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Find video protocols related to scientific articles indexed in Pubmed.
Content discovery and retrieval services at the European Nucleotide Archive.
Nucleic Acids Res.
PUBLISHED: 11-19-2014
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The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is Europe's primary resource for nucleotide sequence information. With the growing volume and diversity of public sequencing data comes the need for increased sophistication in data organisation, presentation and search services so as to maximise its discoverability and usability. In response to this, ENA has been introducing and improving checklists for use during submission and expanding its search facilities to provide targeted search results. Here, we give a brief update on ENA content and some major developments undertaken in data submission services during 2014. We then describe in more detail the services we offer for data discovery and retrieval.
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Histamine impairs midbrain dopaminergic development in vivo by activating histamine type 1 receptors.
Mol Brain
PUBLISHED: 08-12-2014
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Histamine (HA) regulates the sleep-wake cycle, synaptic plasticity and memory in adult mammals. Dopaminergic specification in the embryonic ventral midbrain (VM) coincides with increased HA brain levels. To study the effect of HA receptor stimulation on dopamine neuron generation, we administered HA to dopamine progenitors, both in vitro and in vivo.
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Epidemiology of bacterial meningitis in the USA from 1997 to 2010: a population-based observational study.
Lancet Infect Dis
PUBLISHED: 08-04-2014
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Bacterial meningitis continues to be a substantial cause of morbidity and mortality, but the epidemiological trends after adjunctive dexamethasone recommendations are unknown in the USA. We aimed to describe the changing patterns among the most common bacterial causes in the USA after conjugate vaccination and to assess the association between adjunctive dexamethasone and mortality.
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2-Phenylaminonaphthoquinones and related compounds: synthesis, trypanocidal and cytotoxic activities.
Bioorg. Med. Chem.
PUBLISHED: 07-27-2014
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A series of new 2-aminonaphthoquinones and related compounds were synthesized and evaluated in vitro as trypanocidal and cytotoxic agents. Some tested compounds inhibited epimastigote growth and trypomastigote viability. Several compounds showed similar or higher activity and selectivity as compared with current trypanocidal drug, nifurtimox. Compound 4l exhibit higher selectivity than nifurtimox against Trypanosoma cruzi in comparison with Vero cells. Some of the synthesized quinones were tested against cancer cells and normal fibroblasts, showing that certain chemical modifications on the naphthoquinone moiety induce and excellent increase the selectivity index of the cytotoxicity (4g and 10). The results presented here show that the anti-T. cruzi activity of 2-aminonaphthoquinones derivatives can be improved by the replacement of the benzene ring by a pyridine moiety. Interestingly, the presence of a chlorine atom at C-3 and a highly lipophilic alkyl group or aromatic ring are newly observed elements that should lead to the discovery of more selective cytotoxic and trypanocidal compounds.
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Carrier-envelope-phase stable, high-contrast, double chirped-pulse-amplification laser system.
Opt Lett
PUBLISHED: 07-01-2014
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We present the first carrier-envelope-phase stable chirped-pulse amplifier (CPA) featuring high temporal contrast for relativistic intensity laser-plasma interactions at 1 kHz repetition rate. The laser is based on a double-CPA architecture including cross-polarized wave (XPW) filtering technique and a high-energy grism-based compressor. The 8 mJ, 22 fs pulses feature 10?¹¹ temporal contrast at -20??ps and a carrier-envelope-phase drift of 240 mrad root mean square.
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Reliability of recordings of subgingival calculus detected using an ultrasonic device.
Clin Oral Investig
PUBLISHED: 04-29-2014
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To assess the intra-examiner reliability of recordings of subgingival calculus detected using an ultrasonic device, and to investigate the influence of subject-, tooth- and site-level factors on the reliability of these subgingival calculus recordings.
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InterProScan 5: genome-scale protein function classification.
