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Find video protocols related to scientific articles indexed in Pubmed.
Brucella abortus depends on pyruvate phosphate dikinase and malic enzyme but not on Fbp and GlpX fructose-1,6-bisphosphatases for full virulence in laboratory models.
J. Bacteriol.
PUBLISHED: 06-16-2014
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The brucellae are the etiological agents of brucellosis, a worldwide-distributed zoonosis. These bacteria are facultative intracellular parasites and thus are able to adjust their metabolism to the extra- and intracellular environments encountered during an infectious cycle. However, this aspect of Brucella biology is imperfectly understood, and the nutrients available in the intracellular niche are unknown. Here, we investigated the central pathways of C metabolism used by Brucella abortus by deleting the putative fructose-1,6-bisphosphatase (fbp and glpX), phosphoenolpyruvate carboxykinase (pckA), pyruvate phosphate dikinase (ppdK), and malic enzyme (mae) genes. In gluconeogenic but not in rich media, growth of ?ppdK and ?mae mutants was severely impaired and growth of the double ?fbp-?glpX mutant was reduced. In macrophages, only the ?ppdK and ?mae mutants showed reduced multiplication, and studies with the ?ppdK mutant confirmed that it reached the replicative niche. Similarly, only the ?ppdK and ?mae mutants were attenuated in mice, the former being cleared by week 10 and the latter persisting longer than 12 weeks. We also investigated the glyoxylate cycle. Although aceA (isocitrate lyase) promoter activity was enhanced in rich medium, aceA disruption had no effect in vitro or on multiplication in macrophages or mouse spleens. The results suggest that B. abortus grows intracellularly using a limited supply of 6-C (and 5-C) sugars that is compensated by glutamate and possibly other amino acids entering the Krebs cycle without a critical role of the glyoxylate shunt.
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The identification of wadB, a new glycosyltransferase gene, confirms the branched structure and the role in virulence of the lipopolysaccharide core of Brucella abortus.
Microb. Pathog.
PUBLISHED: 05-03-2014
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Brucellosis is a worldwide extended zoonosis caused by Brucella spp. These gram-negative bacteria are not readily detected by innate immunity, a virulence-related property largely linked to their surface lipopolysaccharide (LPS). The role of the LPS lipid A and O-polysaccharide in virulence is well known. Moreover, mutation of the glycosyltransferase gene wadC of Brucella abortus, although not affecting O-polysaccharide assembly onto the lipid-A core section causes a core oligosaccharide defect that increases recognition by innate immunity. Here, we report on a second gene (wadB) encoding a LPS core glycosyltransferase not involved in the assembly of the O-polysaccharide-linked core section. As compared to wild-type B. abortus, a wadB mutant was sensitive to bactericidal peptides and non-immune serum, and was attenuated in mice and dendritic cells. These observations show that as WadC, WadB is also involved in the assembly of a branch of Brucella LPS core and support the concept that this LPS section is a virulence-related structure.
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Mutants in the lipopolysaccharide of Brucella ovis are attenuated and protect against B. ovis infection in mice.
Vet. Res.
PUBLISHED: 01-23-2014
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Brucella spp. are Gram-negative bacteria that behave as facultative intracellular parasites of a variety of mammals. This genus includes smooth (S) and rough (R) species that carry S and R lipopolysaccharides (LPS), respectively. S-LPS is a virulence factor, and mutants affected in the S-LPS O-polysaccharide (R mutants), core oligosaccharide or both show attenuation. However, B. ovis is naturally R and is virulent in sheep. We studied the role of B. ovis LPS in virulence by mutating the orthologues of wadA, wadB and wadC, three genes known to encode LPS core glycosyltransferases in S brucellae. When mapped with antibodies to outer membrane proteins (Omps) and R-LPS, wadB and wadC mutants displayed defects in LPS structure and outer membrane topology but inactivation of wadA had little or no effect. Consistent with these observations, the wadB and wadC but not the wadA mutants were attenuated in mice. When tested as vaccines, the wadB and wadC mutants protected mice against B. ovis challenge. The results demonstrate that the LPS core is a structure essential for survival in vivo not only of S brucellae but also of a naturally R Brucella pathogenic species, and they confirm our previous hypothesis that the Brucella LPS core is a target for vaccine development. Since vaccine B. melitensis Rev 1 is S and thus interferes in serological testing for S brucellae, wadB mutant represents a candidate vaccine to be evaluated against B. ovis infection of sheep suitable for areas free of B. melitensis.
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Value of a simple method to assess chronic rejection in renal allograft on electron microscopy.
