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Find video protocols related to scientific articles indexed in Pubmed.
Phase Instability and Molecular Kinetics Provoked by Repeated Crossing of the Demixing Transition of PNIPAM Solutions.
Langmuir
PUBLISHED: 09-26-2014
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The demixing process of aqueous poly(N-isopropylacrylamide) (PNIPAM) solutions can occur either via a nucleation and growth process or via spinodal decomposition. The ensuing self-assembly, leading to heterogeneous morphologies within the PNIPAM solution, is codetermined by kinetic processes caused by molecular transport. By subjecting PNIPAM solutions to cyclic changes in temperature leading to repeated crossing of the demixing transition, we are able to assess the importance of kinetics as well as of overheating and supercooling of the phase transition within the metastable range delimited by the binodal and spinodal lines. First indications about the location of these stability limits for the low- and high-temperature phases, separated by about 1.6 K, could be gained by detailed kinetic studies of the refractive index. These investigations are made possible due to the novel technique of temperature-modulated optical refractometry.
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The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers.
Bioinformatics
PUBLISHED: 09-04-2014
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Rapid technological advances have led to an explosion of biomedical data in recent years. The pace of change has inspired new collaborative approaches for sharing materials and resources to help train life scientists both in the use of cutting-edge bioinformatics tools and databases and in how to analyse and interpret large datasets. A prototype platform for sharing such training resources was recently created by the Bioinformatics Training Network (BTN). Building on this work, we have created a centralized portal for sharing training materials and courses, including a catalogue of trainers and course organizers, and an announcement service for training events. For course organizers, the portal provides opportunities to promote their training events; for trainers, the portal offers an environment for sharing materials, for gaining visibility for their work and promoting their skills; for trainees, it offers a convenient one-stop shop for finding suitable training resources and identifying relevant training events and activities locally and worldwide. Availability and implementation: http://mygoblet.org/training-portal CONTACT: manuel.corpas@tgac.ac.uk.
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Recombination between clonal lineages of the asexual fungus Verticillium dahliae detected by genotyping by sequencing.
PLoS ONE
PUBLISHED: 09-02-2014
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Most asexual species of fungi have either lost sexuality recently, or they experience recombination by cryptic sexual reproduction. Verticillium dahliae is a plant-pathogenic, ascomycete fungus with no known sexual stage, even though related genera have well-described sexual reproduction. V. dahliae reproduces mitotically and its population structure is highly clonal. However, previously described discrepancies in phylogenetic relationships among clonal lineages may be explained more parsimoniously by recombination than mutation; therefore, we looked for evidence of recombination within and between clonal lineages. Genotyping by sequencing was performed on 141 V. dahliae isolates from diverse geographic and host origins, resulting in 26,748 single-nucleotide polymorphisms (SNPs). We found a strongly clonal population structure with the same lineages as described previously by vegetative compatibility groups (VCGs) and molecular markers. We detected 443 recombination events, evenly distributed throughout the genome. Most recombination events detected were between clonal lineages, with relatively few recombinant haplotypes detected within lineages. The only three isolates with mating type MAT1-1 had recombinant SNP haplotypes; all other isolates had mating type MAT1-2. We found homologs of eight meiosis-specific genes in the V. dahliae genome, all with conserved or partially conserved protein domains. The extent of recombination and molecular signs of sex in (mating-type and meiosis-specific genes) suggest that V. dahliae clonal lineages arose by recombination, even though the current population structure is markedly clonal. Moreover, the detection of new lineages may be evidence that sexual reproduction has occurred recently and may potentially occur under some circumstances. We speculate that the current clonal population structure, despite the sexual origin of lineages, has arisen, in part, as a consequence of agriculture and selection for adaptation to agricultural cropping systems.
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Lateral lipid organization of the bovine milk fat globule membrane is revealed by washing processes.
J. Dairy Sci.
PUBLISHED: 08-06-2014
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Evidence for the asymmetric distribution of phospholipids in the milk fat globule membrane (MFGM) was obtained by applying 3 washing processes using aqueous solutions with different degrees of stringency (mild, intermediate, and intensive) to milk fat globule (MFG) surfaces in simulated milk ultrafiltrate buffer. We detected no change in the amount of cholesterol after the mild washing process; however, intensive washing yielded a relative enrichment of surface cholesterol with concomitant damage to the outer bilayer of the MFGM. This finding supports the hypothesis of repartitioning of cholesterol on MFG surfaces during mechanical treatments. An updated model system of lipid organization was developed according to the results of relative depletion of individual phospholipids, as analyzed by HPLC.
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Two-level systems and boson peak remain stable in 110-million-year-old amber glass.
Phys. Rev. Lett.
PUBLISHED: 04-22-2014
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The two most prominent and ubiquitous features of glasses at low temperatures, namely the presence of tunneling two-level systems and the so-called boson peak in the reduced vibrational density of states, are shown to persist essentially unchanged in highly stabilized glasses, contrary to what was usually envisaged. Specifically, we have measured the specific heat of 110 million-year-old amber samples from El Soplao (Spain), both at very low temperatures and around the glass transition Tg. In particular, the amount of two-level systems, assessed at the lowest temperatures, was surprisingly found to be exactly the same for the pristine hyperaged amber as for the, subsequently, partially and fully rejuvenated samples.
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Transient expression of Bcl6 is sufficient for oncogenic function and induction of mature B-cell lymphoma.
Nat Commun
PUBLISHED: 04-15-2014
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Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoma and can be separated into two subtypes based upon molecular features with similarities to germinal centre B-cells (GCB-like) or activated B-cells (ABC-like). Here we identify gain of 3q27.2 as being significantly associated with adverse outcome in DLBCL and linked with the ABC-like subtype. This lesion includes the BCL6 oncogene, but does not alter BCL6 transcript levels or target-gene repression. Separately, we identify expression of BCL6 in a subset of human haematopoietic stem/progenitor cells (HSPCs). We therefore hypothesize that BCL6 may act by 'hit-and-run' oncogenesis. We model this hit-and-run mechanism by transiently expressing Bcl6 within murine HSPCs, and find that it causes mature B-cell lymphomas that lack Bcl6 expression and target-gene repression, are transcriptionally similar to post-GCB cells, and show epigenetic changes that are conserved from HSPCs to mature B-cells. Together, these results suggest that BCL6 may function in a 'hit-and-run' role in lymphomagenesis.
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Surgical treatment of borderline and malignant phyllodes tumors: the effect of the extent of resection and tumor characteristics on patient outcome.
Ann. Surg. Oncol.
PUBLISHED: 04-14-2014
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Malignant phyllodes tumors are rare fibroepithelial breast neoplasms. Appropriate surgical management remains a subject of debate. The purpose of our study was to define optimal surgical treatment and to identify factors associated with outcome.
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The role of albuminuria in the follow-up of HIV-infected pediatric patients.
Pediatr. Nephrol.
PUBLISHED: 03-20-2014
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In HIV-infected adults, elevated albumin has been associated with increased inflammatory activity, HIV-related nephropathy, and type 2 diabetes. Data on albuminuria in HIV-infected children are very scarce, and guidelines do not include routine determination of urinary albumin/creatinine ratio in this population.
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Phospholipid Architecture of the Bovine Milk Fat Globule Membrane Using Giant Unilamellar Vesicles as a Model.
J. Agric. Food Chem.
PUBLISHED: 03-20-2014
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Giant unilamellar vesicles (GUVs) were constructed using an electroformation technique to mimic the morphology of the native milk fat globule membrane (MFGM) for the purpose of structural investigation. Bovine milk derived phospholipids were selected to manufacture GUVs which were characterized by confocal laser scanning microscopy after fluorescent staining. Circular nonfluorescent dark regions were observed in a 3/7 (mol/mol) surface mixture of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-dioleoyl-sn-glycero-3 phosphoethanolamine. Linear shaped dark lipid domains were found in GUVs containing sphingomyelin (SM) in the absence of cholesterol. The dark regions were interpreted as a gel phase formed by a high gel-liquid phase transition temperature (Tm) of DPPC and SM. This study provides a strategy for investigating the lipid structural organization within the native MFGM using a model lipid bilayer system and reveals that a SM and cholesterol association network is not the only requirement for nonfluorescent lipid domain formation and that PE is preferably located in the inner leaflet of the phospholipid bilayer.