Bioinformatics
PUBLISHED: 01-21-2014
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Robust large-scale sequence analysis is a major challenge in modern genomic science, where biologists are frequently trying to characterize many millions of sequences. Here, we describe a new Java-based architecture for the widely used protein function prediction software package InterProScan. Developments include improvements and additions to the outputs of the software and the complete reimplementation of the software framework, resulting in a flexible and stable system that is able to use both multiprocessor machines and/or conventional clusters to achieve scalable distributed data analysis. InterProScan is freely available for download from the EMBl-EBI FTP site and the open source code is hosted at Google Code.
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Pentamidine exerts in vitro and in vivo anti Trypanosoma cruzi activity and inhibits the polyamine transport in Trypanosoma cruzi.
Acta Trop.
PUBLISHED: 01-17-2014
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Pentamidine is an antiprotozoal and fungicide drug used in the treatment of leishmaniasis and African trypanosomiasis. Despite its extensive use as antiparasitic drug, little evidence exists about the effect of pentamidine in Trypanosoma cruzi, the etiological agent of Chagas' disease. Recent studies have shown that pentamidine blocks a polyamine transporter present in Leishmania major; consequently, its might also block these transporters in T. cruzi. Considering that T. cruzi lacks the ability to synthesize putrescine de novo, the inhibition of polyamine transport can bring a new therapeutic target against the parasite. In this work, we show that pentamidine decreases, not only the viability of T. cruzi trypomastigotes, but also the parasite burden of infected cells. In T. cruzi-infected mice pentamidine decreases the inflammation and parasite burden in hearts from infected mice. The treatment also decreases parasitemia, resulting in an increased survival rate. In addition, pentamidine strongly inhibits the putrescine and spermidine transport in T. cruzi epimastigotes and amastigotes. Thus, this study points to reevaluate the utility of pentamidine and introduce evidence of a potential new action mechanism. In the quest of new therapeutic strategies against Chagas disease, the extensive use of pentamidine in human has led to a well-known clinical profile, which could be an advantage over newly synthesized molecules that require more comprehensive trials prior to their clinical use.
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Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut.
BMC Genomics
PUBLISHED: 01-16-2014
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The main limitations in the analysis of viral metagenomes are perhaps the high genetic variability and the lack of information in extant databases. To address these issues, several bioinformatic tools have been specifically designed or adapted for metagenomics by improving read assembly and creating more sensitive methods for homology detection. This study compares the performance of different available assemblers and taxonomic annotation software using simulated viral-metagenomic data.
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Toxic and therapeutic effects of Nifurtimox and Benznidazol on Trypanosoma cruzi ex vivo infection of human placental chorionic villi explants.
Acta Trop.
PUBLISHED: 01-13-2014
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Nifurtimox (Nfx) and Benznidazole (Bnz) are the only available drugs in use for the treatment of Chagas disease. These drugs are recommended but not fully validated in evidence-based medicine and reports about the differential toxicity of both drugs are controversial. Here, we evaluated the toxic and therapeutic effects of Nfx and Bnz on human placental chorionic villi explants (HPCVE) during ex vivo infection of Trypanosoma cruzi, performing histopathological, histochemical, immunohistochemical as well as immunofluorescence analysis of the tissue. Additionally, we determined the effect of both drugs on parasite load by real time PCR. Bnz prevents the parasite induced tissue damage in ex vivo infected HPCVE compared to Nfx, which is toxic per se. The presence of T. cruzi antigens and DNA in infected explants suggests that these drugs do not impair parasite invasion into the HPCVE. Additionally, our results confirm reports suggesting that Bnz is less toxic than Nfx and support the need for the development of more effective and better-tolerated drugs.
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Assembly information services in the European Nucleotide Archive.
Nucleic Acids Res.
PUBLISHED: 11-08-2013
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The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is a repository for the world public domain nucleotide sequence data output. ENA content covers a spectrum of data types including raw reads, assembly data and functional annotation. ENA has faced a dramatic growth in genome assembly submission rates, data volumes and complexity of datasets. This has prompted a broad reworking of assembly submission services, for which we now reach the end of a major programme of work and many enhancements have already been made available over the year to components of the submission service. In this article, we briefly review ENA content and growth over 2013, describe our rapidly developing services for genome assembly information and outline further major developments over the last year.
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Carrier-envelope phase stability of hollow fibers used for high-energy few-cycle pulse generation.
