GenomeSpace. Additionally, R objects, for microarray data, and binary alignment format files, for sequencing data, have been generated for a significant proportion of ArrayExpress data.
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Oral cleft prevention program (OCPP).
BMC Pediatr
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Oral clefts are one of the most common birth defects with significant medical, psychosocial, and economic ramifications. Oral clefts have a complex etiology with genetic and environmental risk factors. There are suggestive results for decreased risks of cleft occurrence and recurrence with folic acid supplements taken at preconception and during pregnancy with a stronger evidence for higher than lower doses in preventing recurrence. Yet previous studies have suffered from considerable design limitations particularly non-randomization into treatment. There is also well-documented effectiveness for folic acid in preventing neural tube defect occurrence at 0.4 mg and recurrence with 4 mg. Given the substantial burden of clefting on the individual and the family and the supportive data for the effectiveness of folic acid supplementation as well as its low cost, a randomized clinical trial of the effectiveness of high versus low dose folic acid for prevention of cleft recurrence is warranted.
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Combination therapy for gonorrhoea: in vitro synergy testing.
J. Antimicrob. Chemother.
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Antimicrobial resistance in Neisseria gonorrhoeae is an increasing problem worldwide and combinations of antimicrobial agents have been recommended to delay the onset of treatment failures. The objective of this study was to obtain in vitro data on the activity of current (ceftriaxone or cefixime plus azithromycin) and alternative (gentamicin plus azithromycin) regimens.
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Analysis of genetic ancestry in the admixed Brazilian population from Rio de Janeiro using 46 autosomal ancestry-informative indel markers.
Ann. Hum. Biol.
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The Brazilian population is highly heterogeneous as a result of five centuries of inter-ethnic mating between native Amerindians, European colonizers and Africans arrived during slavery. This study aimed to assess the proportions of inter-ethnic admixture in the Brazilian population of Rio de Janeiro using autosomal Ancestry-Informative Markers (AIMs). The autosomal data were also compared to the results expected from uniparental genetic markers. A total of 413 individuals were genotyped for 46 AIM-Indels and ancestry estimates were then assessed using HGDP-CEPH samples as ancestral reference. Individuals from Rio de Janeiro presented highly diverse admixture patterns. The global admixture estimates showed a predominantly European ancestry, above 55%, followed by African and Amerindian contributions. A separate self-declared Afro-descendant group also included in this study revealed an increased African ancestry, from ?30% to ?50%. The inter-ethnic admixture landscape of Rio de Janeiro captured by autosomal AIM-Indels is in agreement with historical records and similar to that expected from uniparental mtDNA and Y-chromosome information. The AIM-Indel panel proved to be a rapid strategy to estimate autosomal genetic ancestry at individual and population levels in Rio de Janeiro, which is useful in population genetics and in case-control association studies.
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Circadian clock genes Bmal1 and Clock during early chick development.
Dev. Dyn.
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The circadian clock is a well-described temporal organizer in adult organisms. Despite the particularly evident need for temporal control during embryo development, the effect of environmental cues is still greatly neglected. Few studies have reported circadian clock gene expression in early embryonic stages. However, nothing is known about circadian clock gene expression and function in the first stages of avian embryogenesis.
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Assessing paternities with inconclusive STR results: The suitability of bi-allelic markers.
Forensic Sci Int Genet
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In paternity testing the genetic profiles of the individuals are used to compare the relative likelihoods of the alleged father and the child being related as father/offspring against, usually, being unrelated. In the great majority of the cases, analyses with the widely used sets of short tandem repeat markers (STRs) provide powerful statistical evidence favouring one of the alternative hypotheses. Nevertheless, there are situations where the final statistical result is ambiguous, mostly because the alleged father shows incompatible genotypes at a few loci along with a very high paternity index in the remaining systems. In these cases, the possibility that the alleged father is actually a close relative of the real one (son, father or brother) can reasonably be raised. In such cases, when the statistical evidence obtained is considered as insufficient, the common practice is to extend the set of analysed markers. In this context, many authors have suggested that bi-allelic markers, such as single nucleotide (SNP) or insertion/deletion (Indel) polymorphisms, are markers of choice, as they are incomparably less prone to mutation than STRs. In this work we address the soundness of this claim and the consequences of this strategy, analyzing the a priori odds both for (a) expected number of Mendelian incompatibilities, and (b) expected values for the final likelihood ratios. Moreover, one hundred real pairs of second degree relatives, typed for two sets of markers: 15 STRs plus 38 Indels, were used to simulate paternity testing. Our data show that, for the number of markers commonly considered, the results from an extended battery of SNPs or Indels should be interpreted with caution when relatives are possibly involved.
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Refining the genetic portrait of Portuguese Roma through X-chromosomal markers.
Am. J. Phys. Anthropol.