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The testis of greater white-toothed shrew Crocidura russula in Southern European populations: a case of adaptive lack of seasonal involution?
J. Exp. Zool. B Mol. Dev. Evol.
PUBLISHED: 03-14-2014
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Males of all seasonal breeding mammals undergo circannual periods of testis involution resulting in almost complete ablation of the germinative epithelium. We performed a morphometric, histological, hormonal, and gene-expression study of the testes from winter and summer males of the greater white-toothed shrew, Crocidura russula, in populations of the southeastern Iberian Peninsula. Unexpectedly, we found no significant differences between the two study groups. Surprisingly, female data confirmed a non-breeding period in the summer, evidencing that males retain full testis function even when most females are not receptive. This situation, which has not been described before, does not occur in northern populations of the same species where, in addition, the reproductive cycle is inverted with respect to those in the south, as the non-breeding period occurs in winter instead in summer. Considering that the non-reproductive period shortens at lower latitude locations, we hypothesize that in southern populations the non-breeding period is short enough to make testis regression inefficient in terms of energy savings, because: (1) testes of C. russula are very small, a condition derived from their monogamy that implies low investment in spermatogenesis; and (2) the spermatogenic cycle of this species is slow and long. The inverted seasonal breeding cycle and the lack of seasonal testis regression described here are new adaptive processes that deserve further research, and provide evidence that the genetic and hormonal mechanisms controlling reproduction timing in mammals are more plastic and versatile than initially suspected.
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Impact of the timestep in some molecular dynamics simulations on compression of granular systems.
Eur Phys J E Soft Matter
PUBLISHED: 02-20-2014
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We conduct two-dimensional molecular dynamics simulations to study the statistical distribution of the force-moment (defined as stress multiplied by volume) of static granular packings under external isotropic compression. To that end, we generate packings by compressing initially ordered lattices using irregular, randomly generated, walls. Velocity-Verlet algorithm and linear spring-dashpot interactions are employed. With this specific method, the obtained statistical distributions of the force-moment are similar for different initial packings. However they depend on the timestep selection within a range of values. This shows that inadequate molecular dynamic simulations may provide different classes of solutions for the same physical process, and this could cause problems to validate theoretical approaches based on statistical mechanics.
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Comparative analysis of minimally invasive thymectomy versus open resection for early-stage thymoma.
Cir Esp
PUBLISHED: 02-05-2014
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Video-assisted thoracic surgery (VATS) has significantly developed over the last decade. However, a VATS approach for thymoma remains controversial. We present a study to evaluate the feasibility of VATS thymectomy for the treatment of early-stage thymoma and to compare the outcomes with open resection.
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Adsorption of bile salts to milk phospholipid and phospholipid-protein monolayers.
J. Agric. Food Chem.
PUBLISHED: 01-29-2014
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The adsorption of bile salts to milk phospholipid and phospholipid-protein monolayers at the air-water interface was studied under simulated intestinal conditions using a Langmuir trough, epifluorescence microscopy, and atomic force microscopy. Surface pressure changes were affected by temperature, initial surface pressure, and bile composition. The rate of addition of bile salts and the initial surface pressure of the monolayers had an impact on the microstructure of the mixed monolayers. The presence of proteins in monolayers at different ratios did not affect the surface pressure change upon addition of bile. However, at 20 °C, the addition of bile to phospholipid and phospholipid-protein monolayers led to different features with branching and clustering of liquid-ordered domains and possible formation of bile salt-rich areas within liquid-ordered domains. This study provides a basic understanding of the interfacial changes occurring at the surface of milk fat globules and milk phospholipid liposomes during their passage in the duodenum.
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Supercritical fluid extraction provides an enhancement to the immune response for orally-delivered hepatitis B surface antigen.
Vaccine
PUBLISHED: 01-14-2014
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The hepatitis B virus continues to be a major pathogen worldwide despite the availability of an effective parenteral vaccine for over 20 years. Orally-delivered subunit vaccines produced in maize may help to alleviate the disease burden by providing a low-cost, heat-stable alternative to the parenteral vaccine. Oral subunit vaccination has been an elusive goal due to the large amounts of antigen required to induce an immunologic response when administered through the digestive tract. Here we show that high levels of HBsAg were obtained in maize grain, the grain was formed into edible wafers, and wafers were fed to mice at a concentration of approximately 300 ?g/g. When these wafers were made with supercritical fluid extraction (SFE)-treated maize material, robust IgG and IgA responses in sera were observed that were comparable to the injected commercial vaccine (Recombivax(®)). In addition, all mice administered SFE wafers showed high secretory IgA titers in fecal material whereas Recombivax(®) treated mice showed no detectable titer. Increased salivary IgA titers were also detected in SFE-fed mice but not in Recombivax(®) treated mice. Wafers made from hexane-treated or full fat maize material induced immunologic responses, but fecal titers were attenuated relative to those produced by SFE-treated wafers. These responses demonstrate the feasibility of using a two-dose oral vaccine booster in the absence of an adjuvant to induce immunologic responses in both sera and at mucosal surfaces, and highlight the potential limitations of using an exclusively parenteral dosing regime.
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BioJS: an open source standard for biological visualisation - its status in 2014.
F1000Res
PUBLISHED: 01-01-2014
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BioJS is a community-based standard and repository of functional components to represent biological information on the web. The development of BioJS has been prompted by the growing need for bioinformatics visualisation tools to be easily shared, reused and discovered. Its modular architecture makes it easy for users to find a specific functionality without needing to know how it has been built, while components can be extended or created for implementing new functionality. The BioJS community of developers currently provides a range of functionality that is open access and freely available. A registry has been set up that categorises and provides installation instructions and testing facilities at http://www.ebi.ac.uk/tools/biojs/. The source code for all components is available for ready use at https://github.com/biojs/biojs.
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Sequence, a BioJS component for visualising sequences.
F1000Res
PUBLISHED: 01-01-2014
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Sequences are probably the most common piece of information in sites providing biological data resources, particularly those related to genes and proteins. Multiple visual representations of the same sequence can be found across those sites. This can lead to an inconsistency compromising both the user experience and usability while working with graphical representations of a sequence. Furthermore, the code of the visualisation module is commonly embedded and merged with the rest of the application, making it difficult to reuse it in other applications. In this paper, we present a BioJS component for visualising sequences with a set of options supporting a flexible configuration of the visual representation, such as formats, colours, annotations, and columns, among others. This component aims to facilitate a common representation across different sites, making it easier for end users to move from one site to another.
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PsicquicGraph, a BioJS component to visualize molecular interactions from PSICQUIC servers.
F1000Res
PUBLISHED: 01-01-2014
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Protein interaction networks have become an essential tool in large-scale data analysis, integration, and the visualization of high-throughput data in the context of complex cellular networks. Many individual databases are available that provide information on binary interactions of proteins and small molecules. Community efforts such as PSICQUIC aim to unify and standardize information emanating from these public databases. Here we introduce PsicquicGraph, an open-source, web-based visualization component for molecular interactions from PSIQUIC services.
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KEGGViewer, a BioJS component to visualize KEGG Pathways.
F1000Res
PUBLISHED: 01-01-2014
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Signaling pathways provide essential information on complex regulatory processes within the cell. They are moreover widely used to interpret and integrate data from large-scale studies, such as expression or functional screens. We present KEGGViewer a BioJS component to visualize KEGG pathways and to allow their visual integration with functional data.
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The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.
Nucleic Acids Res.
PUBLISHED: 11-13-2013
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IntAct (freely available at http://www.ebi.ac.uk/intact) is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. IntAct has developed a sophisticated web-based curation tool, capable of supporting both IMEx- and MIMIx-level curation. This tool is now utilized by multiple additional curation teams, all of whom annotate data directly into the IntAct database. Members of the IntAct team supply appropriate levels of training, perform quality control on entries and take responsibility for long-term data maintenance. Recently, the MINT and IntAct databases decided to merge their separate efforts to make optimal use of limited developer resources and maximize the curation output. All data manually curated by the MINT curators have been moved into the IntAct database at EMBL-EBI and are merged with the existing IntAct dataset. Both IntAct and MINT are active contributors to the IMEx consortium (http://www.imexconsortium.org).