Ultrastruct Pathol
PUBLISHED: 10-17-2013
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Electron microscopy is a powerful tool for the assessment of complex lesions in nontumor renal pathology, however it is a time-consuming procedure. We evaluated a simple method to assess morphological signs of chronic rejection in renal allograft that seems to have prognostic significance.
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Membranous glomerulopathy in renal allograft: an ultrastructural study of 17 cases.
Ultrastruct Pathol
PUBLISHED: 07-22-2013
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Membranous glomerulopathy is a common complication of renal allograft. However, its incidence and prognosis are not well defined, because an undetermined number of them pass undiagnosed under the generic epigraph of chronic allograft nephropathy.
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Quantifying reproducibility in computational biology: the case of the tuberculosis drugome.
PLoS ONE
PUBLISHED: 01-01-2013
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How easy is it to reproduce the results found in a typical computational biology paper? Either through experience or intuition the reader will already know that the answer is with difficulty or not at all. In this paper we attempt to quantify this difficulty by reproducing a previously published paper for different classes of users (ranging from users with little expertise to domain experts) and suggest ways in which the situation might be improved. Quantification is achieved by estimating the time required to reproduce each of the steps in the method described in the original paper and make them part of an explicit workflow that reproduces the original results. Reproducing the method took several months of effort, and required using new versions and new software that posed challenges to reconstructing and validating the results. The quantification leads to "reproducibility maps" that reveal that novice researchers would only be able to reproduce a few of the steps in the method, and that only expert researchers with advance knowledge of the domain would be able to reproduce the method in its entirety. The workflow itself is published as an online resource together with supporting software and data. The paper concludes with a brief discussion of the complexities of requiring reproducibility in terms of cost versus benefit, and a desiderata with our observations and guidelines for improving reproducibility. This has implications not only in reproducing the work of others from published papers, but reproducing work from ones own laboratory.
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The cognitive atlas: toward a knowledge foundation for cognitive neuroscience.
Front Neuroinform
PUBLISHED: 03-31-2011
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Cognitive neuroscience aims to map mental processes onto brain function, which begs the question of what "mental processes" exist and how they relate to the tasks that are used to manipulate and measure them. This topic has been addressed informally in prior work, but we propose that cumulative progress in cognitive neuroscience requires a more systematic approach to representing the mental entities that are being mapped to brain function and the tasks used to manipulate and measure mental processes. We describe a new open collaborative project that aims to provide a knowledge base for cognitive neuroscience, called the Cognitive Atlas (accessible online at http://www.cognitiveatlas.org), and outline how this project has the potential to drive novel discoveries about both mind and brain.
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Brucella abortus ornithine lipids are dispensable outer membrane components devoid of a marked pathogen-associated molecular pattern.
PLoS ONE
PUBLISHED: 01-07-2011
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The brucellae are ?-Proteobacteria facultative intracellular parasites that cause an important zoonosis. These bacteria escape early detection by innate immunity, an ability associated to the absence of marked pathogen-associated molecular patterns in the cell envelope lipopolysaccharide, lipoproteins and flagellin. We show here that, in contrast to the outer membrane ornithine lipids (OL) of other Gram negative bacteria, Brucella abortus OL lack a marked pathogen-associated molecular pattern activity. We identified two OL genes (olsB and olsA) and by generating the corresponding mutants found that olsB deficient B. abortus did not synthesize OL or their lyso-OL precursors. Liposomes constructed with B. abortus OL did not trigger IL-6 or TNF-? release by macrophages whereas those constructed with Bordetella pertussis OL and the olsB mutant lipids as carriers were highly active. The OL deficiency in the olsB mutant did not promote proinflammatory responses or generated attenuation in mice. In addition, OL deficiency did not increase sensitivity to polymyxins, normal serum or complement consumption, or alter the permeability to antibiotics and dyes. Taken together, these observations indicate that OL have become dispensable in the extant brucellae and are consistent within the trend observed in ?-Proteobacteria animal pathogens to reduce and eventually eliminate the envelope components susceptible of recognition by innate immunity.
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Parameterized Specification, Configuration and Execution of Data-Intensive Scientific Workflows.
Cluster Comput
PUBLISHED: 09-01-2010
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Data analysis processes in scientific applications can be expressed as coarse-grain workflows of complex data processing operations with data flow dependencies between them. Performance optimization of these workflows can be viewed as a search for a set of optimal values in a multidimensional parameter space consisting of input performance parameters to the applications that are known to affect their execution times. While some performance parameters such as grouping of workflow components and their mapping to machines do not affect the accuracy of the analysis, others may dictate trading the output quality of individual components (and of the whole workflow) for performance. This paper describes an integrated framework which is capable of supporting performance optimizations along multiple such parameters. Using two real-world applications in the spatial, multidimensional data analysis domain, we present an experimental evaluation of the proposed framework.