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Due to differences in transmission between X-chromosomal and autosomal DNA, the comparison of data derived from both markers allows deeper insight into the forces that shape the patterns of genetic diversity in populations. In this study, we applied this comparative approach to a sample of Portuguese Roma (Gypsies) by analyzing 43 X-chromosomal markers and 53 autosomal markers. Portuguese individuals of non-Gypsy ancestry were also studied. Compared with the host population, reduced levels of diversity on the X chromosome and autosomes were detected in Gypsies; this result was in line with known patterns of genetic diversity typical of Roma groups. As a consequence of the complex demographic past of the Roma, during which admixture and genetic drift played major roles, the amount of linkage disequilibrium (LD) on the X chromosome in Gypsies was considerably higher than that observed in non-Gypsies. When the pattern of differentiation on the X chromosome was compared with that of autosomes, there was evidence for asymmetries in female and male effective population sizes during the admixture between Roma and non-Roma. This result supplements previous data provided by mtDNA and the Y chromosome, underlining the importance of using combined information from the X chromosome and autosomes to dissect patterns of genetic diversity. Following the out-of-India dispersion, the Roma acquired a complex genetic pattern that was influenced by drift and introgression with surrounding populations, with important contributions from both males and females. We provide evidence that a sex-biased admixture with Europeans is probably associated with the founding of the Portuguese Gypsies.
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Structural, physical, and chemical modifications induced by microwave heating on native agar-like galactans.
J. Agric. Food Chem.
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Native agars from Gracilaria vermiculophylla produced in sustainable aquaculture systems (IMTA) were extracted under conventional (TWE) and microwave (MAE) heating. The optimal extracts from both processes were compared in terms of their properties. The agars structure was further investigated through Fourier transform infrared and NMR spectroscopy. Both samples showed a regular structure with an identical backbone, ?-d-galactose (G) and 3,6-anhydro-?-l-galactose (LA) units; a considerable degree of methylation was found at C6 of the G units and, to a lesser extent, at C2 of the LA residues. The methylation degree in the G units was lower for MAE(opt) agar; the sulfate content was also reduced. MAE led to higher agar recoveries with drastic extraction time and solvent volume reductions. Two times lower values of [?] and M(v) obtained for the MAE(opt) sample indicate substantial depolymerization of the polysaccharide backbone; this was reflected in its gelling properties; yet it was clearly appropriate for commercial application in soft-texture food products.
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What drives the precipitation of long-chain calcium carboxylates (soaps) in aqueous solution?
Phys Chem Chem Phys
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The interaction of sodium octanoate, decanoate or dodecanoate with calcium(ii) in aqueous solutions has been studied using turbidity, conductivity and potentiometric measurements. These show a marked alkyl chain length dependence on the behaviour. At the calcium concentration used (1.0 mM), there is little interaction with the octanoate, the decanoate shows initially formation of a 1:1 complex, followed by precipitation, while the dodecanoate precipitates at low surfactant concentrations. The solid calcium carboxylates were prepared, and show lamellar, bilayer structures with planes of calcium(II) ions coordinated to carboxylate groups through bidentate chelate linkages. Thermogravimetry and elemental analyses indicate the presence of coordinated water with the calcium decanoate but not with longer chain carboxylates. The results of both the solution and solid state studies suggest that precipitation of long-chain carboxylates depends on a balance between hydration effects and hydrophobic (largely van der Waals) interactions. Electrostatic effects make little energetic contribution but play the important structural role of ordering the carboxylate anions before precipitation. Differences are observed in the interactions between calcium(II) and long chain alkylcarboxylates and alkylsulfates, and are interpreted in terms of stronger binding to the metal of the carboxylate group. A general mechanism is proposed for calcium carboxylate precipitation from aqueous solution based on this and previous studies.
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The anti-ageing potential of a new jasmonic acid derivative (LR2412): in vitro evaluation using reconstructed epidermis Episkin™.
Exp. Dermatol.
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Jasmonic acid is involved in plant wound repair and tissue regeneration, but no study has been reported in human skin. The effect of a jasmonic acid derivative, tetra-hydro-jasmonic acid (LR2412, 1 and 10 ?m) was investigated on an in vitro reconstructed skin model, Episkin™. Using real time RTQPCR studies, results showed an increase in hyaluronan synthase 2 (HAS2) and hyaluronase synthase 3 (HAS3) expression. Furthermore, an increase in hyaluronic acid (HA) deposits in basal and suprabasal layers of the epidermis was observed. The percentage of positive Ki67 keratinocytes in the basal layer as well as the epidermis thickness were seen to increase. Immunohistochemistry studies showed that the synthesis of late differentiation proteins filaggrin and transglutaminase 1 was not modified. The human epidermis is known to thin with age while HA content has been reported to decrease. These results illustrate the potential of LR2412 in counteracting signs of skin ageing.
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Optimization approaches for the in silico discovery of optimal targets for gene over/underexpression.