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Gallium induces the production of virulence factors in Pseudomonas aeruginosa.
Pathog Dis
PUBLISHED: 08-27-2013
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The novel antimicrobial gallium is a nonredox iron III analogue with bacteriostatic and bactericidal properties, effective for the treatment of Pseudomonas aeruginosa in vitro and in vivo in mouse and rabbit infection models. It interferes with iron metabolism, transport, and presumably its homeostasis. As gallium exerts its antimicrobial effects by competing with iron, we hypothesized that it ultimately will lead cells to an iron deficiency status. As iron deficiency promotes the expression of virulence factors in vitro and promotes the pathogenicity of P. aeruginosa in animal models, it is anticipated that treatment with gallium will also promote the production of virulence factors. To test this hypothesis, the reference strain PA14 and two clinical isolates from patients with cystic fibrosis were exposed to gallium, and their production of pyocyanin, rhamnolipids, elastase, alkaline protease, alginate, pyoverdine, and biofilm was determined. Gallium treatment induced the production of all the virulence factors tested in the three strains except for pyoverdine. In addition, as the Ga-induced virulence factors are quorum sensing controlled, co-administration of Ga and the quorum quencher brominated furanone C-30 was assayed, and it was found that C-30 alleviated growth inhibition from gallium. Hence, adding both C-30 and gallium may be more effective in the treatment of P. aeruginosa infections.
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Bovine milk fat globule membrane proteins are affected by centrifugal washing processes.
J. Agric. Food Chem.
PUBLISHED: 08-23-2013
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The impact of washing on the release of proteins from the milk fat globule membrane (MFGM) was examined by applying washing procedures with different degrees of stringency to milk fat globule (MFG) surfaces in simulated milk ultrafiltrate buffer solution. Three washing methods, M1 (3000g, 5 min, three washes), M2 (3750g, 15 min, one wash), and M3 (15000g, 20 min, three washes) were chosen. MFG ?-potential increased after M3 washing (P < 0.05), suggesting surface damage. For M1, in which the native MFG surface was least damaged, cluster of differentiation 36 (CD 36) and periodic acid schiff 6/7 proteins were more strongly bound to the MFGM compared with other major membrane proteins. For M3, CD 36 together with fatty acid-binding protein was more strongly bound to the MFGM. Washing by centrifugation and redispersal of the fat globules damaged the MFGM, with release into the aqueous phase of some membrane-associated proteins. The current results show the impact of washing processes on retention of functional MFGM proteins.
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Integration of cardiac proteome biology and medicine by a specialized knowledgebase.
Circ. Res.
PUBLISHED: 08-21-2013
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Omics sciences enable a systems-level perspective in characterizing cardiovascular biology. Integration of diverse proteomics data via a computational strategy will catalyze the assembly of contextualized knowledge, foster discoveries through multidisciplinary investigations, and minimize unnecessary redundancy in research efforts.
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Plasma triglyceride/HDL-cholesterol ratio, insulin resistance, and cardiometabolic risk in young adults.
J. Lipid Res.
PUBLISHED: 07-17-2013
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Studies in mature adults suggest that the plasma concentration ratio of triglyceride (TG)/HDL-cholesterol (HDL-C) provides a simple way to identify apparently healthy individuals who are insulin resistant (IR) and at increased cardiometabolic risk. This study extends these observations by examining the clinical utility of the TG/HDL-C ratio and the metabolic syndrome (MetS) in 2,244 healthy college students (17-24 years old) of Mexican Mestizo ancestry. The TG/HDL-C ratio separating the 25% with the highest value was used to identify IR and increased cardiometabolic risk. Cardiometabolic risk factors were more adverse in men and women whose TG/HDL-C ratios exceeded 3.5 and 2.5, respectively, and approximately one third were identified as being IR. The MetS identified fewer individuals as being IR, but their risk profile was accentuated. In conclusion, both a higher TG/HDL-C ratio and a diagnosis of the MetS identify young IR individuals with an increased cardiometabolic risk profile. The TG/HDL-C ratio identified a somewhat greater number of "high risk" subjects, whereas the MetS found a group whose risk profile was somewhat magnified. These findings suggest that the TG/HDL-C ratio may serve as a simple and clinically useful approach to identify apparently healthy, young individuals who are IR and at increased cardiometabolic risk.
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Low-temperature thermal properties of a hyperaged geological glass.
J Phys Condens Matter
PUBLISHED: 07-02-2013
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We have measured the specific heat of amber from the Dominican Republic, an ancient geological glass about 20 million years old, in the low-temperature range 0.6 K ? T ? 26 K, in order to assess the effects of its natural stabilization (hyperageing) process on the low-temperature glassy properties, i.e. boson peak and two-level systems. We have also conducted modulated differential scanning calorimetry experiments to characterize the thermodynamic state of our samples. We found that calorimetric curves exhibit a huge ageing signal ?H ? 5 J g(-1) in the first upscan at the glass transition Tg = 389 K, that completely disappears after heating up (rejuvenating) the sample to T = 395 K for 3 h. To independently evaluate the phonon contribution to the specific heat, Brillouin spectroscopy was performed in the temperature range 80 K ? T ? 300 K. An expected increase in the Debye level was observed after rejuvenating the Dominican amber. However, no significant change was observed in the low-temperature specific heat of glassy amber after erasing its thermal history: both its boson peak (i.e., the maximum in the Cp/T(3) representation) and the density of tunnelling two-level systems (i.e., the Cp ? T contribution at the lowest temperatures) remained essentially the same. Also, a consistent analysis using the soft-potential model of our Cp data and earlier thermal-conductivity data found in the literature further supports our main conclusion, namely, that these glassy anomalous properties at low temperatures remain essentially invariant after strong relaxational processes such as hyperageing.
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Best practices in bioinformatics training for life scientists.
Brief. Bioinformatics
PUBLISHED: 06-25-2013
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The mountains of data thrusting from the new landscape of modern high-throughput biology are irrevocably changing biomedical research and creating a near-insatiable demand for training in data management and manipulation and data mining and analysis. Among life scientists, from clinicians to environmental researchers, a common theme is the need not just to use, and gain familiarity with, bioinformatics tools and resources but also to understand their underlying fundamental theoretical and practical concepts. Providing bioinformatics training to empower life scientists to handle and analyse their data efficiently, and progress their research, is a challenge across the globe. Delivering good training goes beyond traditional lectures and resource-centric demos, using interactivity, problem-solving exercises and cooperative learning to substantially enhance training quality and learning outcomes. In this context, this article discusses various pragmatic criteria for identifying training needs and learning objectives, for selecting suitable trainees and trainers, for developing and maintaining training skills and evaluating training quality. Adherence to these criteria may help not only to guide course organizers and trainers on the path towards bioinformatics training excellence but, importantly, also to improve the training experience for life scientists.
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iAnn: an event sharing platform for the life sciences.
Bioinformatics
PUBLISHED: 06-05-2013
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We present iAnn, an open source community-driven platform for dissemination of life science events, such as courses, conferences and workshops. iAnn allows automatic visualisation and integration of customised event reports. A central repository lies at the core of the platform: curators add submitted events, and these are subsequently accessed via web services. Thus, once an iAnn widget is incorporated into a website, it permanently shows timely relevant information as if it were native to the remote site. At the same time, announcements submitted to the repository are automatically disseminated to all portals that query the system. To facilitate the visualization of announcements, iAnn provides powerful filtering options and views, integrated in Google Maps and Google Calendar. All iAnn widgets are freely available.
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Bioinformatics workflows and web services in systems biology made easy for experimentalists.
Methods Mol. Biol.
PUBLISHED: 05-30-2013
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Workflows are useful to perform data analysis and integration in systems biology. Workflow management systems can help users create workflows without any previous knowledge in programming and web services. However the computational skills required to build such workflows are usually above the level most biological experimentalists are comfortable with. In this chapter we introduce workflow management systems that reuse existing workflows instead of creating them, making it easier for experimentalists to perform computational tasks.