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Fine-needle aspiration cytology diagnosis of metastatic nonhaematological neoplasms of the breast: a series of seven cases.
Diagn. Cytopathol.
PUBLISHED: 07-06-2010
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Metastatic neoplasms of the breast are rare. Mammary metastases as the initial presentation are even more infrequent and can simulate a primary malignancy clinically and radiologically. Recognition of metastatic tumors in the breast is important because it would prevent unnecessary mutilating surgery and would lead to appropriate treatment of the primary tumor. There is a broad variety of cytological appearances reported about primary tumors and few reports about secondary breast malignancies, specially diagnosed by FNAC. This study was carried out to examine the clinical and cytomorphologic features of metastatic breast tumors found in 12 de Octubre University Hospital during a period of 20 years. It confirms the utility of FNAC and describes findings that can help in the differential diagnosis that sometimes can be very difficult. Seven cases of nonhematological metastatic neoplasms of the breast were identified from the files of the Department of Pathology of the 12 de Octubre University Hospital from a total of 64,000 aspirates. We included only metastatic tumors from extramammary nonhematological neoplasms. There were nine cases of hematological metastatic neoplasm that were excluded. They were diagnosed with FNAC and confirmed by histopathology, with at least three years of follow up. The breast lump was the first manifestation of malignancy in one case of synovial sarcoma. The other six cases had been previously diagnosed of cancer. These included one malignant melanoma, one alveolar rhabdomyosarcoma, one mixed müllerian tumor, one medullary carcinoma of thyroid, one colonic adenocarcinoma, and one gastric adenocarcinoma. The period of time between primary tumor and metastases ranged from one month to eight years. An accurate cytologic diagnosis was made in all the cases. Immunocytochemistry was available but diagnosis could be made with cytomorphology alone in the seven cases. Fine-needle aspiration cytology is an excellent first line diagnostic modality that is particularly informative when clinical previous data are known. If metastatic disease is suspected, the material obtained by FNAC may provide a definitive diagnosis and prevent open surgical biopsy or mastectomy. We concur with previous reports that FNAC is a reliable, rapid, secure, and cost-effective approach to the diagnosis of palpable metastatic breast tumors.
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Lichtheimia corymbifera subcutaneous infection successfully treated with amphotericin B, early debridement, and vacuum-assisted closure.
J. Pediatr. Surg.
PUBLISHED: 05-10-2010
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Lichtheimia corymbifera (syn. Absidia corymbifera, Mycocladus corymbifer) is an ubiquitous cosmopolitan mold that can cause primary cutaneous and deep tissue infection in healthy individuals. We report a subcutaneous L. corymbifera infection in a 13-year-old immune-competent child, with a severe traumatic injury, with a successful outcome after early diagnosis and treatment with lipid amphotericin B, early debridement, and vacuum-assisted closure (VAC).
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Primary retroperitoneal liposarcoma: clinical and histological analysis of ten cases.
Gastroenterol Hepatol
PUBLISHED: 03-04-2010
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Retroperitoneal liposarcoma constitutes an uncommon and locally aggressive malignancy. We performed a retrospective analysis of 10 patients (6 males; mean age: 63.2+/-11 years) with histologically proven retroperitoneal liposarcoma seen at our institution between 1999 and 2007. Presence of a palpable abdominal mass was the main symptom at diagnosis. All patients underwent complete surgical resection. Negative microscopic margin was achieved in four cases. Histological analysis revealed the following subtypes: well-differentiated (6 cases), dedifferentiated (two cases), pleomorphic, and myxoid/round cell (one case each). Concomitant resection of adjacent organs was needed in five cases. Half of the patients developed tumor recurrence, mainly limited to the retroperitoneum or abdominal cavity. The mean recurrence-free survival was 43.3 months (95%CI: 25.7-60.8), with 3- and 5-year overall survival rates of 79% and 61%, respectively. Patients undergoing complete resection with clear margins showed a near-significant trend toward increased recurrence-free survival (62.9 vs. 29.3 months; P=0.06).
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HPC AND GRID COMPUTING FOR INTEGRATIVE BIOMEDICAL RESEARCH.
Int J High Perform Comput Appl
PUBLISHED: 12-08-2009
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Integrative biomedical research projects query, analyze, and integrate many different data types and make use of datasets obtained from measurements or simulations of structure and function at multiple biological scales. With the increasing availability of high-throughput and high-resolution instruments, the integrative biomedical research imposes many challenging requirements on software middleware systems. In this paper, we look at some of these requirements using example research pattern templates. We then discuss how middleware systems, which incorporate Grid and high-performance computing, could be employed to address the requirements.