J. Comput. Biol.
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Metabolic engineering (ME) efforts have been recently boosted by the increase in the number of annotated genomes and by the development of several genome-scale metabolic models for microbes of interest in industrial biotechnology. Based on these efforts, strain optimization methods have been proposed to reach the best set of genetic changes to apply to selected host microbes, in order to create strains that are able to overproduce metabolites of industrial interest. Previous work in strain optimization has been mostly based in finding sets of gene (or reaction) deletions that lead to desired phenotypes in computational simulations. In this work, we focus on enlarging the set of possible genetic changes, considering gene over and underexpression. A gene is considered under (over) expressed if its expression value is constrained to be significantly lower (higher) than the one in the wild-type strain, used as a reference. A method is proposed to propagate relative gene expression values to flux constraints over related reactions, making use of the available transcriptional/translational information. The algorithms chosen for the optimization tasks are metaheuristics such as Evolutionary Algorithms (EA) and Simulated Annealing (SA), based on previous successful work on gene knockout optimization. These methods were modified appropriately to accommodate the novel optimization tasks and were applied to study the optimization of succinic and lactic acid production using Escherichia coli as the host. The results are compared with previous ones obtained in gene knockout optimization, thus showing the usefulness of the approach. The methods proposed in this work were implemented in a novel plug-in for OptFlux, an open-source software framework for ME. Supplementary Material is available at www.liebertonline.com/cmb.
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Indel markers: genetic diversity of 38 polymorphisms in Brazilian populations and application in a paternity investigation with post mortem material.
Forensic Sci Int Genet
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Aiming to evaluate the usefulness of 38 non-coding bi-allelic autosomal indels in genetic identification and kinship testing, three Brazilian population samples were studied: two from Rio de Janeiro (including a sample of individuals with self-declared African ancestry) and one Native American population of Terena from Mato Grosso do Sul. Based on the observed allele frequencies, parameters of forensic relevance were calculated. The combined power of discrimination of the 38 indels was high in all studied groups (PD?0.9999999999997), although slightly lower in Native Americans. Genetic distance analysis showed significant differences between the allele frequencies in the Rio de Janeiro population and those previously reported for Europeans, Africans and Asians explained by its intermediate position between Europeans and Africans. As expected, the Terena sample was significantly different from all the other populations: Brazilians from Rio de Janeiro general population and with self-declared African ancestry, Europeans, Africans and East Asians. Finally, the performance of the 38-indel multiplex assay was tested in post-mortem material with positive results, supporting the use of short amplicon bi-allelic markers as an additional tool to STR analysis when DNA molecules are degraded.
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Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing.
PLoS ONE
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Ancestry-informative markers (AIMs) show high allele frequency divergence between different ancestral or geographically distant populations. These genetic markers are especially useful in inferring the likely ancestral origin of an individual or estimating the apportionment of ancestry components in admixed individuals or populations. The study of AIMs is of great interest in clinical genetics research, particularly to detect and correct for population substructure effects in case-control association studies, but also in population and forensic genetics studies. This work presents a set of 46 ancestry-informative insertion deletion polymorphisms selected to efficiently measure population admixture proportions of four different origins (African, European, East Asian and Native American). All markers are analyzed in short fragments (under 230 basepairs) through a single PCR followed by capillary electrophoresis (CE) allowing a very simple one tube PCR-to-CE approach. HGDP-CEPH diversity panel samples from the four groups, together with Oceanians, were genotyped to evaluate the efficiency of the assay in clustering populations from different continental origins and to establish reference databases. In addition, other populations from diverse geographic origins were tested using the HGDP-CEPH samples as reference data. The results revealed that the AIM-INDEL set developed is highly efficient at inferring the ancestry of individuals and provides good estimates of ancestry proportions at the population level. In conclusion, we have optimized the multiplexed genotyping of 46 AIM-INDELs in a simple and informative assay, enabling a more straightforward alternative to the commonly available AIM-SNP typing methods dependent on complex, multi-step protocols or implementation of large-scale genotyping technologies.
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Local strategies to address health needs of individuals with orofacial clefts in alagoas, Brazil.
Cleft Palate Craniofac. J.
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Objective : To describe demographic and clinical-genetic characteristics of patients from a poor area of Brazil and to share experience on how the local genetic unit has addressed their major health needs. Design : Descriptive cohort. Setting : A clinical-genetic unit, a cytogenetics unit, and a regional cleft team located in the northeast and southeast of Brazil. Participants : A total of 133 individuals with orofacial clefts who attended the surgical call of a nongovernmental organization. From this group, 125, 77, and 13 patients completed phases 1, 2, and 3, respectively. Methods : Phase 1 comprised a description of demographic characteristics recorded through interviews. Phase 2 included a clinical-genetic evaluation using a pretested form, as well as cytogenetic analyses of selected patients. Phase 3 comprised collaborative action to address major health needs of patients without primary surgery. The Fisher test was used for statistics with p value < .05. Results : A majority of patients were rural residents with isolated cleft lip with cleft palate. Ages ranged between 0 and 30 years. Fifty percent had never undergone surgery; whereas, 100% had never attended a genetic evaluation. Isolated cleft was diagnosed in 77.9%, syndromes in 14.3%, and multiple congenital abnormalities in 7.8%. Positive familial history of clefts occurred in 28%; whereas, parental consanguinity was present in 7.8% cases. A total of 23 individuals without cleft surgery were registered for multidisciplinary treatment. Conclusions : Findings revealed high levels of unmet medical needs and provided an evidence base for health care planning. Collaborative action was crucial and might be applied to other regions in Brazil.
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JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.