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Use of an Intraoperative Ultrasonography-Guided Localization and Tissue Fixation Device Demonstrates Less Margin Positivity During Breast-Conserving Surgery for Invasive Breast Cancer Than Standard Preoperative Needle-Wire Localization: A Retrospective Co
Clin. Breast Cancer
PUBLISHED: 05-26-2013
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To retrospectively compare 2 methods of pre-resection, image-guided tumor localization-preoperative needle-wire localization (PNWL) and intraoperative ultrasonography-guided localization and tissue fixation (IUGLTF)-for patients with invasive breast cancer at the time of breast-conserving surgery (BCS).
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Long-Term Cost-Effectiveness Analysis of Etanercept and Adalimumab for Plaque Psoriasis not Associated with Arthritis.
Dermatol Ther (Heidelb)
PUBLISHED: 05-17-2013
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Pharmacoeconomic studies examining the cost-effectiveness of biological agents to treat moderate-to-severe psoriasis in real-life clinical practice are scarce. The aim of this study was to assess the efficiency, in terms of incremental cost-effectiveness, of etanercept and adalimumab in a real clinical setting.
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Proteomics data exchange and storage: the need for common standards and public repositories.
Methods Mol. Biol.
PUBLISHED: 05-14-2013
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Both the existence of data standards and public databases or repositories have been key factors behind the development of the existing "omics" approaches. In this book chapter we first review the main existing mass spectrometry (MS)-based proteomics resources: PRIDE, PeptideAtlas, GPMDB, and Tranche. Second, we report on the current status of the different proteomics data standards developed by the Proteomics Standards Initiative (PSI): the formats mzML, mzIdentML, mzQuantML, TraML, and PSI-MI XML are then reviewed. Finally, we present an easy way to query and access MS proteomics data in the PRIDE database, as a representative of the existing repositories, using the workflow management system (WMS) tool Taverna. Two different publicly available workflows are explained and described.
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A new reference implementation of the PSICQUIC web service.
Nucleic Acids Res.
PUBLISHED: 05-13-2013
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The Proteomics Standard Initiative Common QUery InterfaCe (PSICQUIC) specification was created by the Human Proteome Organization Proteomics Standards Initiative (HUPO-PSI) to enable computational access to molecular-interaction data resources by means of a standard Web Service and query language. Currently providing >150 million binary interaction evidences from 28 servers globally, the PSICQUIC interface allows the concurrent search of multiple molecular-interaction information resources using a single query. Here, we present an extension of the PSICQUIC specification (version 1.3), which has been released to be compliant with the enhanced standards in molecular interactions. The new release also includes a new reference implementation of the PSICQUIC server available to the data providers. It offers augmented web service capabilities and improves the user experience. PSICQUIC has been running for almost 5 years, with a user base growing from only 4 data providers to 28 (April 2013) allowing access to 151 310 109 binary interactions. The power of this web service is shown in PSICQUIC View web application, an example of how to simultaneously query, browse and download results from the different PSICQUIC servers. This application is free and open to all users with no login requirement (http://www.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml).
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An Lrp-type transcriptional regulator controls expression of the Bacillus subtilis chromate transporter.
Antonie Van Leeuwenhoek
PUBLISHED: 04-25-2013
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The Bacillus subtilis strain 168 genome contains the chr3N-chr3C genes encoding the Chr3N/Chr3C protein pair of the chromate ion transporter (CHR) superfamily. Chr3N/Chr3C confers chromate resistance in Escherichia coli only when both proteins are expressed. Upstream of chr3N is the chrS gene encoding ChrS, a protein with homology to the Lrp/AsnC family of transcriptional regulators. When the chrS-chr3N-chr3C gene cluster was transferred to E. coli, a diminished level of chromate resistance was observed, as compared with E. coli transformants bearing only the chromate resistance genes, which displayed full resistance. These data suggested that the chrS gene product acts as negative regulator. RT-PCR assays demonstrated that expression of chrS diminishes transcription of the chromate resistance genes in E. coli, and that this repression was overcome by chromate. Electrophoretic mobility shift assays showed that purified ChrS protein specifically binds to the 5 region of chrS. These results indicate that the chr gene cluster forms an operon regulated negatively by ChrS binding to its own genes regulatory region, and positively by chromate ions. Sequence analysis revealed similar operons in many Bacillales strains, suggesting some adaptive advantage. This is the first example of a bacterial heavy-metal resistance system controlled by an Lrp-type transcriptional regulator.
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Increased concentrations of soluble CD40 ligand platelet in patients with primary antiphospholipidic syndrome.
Reumatol Clin
PUBLISHED: 03-01-2013
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To determine the concentrations of sCD40L in patients with PAPS, and establish its association with the number of thrombosis.
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BioJS: an open source JavaScript framework for biological data visualization.
Bioinformatics
PUBLISHED: 02-23-2013
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BioJS is an open-source project whose main objective is the visualization of biological data in JavaScript. BioJS provides an easy-to-use consistent framework for bioinformatics application programmers. It follows a community-driven standard specification that includes a collection of components purposely designed to require a very simple configuration and installation. In addition to the programming framework, BioJS provides a centralized repository of components available for reutilization by the bioinformatics community. Availability and implementation: http://code.google.com/p/biojs/.
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Experience and Development of the Video-Assisted Thoracic Surgery Lobectomy Technique: Comparative Study With Conventional Surgery in StageI Non-Small Cell Lung Cancer.
Arch. Bronconeumol.
PUBLISHED: 02-10-2013
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Surgical treatment of stageI non-small cell lung cancer (NSCLC) can be performed either by thoracotomy or by employing video-assisted thoracic surgery (VATS). The aim of this study was to compare long and short-term results of conventional surgery (CS) vs. VATS lobectomy in the treatment of stageI NSCLC.
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The different morphologies of urachal adenocarcinoma do not discriminate genomically by micro-RNA expression profiling.
Hum. Pathol.
PUBLISHED: 01-07-2013
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Urachal adenocarcinoma has several morphologic presentations that include mucinous, enteric, signet ring cell, and not otherwise specified. Mixtures of these morphologies can occur, and percentage cut-offs are used for classification. The clinical significance of these morphologic types is currently unknown, and genetic analysis that could elucidate possible intertumoral differences has not been performed. In this study, we analyzed the micro-RNA expression profiles of 12 urachal adenocarcinomas classified using strict morphologic criteria (3 pure enteric, 3 pure mucinous, 2 signet ring cell [both 90% signet ring cell], 2 pure not otherwise specified, and 2 mixed cell types). Of 598 unique human micro-RNAs, 333 were expressed in more than 50% of the samples. Hierarchal clustering showed no distinct patterns in the genetic profiles of the morphologic types. However, there were individual micro-RNA differences when the different types were compared individually or grouped together, either by intracellular mucin production or by grouping enteric and signet ring cell together. In the later group, 13 messenger RNA species were differentially expressed (adjusted P value of ?.05). However, these micro-RNA differences were small, suggesting more biologic similarity than differences among these entities. Thus, this study suggests that the different morphological subtypes may represent patterns of differentiation or a continuum of a single biological tumor type rather than several distinct types that arose from the urachal remnant epithelium. This finding, if further validated in larger studies, may have implications in future clinical therapeutic trials for urachal adenocarcinoma with regard to patient grouping and choice of therapy.
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A microRNA (mmu-miR-124) prevents Sox9 expression in developing mouse ovarian cells.
Biol. Reprod.
PUBLISHED: 01-01-2013
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In mammals, sex differentiation depends on gonad development, which is controlled by two groups of sex-determining genes that promote one gonadal sex and antagonize the opposite one. SOX9 plays a key role during testis development in all studied vertebrates, whereas it is kept inactive in the XX gonad at the critical time of sex determination, otherwise, ovary-to-testis gonadal sex reversal occurs. However, molecular mechanisms underlying repression of Sox9 at the beginning of ovarian development, as well as other important aspects of gonad organogenesis, remain largely unknown. Because there is indirect evidence that micro-RNAs (miRNA) are necessary for testicular function, the possible involvement of miRNAs in mammalian sex determination deserved further research. Using microarray technology, we have identified 22 miRNAs showing sex-specific expression in the developing gonads during the critical period of sex determination. Bioinformatics analyses led to the identification of miR-124 as the candidate gene for ovarian development. We knocked down or overexpressed miR-124 in primary gonadal cell cultures and observed that miR-124 is sufficient to induce the repression of both SOX9 translation and transcription in ovarian cells. Our results provide the first evidence of the involvement of a miRNA in the regulation of the gene controlling gonad development and sex determination. The miRNA microarray data reported here will help promote further research in this field, to unravel the role of other miRNAs in the genetic control of mammalian sex determination.