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Lines of cell differentiation in solitary fibrous tumor: an ultrastructural and immunohistochemical study of 10 cases.
Ultrastruct Pathol
PUBLISHED: 11-26-2009
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Solitary fibrous tumor (SFT) is a rare ubiquitous mesenchymal neoplasm of probable fibroblastic type with a prominent hemangiopericytoma-like vascular pattern. Since their initial description as arising from the pleura, SFTs have been reported in many extraserosal sites. It is now accepted that this neoplasm is derived from mesenchymal cells but its histogenesis is still not known.
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[Comparison between agar dilution and three other methods for determining the susceptibility of 228 clinical isolates of non-fermenting gram-negative rods].
Enferm. Infecc. Microbiol. Clin.
PUBLISHED: 05-05-2009
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Susceptibility testing for non-fermenting gram-negative rods (NFGNR) is problematic; valid methods are needed for this purpose.
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Lipopolysaccharide as a target for brucellosis vaccine design.
Microb. Pathog.
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The gram-negative bacteria of the genus Brucella are facultative intracellular parasites that cause brucellosis, a world wide-distributed zoonotic disease that represents a serious problem for animal and human health. There is no human-to-human contagion and, since there is no human vaccine, animal vaccination is essential to control brucellosis. However, current vaccines (all developed empirically) do not provide 100% protection and are infectious in humans. Attempts to generate new vaccines by obtaining mutants lacking the lipopolysaccharide O-polysaccharide, in purine metabolism or in Brucella type IV secretion system have not been successful. Here we propose a new approach to develop brucellosis vaccines based on the concept that Brucella surface molecules evade efficient detection by innate immunity, thus delaying protective Th1 responses and opening a time window to reach sheltered intracellular compartments. We showed recently that a branch of the core oligosaccharide section of Brucella lipopolysaccharide hampers recognition by TLR4-MD2. Mutation of glycosyltransferase WadC, involved in the synthesis of this branch, results in a lipopolysaccharide that, while keeping the O-polysaccharide essential for optimal protection, shows a truncated core, is more efficiently recognized by MD2 and triggers an increased cytokine response. In keeping with this, the wadC mutant is attenuated in dendritic cells and mice. In the mouse model of brucellosis vaccines, the Brucella abortus wadC mutant conferred protection similar to that provided by S19, the best cattle vaccine available. The properties of the wadC mutant provide the proof of concept for this new approach and open the way for more effective brucellosis vaccines.
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[Diseases associated with bloodstream infections caused by the new species included in the old Streptococcus bovis group].
Enferm. Infecc. Microbiol. Clin.
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We sought to identify possible diseases associated with bloodstream infections caused by new species of S. bovis group isolated in blood cultures and by studying patient records
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Identification and functional analysis of the cyclopropane fatty acid synthase of Brucella abortus.
Microbiology (Reading, Engl.)
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The brucellae are facultative intracellular pathogens of mammals that are transmitted by contact with infected animals or contaminated materials. Several major lipidic components of the brucella cell envelope are imperfectly recognized by innate immunity, thus contributing to virulence. These components carry large proportions of acyl chains of lactobacillic acid, a long chain cyclopropane fatty acid (CFA). CFAs result from addition of a methylene group to unsaturated acyl chains and contribute to resistance to acidity, dryness and high osmolarity in many bacteria and to virulence in mycobacteria. We examined the role of lactobacillic acid in Brucella abortus virulence by creating a mutant in ORF BAB1_0476, the putative CFA synthase gene. The mutant did not incorporate [(14)C]methyl groups into lipids, lacked CFAs and synthesized the unsaturated precursors, proving that BAB1_0476 actually encodes a CFA synthase. BAB1_0476 promoter-luxAB fusion studies showed that CFA synthase expression was promoted by acid pH and high osmolarity. The mutant was not attenuated in macrophages or mice, strongly suggesting that CFAs are not essential for B. abortus intracellular life. However, when the mutant was tested under high osmolarity on agar and acid pH, two conditions likely to occur on contaminated materials and fomites, they showed reduced ability to grow or survive. Since CFA synthesis entails high ATP expenses and brucellae produce large proportions of lactobacillic acyl chains, we speculate that the CFA synthase has been conserved because it is useful for survival extracellularly, thus facilitating persistence in contaminated materials and transmission to new hosts.
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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.

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

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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.