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Microbial communities in pre-columbian coprolites.
PLoS ONE
PUBLISHED: 01-01-2013
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The study of coprolites from earlier cultures represents a great opportunity to study an "unaltered" composition of the intestinal microbiota. To test this, pre-Columbian coprolites from two cultures, the Huecoid and Saladoid, were evaluated for the presence of DNA, proteins and lipids by cytochemical staining, human and/or dog-specific Bacteroides spp. by PCR, as well as bacteria, fungi and archaea using Terminal Restriction Fragment analyses. DNA, proteins and lipids, and human-specific Bacteroides DNA were detected in all coprolites. Multidimensional scaling analyses resulted in spatial arrangements of microbial profiles by culture, further supported by cluster analysis and ANOSIM. Differences between the microbial communities were positively correlated with culture, and SIMPER analysis indicated 68.8% dissimilarity between the Huecoid and Saladoid. Proteobacteria, Bacteroidetes and methanogens were found in all coprolite samples. Propionebacteria, Shewanella and lactic acid bacteria dominated in the Huecoid samples, while Acidobacteria, and peptococci were dominant in Saladoid samples. Yeasts, including Candida albicans and Crypotococcus spp. were found in all samples. Basidiomycetes were the most notable fungi in Huecoid samples while Ascomycetes predominated in Saladoid samples, suggesting differences in dietary habits. Our study provides an approach for the study of the microbial communities of coprolite samples from various cultures.
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Quantitative and microscopic assessment of compatible and incompatible interactions between chickpea cultivars and Fusarium oxysporum f. sp. ciceris races.
PLoS ONE
PUBLISHED: 01-01-2013
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Fusarium wilt caused by Fusarium oxysporum f. sp. ciceris, a main threat to global chickpea production, is managed mainly by resistant cultivars whose efficiency is curtailed by Fusarium oxysporum f. sp. ciceris races.
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Identification of live germ-cell desquamation as a major mechanism of seasonal testis regression in mammals: a study in the Iberian mole (Talpa occidentalis).
Biol. Reprod.
PUBLISHED: 01-01-2013
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In males of seasonally breeding species, testes undergo a severe involution at the end of the breeding season, with a major volume decrease due to massive germ-cell depletion associated with photoperiod-dependent reduced levels of testosterone and gonadotropins. Although it has been repeatedly suggested that apoptosis is the principal effector of testicular regression in vertebrates, recent studies do not support this hypothesis in some mammals. The purpose of our work is to discover alternative mechanisms of testis regression in these species. In this paper, we have performed a morphological, hormonal, ultrastructural, molecular, and functional study of the mechanism of testicular regression and the role that cell junctions play in the cell-content dynamics of the testis of the Iberian mole, Talpa occidentalis, throughout the seasonal breeding cycle. Desquamation of live, nonapoptotic germ cells has been identified here as a new mechanism for seasonal testis involution in mammals, indicating that testis regression is regulated by modulating the expression and distribution of the cell-adhesion molecules in the seminiferous epithelium. During this process, which is mediated by low intratesticular testosterone levels, Sertoli cells lose their nursing and supporting function, as well as the impermeability of the blood-testis barrier. Our results contradict the current paradigm that apoptosis is the major testis regression effector in vertebrates, as it is clearly not true in all mammals. The new testis regression mechanism described here for the mole could then be generalized to other mammalian species. Available data from some previously studied mammals should be reevaluated.
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Anthropogenic contamination of metals in sediments of the Santa Rosalía harbor, Baja California peninsula.
Bull Environ Contam Toxicol
PUBLISHED: 01-01-2013
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To know the environment impact on a harbor of the Santa Rosalía port on the Baja California peninsula, the concentrations of metals (Cd, Co, Cu, Mn, Pb, U and Zn) in harbor sediments were determined for 13 stations and compared with their average upper Earth´s crust abundance. The mean enrichment factors, calculated using Al as a normalizer, were higher than the unity for Ag, Ba, Bi, Cd, Co, Cu, Mn, Ni, Pb, Sb, U, V and Zn. Concentrations of slightly enriched Cd in the sediments are below the effect range low (ERL) sediment quality guidelines value only at three stations. The levels of Pb in the harbor sediments at four stations (1, 6, 9 and 11) are between the ERL (46.7 mg kg(-1)) and the effect range medium (ERM) (218 mg kg(-1)), and Pb content in the rest of the sediment samples is higher than the ERM, demonstrating the high extent of the anthropogenic impact of this metal on the sedimentary environment. The total concentrations of the potentially toxic elements Cu (3,390 ± 804 mg kg(-1)) and Zn (1,916 ± 749 mg kg(-1)) very strongly exceed their ERM, showing a high possibility of toxicological danger for marine biota, living inside or entering the harbor.
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The IntAct molecular interaction database in 2012.
Nucleic Acids Res.
PUBLISHED: 11-24-2011
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IntAct is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. Two levels of curation are now available within the database, with both IMEx-level annotation and less detailed MIMIx-compatible entries currently supported. As from September 2011, IntAct contains approximately 275,000 curated binary interaction evidences from over 5000 publications. The IntAct website has been improved to enhance the search process and in particular the graphical display of the results. New data download formats are also available, which will facilitate the inclusion of IntActs data in the Semantic Web. IntAct is an active contributor to the IMEx consortium (http://www.imexconsortium.org). IntAct source code and data are freely available at http://www.ebi.ac.uk/intact.
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Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers.
Brief. Bioinformatics
PUBLISHED: 11-22-2011
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Funding bodies are increasingly recognizing the need to provide graduates and researchers with access to short intensive courses in a variety of disciplines, in order both to improve the general skills base and to provide solid foundations on which researchers may build their careers. In response to the development of high-throughput biology, the need for training in the field of bioinformatics, in particular, is seeing a resurgence: it has been defined as a key priority by many Institutions and research programmes and is now an important component of many grant proposals. Nevertheless, when it comes to planning and preparing to meet such training needs, tension arises between the reward structures that predominate in the scientific community which compel individuals to publish or perish, and the time that must be devoted to the design, delivery and maintenance of high-quality training materials. Conversely, there is much relevant teaching material and training expertise available worldwide that, were it properly organized, could be exploited by anyone who needs to provide training or needs to set up a new course. To do this, however, the materials would have to be centralized in a database and clearly tagged in relation to target audiences, learning objectives, etc. Ideally, they would also be peer reviewed, and easily and efficiently accessible for downloading. Here, we present the Bioinformatics Training Network (BTN), a new enterprise that has been initiated to address these needs and review it, respectively, to similar initiatives and collections.
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Posterolateral thoracotomy without muscle division: a new approach to complex procedures.
Interact Cardiovasc Thorac Surg
PUBLISHED: 11-16-2011
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Today, there is a strong increase in video-assisted thoracic surgery; however, there are still some diseases and interventions that need a wide pleural cavity exposure (i.e. sulcus tumours and extended resections). These complex procedures are usually performed via a standard posterolateral thoracotomy, which is a good approach but has significant disadvantage due to pain and difficulty coughing. We propose a new thoracotomy that avoids a dorsal muscle division but has the same intrathoracic exposure as a posterolateral thoracotomy.
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Mental disorders among frequent attenders in primary care: a comparison with routine attenders.
J. Nerv. Ment. Dis.
PUBLISHED: 10-04-2011
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Frequent attenders account for a large proportion of primary care (PC) contacts, referrals, and prescriptions. Psychosocial and emotional distress is related to the high use of health services. Few studies have focused on the association between mental disorders assessed using structured interviews and frequent use of PC services.The aim of this study was to determine the factors associated with frequent attendance at primary healthcare units, focusing specifically on mental disorders. A two-phase screening epidemiological study comparing frequent attenders and routine attenders in five primary health care units was designed. Three hundred eighteen frequent attenders and 203 patients who attended the same units on a routine basis were compared. Sociodemographic and clinical data were obtained from statistical records and medical charts. Patients with a total score equal or higher than 7 points on the General Health Questionnaire-28 (GHQ-28) were interviewed using the Schedules for Clinical Assessment in Neuropsychiatry. All the scores obtained on the GHQ were statistically different in the two populations. Frequency of mental disorders also differed significantly between both groups, with somatoform and affective disorders being the most prevalent ICD-10 categories among frequent attenders. The presence of depressive disorders and somatoform disorders is the most powerful predictive factor for frequent attendance. High comorbidity was found among frequent attenders with somatoform disorder. Frequent attendance at primary healthcare units is associated with depressive and somatoform disorders. Psychiatric comorbidity could be a confounder, particularly because affective and somatoform disorders often overlap in PC patients.
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[Self-care ability in the hypertensive patient control].
Rev. Invest. Clin.
PUBLISHED: 10-03-2011
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Trough an analytical cross-sectional study the association of self-care ability and the blood pressure control was evaluated. We studied controlled and uncontrolled hypertensive patients, both groups with 79 subjects. Self-care basic conditioning factors and capacities scale in patients with hypertension was used.
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PerC and GrlA independently regulate Ler expression in enteropathogenic Escherichia coli.
Mol. Microbiol.
PUBLISHED: 09-13-2011
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Ler, encoded by the locus of enterocyte effacement (LEE) of attaching and effacing (A/E) pathogens, induces the expression of LEE genes by counteracting the silencing exerted by H-NS. Ler expression is modulated by several global regulators, and is activated by GrlA, which is also LEE-encoded. Typical enteropathogenic Escherichia coli (EPEC) strains contain the EAF plasmid, which carries the perABC locus encoding PerC. The precise role of PerC in EPEC virulence gene regulation has remained unclear, mainly because EPEC strains lacking the pEAF still express the LEE genes and because PerC is not present in other A/E pathogens such as Citrobacter rodentium. Here, we describe that either PerC or GrlA can independently activate ler expression and, in consequence, of LEE genes depending on the growth conditions. Both PerC and GrlA, with the aid of IHF, counteract the repression exerted by H-NS on ler and can also further increase its activity. Our results substantiate the role of PerC and GrlA in EPEC virulence gene regulation and suggest that these convergent regulatory mechanisms may have represented an evolutionary adaptation in EPEC to co-ordinate the expression of plasmid- and chromosome-encoded virulence factors needed to successfully colonize its intestinal niche.
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Impact of CD4 T cell count on the outcome of planned treatment interruptions in early-treated human immunodeficiency virus-infected children.
Pediatr. Infect. Dis. J.
PUBLISHED: 07-29-2011
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Early highly active antiretroviral therapy is recommended in all vertically human immunodeficiency virus (HIV)-infected infants. We describe the long-term immunologic outcome after planned treatment interruption (PTI) in 7 children diagnosed and treated during acute HIV infection (age <12 weeks). Children had remained a median of 57 months off treatment, 3 of them indefinitely. The 2 patients with the lowest nadir CD4% reinitiated highly active antiretroviral therapy because of a CD4 cell decline of <20%; 2 children resumed treatment because of clinical progression and parents wishes. All patients experienced a decrease in CD4% after PTI, which particularly affected the naive subpopulation. The interferon-? response against HIV-p24 antigen directly correlated with nadir CD4%. Our results suggest that early treatment in HIV-infected infants increases their potential to safely control viral replication after PTI for long periods.
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Dasty3, a WEB framework for DAS.
Bioinformatics
PUBLISHED: 07-28-2011
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Dasty3 is a highly interactive and extensible Web-based framework. It provides a rich Application Programming Interface upon which it is possible to develop specialized clients capable of retrieving information from DAS sources as well as from data providers not using the DAS protocol. Dasty3 provides significant improvements on previous Web-based frameworks and is implemented using the 1.6 DAS specification.
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Impact of human immunodeficiency virus coinfection on the progression of mother-to-child transmitted hepatitis C virus infection.
Pediatr. Infect. Dis. J.
PUBLISHED: 07-21-2011
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Data on mother-to-child transmitted human immunodeficiency virus/hepatitis C virus (HIV/HCV) coinfection are scarce. A prospective observational study with a cohort of 70 HCV-infected children (13 of whom were HIV/HCV-coinfected; mean follow-up: 7.3 years) is presented. In our series, surrogate markers of disease progression (HCV viremia, maximum alanine aminotransferase values, and spontaneous HCV infection clearance) suggest that the evolution of liver disease in HIV/HCV-coinfected pediatric patients is more aggressive than it is in HCV-only infected children.
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Circumventing the polydactyly constraint: the moles thumb.
Biol. Lett.
PUBLISHED: 07-13-2011
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Talpid moles across all northern continents exhibit a remarkably large, sickle-like radial sesamoid bone anterior to their five digits, always coupled with a smaller tibial sesamoid bone. A possible developmental mechanism behind this phenomenon was revealed using molecular markers during limb development in the Iberian mole (Talpa occidentalis) and a shrew (Cryptotis parva), as shrews represent the closest relatives of moles but do not show these conspicuous elements. The moles radial sesamoid develops later than true digits, as shown by Sox9, and extends into the digit area, developing in relation to an Msx2-domain at the anterior border of the digital plate. Fgf8 expression, marking the apical ectodermal ridge, is comparable in both species. Developmental peculiarities facilitated the inclusion of the moles radial sesamoid into the digit series; talpid moles circumvent the almost universal pentadactyly constraint by recruiting wrist sesamoids into their digital region using a novel developmental pathway and timing.
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Microarray analysis of genes associated with cell surface NIS protein levels in breast cancer.
BMC Res Notes
PUBLISHED: 07-06-2011
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Na+/I- symporter (NIS)-mediated iodide uptake allows radioiodine therapy for thyroid cancer. NIS is also expressed in breast tumors, raising potential for radionuclide therapy of breast cancer. However, NIS expression in most breast cancers is low and may not be sufficient for radionuclide therapy. We aimed to identify biomarkers associated with NIS expression such that mechanisms underlying NIS modulation in human breast tumors may be elucidated.
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myKaryoView: a light-weight client for visualization of genomic data.
PLoS ONE
PUBLISHED: 06-01-2011
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The Distributed Annotation System (DAS) is a protocol for easy sharing and integration of biological annotations. In order to visualize feature annotations in a genomic context a client is required. Here we present myKaryoView, a simple light-weight DAS tool for visualization of genomic annotation. myKaryoView has been specifically configured to help analyse data derived from personal genomics, although it can also be used as a generic genome browser visualization. Several well-known data sources are provided to facilitate comparison of known genes and normal variation regions. The navigation experience is enhanced by simultaneous rendering of different levels of detail across chromosomes. A simple interface is provided to allow searches for any SNP, gene or chromosomal region. User-defined DAS data sources may also be added when querying the system. We demonstrate myKaryoView capabilities for adding user-defined sources with a set of genetic profiles of family-related individuals downloaded directly from 23andMe. myKaryoView is a web tool for visualization of genomic data specifically designed for direct-to-consumer genomic data that uses publicly available data distributed throughout the Internet. It does not require data to be held locally and it is capable of rendering any feature as long as it conforms to DAS specifications. Configuration and addition of sources to myKaryoView can be done through the interface. Here we show a proof of principle of myKaryoViews ability to display personal genomics data with 23andMe genome data sources. The tool is available at: http://mykaryoview.com.
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Identification of Helicobacter pylori strain cagPAI+ and cagPAI- Antigens by IgG antibodies from sera of experimentally colonized meriones unguiculatus (Mongolian gerbils).
Helicobacter
PUBLISHED: 05-19-2011
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?Mongolian gerbils that are experimentally infected with Helicobacter pylori develop a chronic inflammation that is similar to natural infections in humans. The aim of this study was to compare the antigens of H. pylori cagPAI+ and cagPAI- strains that are expressed during Meriones unguiculatus colonization.
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Immunohistochemical analysis in a morphologic spectrum of urachal epithelial neoplasms: diagnostic implications and pitfalls.
Am. J. Surg. Pathol.
PUBLISHED: 05-17-2011
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The vast majority of urachal epithelial neoplasms are adenocarcinomas with several described morphologic subtypes that include both enteric and nonenteric histologies. Adenocarcinoma from several other primaries may mimic any of these urachal adenocarcinoma subtypes in the bladder or at distant sites. However, data regarding the immunohistochemical profile of urachal carcinoma are limited, let alone its correlation with the different histologic subtypes that may have implications in the differential diagnostic workup with their morphologic mimics. Herein, we performed an immunohistochemical analysis in a broad spectrum of 39 urachal epithelial neoplasms (34 adenocarcinomas, 1 urothelial carcinoma, and 4 noninvasive mucinous cystic tumors), 13 urachal remnants, and 6 secondary colonic adenocarcinomas of the bladder, using an antibody panel that included novel and traditional gastrointestinal tract-associated markers. Expression levels of p63, CK7, CK20, CDX2, nuclear ?-catenin, claudin-18, and Reg IV in urachal adenocarcinoma were as follows: 3%, 50%, 100%, 85%, 6%, 53%, and 85%. In urachal adenocarcinoma subtypes, expression levels of CDX2, nuclear ?-catenin, claudin-18, and Reg IV were as follows: mucinous (8/8, 0/8, 6/8, 8/8), enteric (10/11, 1/11, 3/11, 8/11), not otherwise specified (5/7, 0/7, 3/7, 5/7), and signet ring cell (4/6, 0/6, 4/6, 6/6) type. All urachal adenocarcinomas had membrano-cytoplasmic ?-catenin staining and only 2 tumors had nuclear localization that were focal to moderate, in contrast to secondary colonic adenocarcinoma of the bladder, which mostly had both membrano-cytoplasmic and nuclear positivity. Claudin-18 positivity was observed only in frankly malignant tumors and not in noninvasive urachal tumors and urachal remnants. Reg IV expression seemed to be related to mucin production, which was often diffuse in mucinous and signet ring cell subtypes and focal in enteric subtype, with goblet cell-like reactivity similar to secondary colonic adenocarcinoma. p63 expression was present in urothelial urachal remnants (3/3) and contrasted with CDX2 expression seen in glandular (5/6) and mixed urothelial/glandular remnants (2/4). Thus, this study showed that CDX2 is expressed by urachal remnants of glandular type, noninvasive urachal mucinous cystic tumors and urachal adenocarcinomas, and can be diffuse in urachal adenocarcinomas, even without the classic enteric morphology. Nuclear localization of ?-catenin can rarely occur in urachal adenocarcinoma; however, diffuse nuclear reactivity argues against its diagnosis. The novel gastrointestinal tract markers claudin-18 and Reg IV are both expressed in urachal adenocarcinoma, including in signet ring cell carcinoma, and thus refutes the suggested specificity for gastrointestinal tract signet ring cell carcinomas. An immunohistochemical panel that includes ?-catenin and CK7 may have value in differentiating urachal adenocarcinoma of enteric morphology from colonic adenocarcinoma. Overall, this study suggests that the different morphologic presentations of urachal adenocarcinomas have a relatively similar or overlapping immunophenotype. Knowledge of the similarity in immunostaining to its different morphologic mimics may help avoid misdiagnosis in urachal adenocarcinoma.
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Sympathetic chain clipping for hyperhidrosis is not a reversible procedure.
Surg Endosc
PUBLISHED: 05-15-2011
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Many techniques have been used to treat palmar hyperhidrosis. Compensatory sweating is a difficult adverse effect. Clipping has been proposed because of its supposed reversibility when clips are removed at a later date. The primary aims of this article are to investigate the neuronal lesion of the sympathetic chain caused by clipping and to study the possibility of regeneration after removal of the clips.
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DAS writeback: a collaborative annotation system.
BMC Bioinformatics
PUBLISHED: 05-10-2011
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Centralised resources such as GenBank and UniProt are perfect examples of the major international efforts that have been made to integrate and share biological information. However, additional data that adds value to these resources needs a simple and rapid route to public access. The Distributed Annotation System (DAS) provides an adequate environment to integrate genomic and proteomic information from multiple sources, making this information accessible to the community. DAS offers a way to distribute and access information but it does not provide domain experts with the mechanisms to participate in the curation process of the available biological entities and their annotations.
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Evaluation of compliance with the EGS guidelines in Spain, using Achievable Benchmarks of Care (ABC®) methodology: the IMCA Study.
Eur J Ophthalmol
PUBLISHED: 05-03-2011
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To evaluate compliance with diagnostic and therapeutic recommendations of the European Glaucoma Society (EGS) for the management of glaucoma in Spain, as determined using the Achievable Benchmarks of Care approach.
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Flat urothelial carcinoma in situ of the bladder with glandular differentiation.
Hum. Pathol.
PUBLISHED: 04-29-2011
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We present the clinicopathologic and immunonohistochemical features of 25 cases of flat urothelial carcinoma in situ with glandular differentiation. Previously, cases on this category have been reported as in situ adenocarcinoma (a term not currently preferred). Fourteen of 25 cases had concurrent conventional urothelial carcinoma in situ. Five of the cases were primary carcinoma in situ with glandular differentiation; twenty cases of secondary carcinoma in situ with glandular differentiation were associated with urothelial carcinoma alone (n = 11) or with glandular differentiation (n = 7), discohesive (n = 1) or micropapillary carcinoma (n = 1). The individual tumor cells were columnar. The architectural pattern of the carcinoma in situ with glandular differentiation consisted of 1 or more papillary, flat or cribriform glandular patterns. Univariate statistical analysis showed no survival differences between urothelial carcinoma in situ with glandular differentiation and conventional urothelial carcinoma in situ (log-rank 0.810; P = .368). Carcinoma in situ with glandular differentiation showed high ki-67 index and p53 accumulation, high nuclear and cytoplasmic p16 expression and diffuse PTEN expression, a phenotype that also characterized concurrent conventional carcinoma in situ. MUC5A, MUC2, CK20, and c-erbB2 were positive in all 25 cases of urothelial carcinoma in situ with glandular differentiation, and CDX-2 was present in 19 cases; MUC1, CK7, or 34?E12 was focally present in 21, 19, and 18 cases, respectively. MUC1core was negative in all cases. We concluded that urothelial carcinoma in situ with glandular differentiation is a variant of carcinoma in situ that follows the natural history of conventional urothelial carcinoma in situ. The immunophenotype suggests urothelial origin with the expression of MUC5A and CDX2 as signature for glandular differentiation.
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Region-wide analysis of genetic diversity in Verticillium dahliae populations infecting olive in southern Spain and agricultural factors influencing the distribution and prevalence of vegetative compatibility groups and pathotypes.
Phytopathology
PUBLISHED: 04-16-2011
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Severity of Verticillium wilt in olive trees in Andalusia, southern Spain is associated with the spread of a highly virulent, defoliating (D) Verticillium dahliae pathotype of vegetative compatibility group 1A (VCG1A) but the extent of this spread and the diversity of the pathogen population have never been documented. VCG typing of 637 V. dahliae isolates from 433 trees in 65 orchards from five olive-growing provinces in Andalusia indicated that 78.1% were of VCG1A, 19.8% of VCG2A, 0.6% of VCG2B, 1.4% of VCG4B, and one isolate was heterokaryon self-incompatible. A single VCG prevailed among isolates within most orchards but two and three VCGs were identified in 12 and 3 orchards, respectively, with VCG1A+VCG2A occurring in 10 orchards. VCG1A was the predominant VCG in the three most important olive-growing provinces, and was almost as prevalent as VCG2A in another one. Molecular pathotyping of the 637 isolates using specific polymerase chain reaction assays indicated that VCG1A isolates were of the D pathotype whereas isolates of VCG2A, -2B, and -4B were of the less virulent nondefoliating (ND) pathotype. The pathotype of isolates correlated with the disease syndrome affecting sampled trees. Only three (seq1, seq2, and seq4) of the seven known sequences of the V. dahliae-specific 539- or 523-bp amplicon were identified among the 637 isolates. Distribution and prevalence of VCGs and seq sequences among orchards indicated that genetic diversity within olive V. dahliae in Andalusia is higher in provinces where VCG1A is not prevalent. Log-linear analysis revealed that irrigation management, source of irrigation water, source of planting stock, and cropping history of soil were significantly associated with the prevalence of VCG1A compared with that of VCG2A. Multivariate analyses using a selected set of agricultural factors as variables allowed development of a discriminant model for predicting the occurrence of D and ND pathotypes in the area of the study. Blind tests using this model correctly indentified the V. dahliae pathotype occurring in an orchard. The widespread occurrence and high prevalence of VCG1A/D pathotype in Andalusia have strong implications for the management of the disease.
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Ultrasound-guided diagnostic breast biopsy methodology: retrospective comparison of the 8-gauge vacuum-assisted biopsy approach versus the spring-loaded 14-gauge core biopsy approach.
World J Surg Oncol
PUBLISHED: 04-08-2011
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Ultrasound-guided diagnostic breast biopsy technology represents the current standard of care for the evaluation of indeterminate and suspicious lesions seen on diagnostic breast ultrasound. Yet, there remains much debate as to which particular method of ultrasound-guided diagnostic breast biopsy provides the most accurate and optimal diagnostic information. The aim of the current study was to compare and contrast the 8-gauge vacuum-assisted biopsy approach and the spring-loaded 14-gauge core biopsy approach.
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Comparison of Monte Carlo ray-tracing and photon-tracing methods for calculation of the impulse response on indoor wireless optical channels.
Opt Express
PUBLISHED: 03-04-2011
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We present a comparison between the modified Monte Carlo algorithm (MMCA) and a recently proposed ray-tracing algorithm named as photon-tracing algorithm. Both methods are compared exhaustively according to error analysis and computational costs. We show that the new photon-tracing method offers a solution with a slightly greater error but requiring from considerable less computing time. Moreover, from a practical point of view, the solutions obtained with both algorithms are approximately equivalent, demonstrating the goodness of the new photon-tracing method.
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A proteomic study of in-root interactions between chickpea pathogens: the root-knot nematode Meloidogyne artiellia and the soil-borne fungus Fusarium oxysporum f. sp. ciceris race 5.
J Proteomics
PUBLISHED: 03-01-2011
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Fusarium wilt caused by the fungus Fusarium oxysporum f. sp. ciceris (Foc) is the main soil-borne disease limiting chickpea production. Management of this disease is achieved mainly by the use of resistant cultivars. However, co-infection of a Foc-resistant plant by the fungus and the root-knot nematode Meloidogyne artiellia (Ma) causes breakdown of the resistance and thus limits its efficacy in the control of Fusarium wilt. In this work we aimed to reveal key aspects of chickpea:Foc:Ma interactions, studying fungal- and nematode-induced changes in root proteins, using chickpea lines CA 336.14.3.0 and ICC 14216K that show similar resistant (Foc race 5) and susceptible (Ma) responses to either pathogen alone but a differential response after co-infection with both pathogens. CA 336.14.3.0 and ICC 14216K chickpea plants were challenged with Foc race 5 and Ma, either in single or in combined inoculations, and the root proteomes were analyzed by two-dimensional gel electrophoresis using three biological replicates. Pairwise comparisons of treatments indicated that 47 protein spots in CA 336.14.3.0 and 31 protein spots in ICC 14216K underwent significant changes in intensity. The responsive protein spots tentatively identified by MALDI TOF-TOF MS (27 spots for CA 336.14.3.0 and 15 spots for ICC 14216K) indicated that same biological functions were involved in the responses of either chickpea line to Foc race 5 and Ma, although common as well as line-specific responsive proteins were found within the different biological functions. To the best of our knowledge, this is the first study at the root proteome level of chickpea response to a biotic stress imposed by single and joint infections by two major soil-borne pathogens.
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[Pericardial window by videothorascopy].
Cir Esp
PUBLISHED: 02-06-2011
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Pericardial effusion is a clinical condition requiring multidisciplinary management. There are several surgical techniques for its diagnosis and treatment. In the present study we report our experience in performing a pericardial window (PW) by videothorascopy.
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easyDAS: automatic creation of DAS servers.
BMC Bioinformatics
PUBLISHED: 01-18-2011
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The Distributed Annotation System (DAS) has proven to be a successful way to publish and share biological data. Although there are more than 750 active registered servers from around 50 organizations, setting up a DAS server comprises a fair amount of work, making it difficult for many research groups to share their biological annotations. Given the clear advantage that the generalized sharing of relevant biological data is for the research community it would be desirable to facilitate the sharing process.
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First rib resection using videothorascopy for the treatment of thoracic outlet syndrome.
Arch. Bronconeumol.
PUBLISHED: 01-16-2011
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Thoracic outlet syndrome is a condition caused by compression of the subclavian artery, subclavian vein and/or the brachial plexus. Scalene muscle section and first rib removal is the most effective treatment. The objective of this article is to demonstrate first rib resection using videothoracoscopy.
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In planta and soil quantification of Fusarium oxysporum f. sp. ciceris and evaluation of Fusarium wilt resistance in chickpea with a newly developed quantitative polymerase chain reaction assay.
Phytopathology
PUBLISHED: 01-12-2011
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Fusarium wilt of chickpea caused by Fusarium oxysporum f. sp. ciceris can be managed by risk assessment and use of resistant cultivars. A reliable method for the detection and quantification of F. oxysporum f. sp. ciceris in soil and chickpea tissues would contribute much to implementation of those disease management strategies. In this study, we developed a real-time quantitative polymerase chain reaction (q-PCR) protocol that allows quantifying F. oxysporum f. sp. ciceris DNA down to 1 pg in soil, as well as in the plant root and stem. Use of the q-PCR protocol allowed quantifying as low as 45 colony forming units of F. oxysporum f. sp. ciceris per gram of dry soil from a field plot infested with several races of the pathogen. Moreover, the q-PCR protocol clearly differentiated susceptible from resistant chickpea reactions to the pathogen at 15 days after sowing in artificially infested soil, as well as the degree of virulence between two F. oxysporum f. sp. ciceris races. Also, the protocol detected early asymptomatic root infections and distinguished significant differences in the level of resistance of 12 chickpea cultivars that grew in that same field plot infested with several races of the pathogen. Use of this protocol for fast, reliable, and cost-effective quantification of F. oxysporum f. sp. ciceris in asymptomatic chickpea tissues at early stages of the infection process can be of great value for chickpea breeders and for epidemiological studies in growth chambers, greenhouses and field-scale plots.
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[Incisions and routes of surgical access].
Arch. Bronconeumol.
PUBLISHED: 01-01-2011
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The correct choice of the incision to the chest is essential for surgical success and a favorable postoperative course. The route of access to the thorax must be adapted both to the disease and to the thoracic surgeons experience, striking a balance between aggressiveness and the safety of the technique. This article describes the characteristics of surgical incisions, including classical thoracotomy, sternotomy and its variants, thoracoscopy and minimally-invasive surgery. The distinct techniques used to explore mediastinal lymphatic areas, including video-assisted mediastinal lymphadenectomy and transcervical extended mediastinal lymphadenectomy, are also described.
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The age of the target cell affects B-cell leukaemia malignancy.
Aging (Albany NY)
PUBLISHED: 12-18-2010
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The incidence, malignancy and treatment resistance of many types of human B-cell leukaemias (B-ALL) are directly related to patient age. A major obstacle to elucidate the contribution of age to the development and evolution of leukaemias is the lack of appropriate mouse models where precise control of the timing of oncogene expression is possible. Here we present proof-of-principle experiments showing how a conditional transgenic mouse model of BCR-ABLp190-driven B-ALL offers the opportunity to test the hypothesis that the age of the leukemic cells-of-origin of B-ALL influences B-ALL malignancy. B-ALLs generated from 12- and 20-month-old progenitors gave rise to a more invasive B-ALL than the one developed from 4-month old precursors. This was evidenced by survival analysis revealing the increased malignancy of B-ALLs generated from 20 or 12-month-old transformed progenitors compared with the 4-month equivalents (median survival of 88 days versus 50.5 and 33 days, respectively). Our study shows that the age of target cells at the time of transformation affects B-ALL malignancy.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

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.