Opt Lett
PUBLISHED: 10-02-2013
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We investigated the carrier-envelope phase (CEP) stability of hollow-fiber compression for high-energy few-cycle pulse generation. Saturation of the output pulse energy is observed at 0.6 mJ for a 260 ?m inner-diameter, 1 m long fiber, statically filled with neon. The pressure is adjusted to achieve output spectra supporting sub-4-fs pulses. The maximum output pulse energy can be increased to 0.8 mJ by either differential pumping (DP) or circularly polarized input pulses. We observe the onset of an ionization-induced CEP instability, which saturates beyond input pulse energies of 1.25 mJ. There is no significant difference in the CEP stability with DP compared to static-fill.
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Medicinal plants of Chile: evaluation of their anti-Trypanosoma cruzi activity.
Z. Naturforsch., C, J. Biosci.
PUBLISHED: 08-09-2013
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The extracts of several plants of Central Chile exhibited anti-Trypanosoma cruzi trypomastigotes activity. Most active extracts were those obtained from Podanthus ovatifolius, Berberis microphylla, Kageneckia oblonga, and Drimys winteri. The active extract of Drimys winteri (IC50 51.2 microg/mL) was purified and three drimane sesquiterpenes were obtained: polygodial, drimenol, and isodrimenin. Isodrimenin and drimenol were found to be active against the trypomastigote form of T. cruzi with IC50 values of 27.9 and 25.1 microM, respectively.
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Reliability of direct and indirect clinical attachment level measurements.
J. Clin. Periodontol.
PUBLISHED: 06-22-2013
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To investigate the influence of subject-, tooth- and site-level characteristics on intra-examiner reproducibility of direct and indirect clinical attachment level (CALDIR and CALIND ) recordings, and to quantify the impact of less-than-perfect reliability on our ability to assess periodontitis progression.
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Study of the viral and microbial communities associated with Crohns disease: a metagenomic approach.
Clin Transl Gastroenterol
PUBLISHED: 06-14-2013
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This study aimed to analyze and compare the diversity and structure of the viral and microbial communities in fecal samples from a control group of healthy volunteers and from patients affected by Crohns disease (CD).
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Analysis Tool Web Services from the EMBL-EBI.
Nucleic Acids Res.
PUBLISHED: 05-13-2013
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Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods.
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Energy-scalable temporal cleaning device for femtosecond laser pulses based on cross-polarized wave generation.
Rev Sci Instrum
PUBLISHED: 05-03-2013
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We report on a compact energy-scalable device for generating high-fidelity femtosecond laser pulses based on spatial filtering through a hollow-core fiber followed by a nonlinear crystal for cross-polarized wave (XPW) generation. This versatile device is suited for temporal pulse cleaning over a wide range of input energies (from 0.1 to >10 mJ) and is successfully qualified on different ultrafast laser systems. Full characterization of the XPW output is presented. In particular, we demonstrate the generation of 1.6 mJ energy pulses starting from 11 mJ input pulse energy. The temporal contrast of the pulses is enhanced by more than 4 orders of magnitude. In addition, pulse shortening from 40 fs down to 15 fs Fourier-transform limit yields an overall peak-power transmission of up to 50%. This device not only serves as an integrated pulse contrast filter inside an ultrafast laser amplifier but also as a simple back-end solution for temporal post-compression of amplified pulses.
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Protection of vascular endothelium by aspirin in a murine model of chronic Chagas disease.
Parasitol. Res.
PUBLISHED: 04-26-2013
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Chronic Chagas disease affects 10-30 % of patients infected with Trypanosoma cruzi, and it mainly manifests as cardiomyopathy. Important pathophysiological mechanisms involved in the cardiac lesions include activation of the endothelium and induced microvascular alterations. These processes involve the production of endothelial adhesion molecules and thromboxane A2, which are involved in inflammatory cell recruitment and platelet aggregation, respectively. Cyclooxygenase inhibitors such as aspirin decrease thromboxane production and alter the course of Chagas disease, both in the acute and chronic phases. We studied the effects of the administration of low and high doses of aspirin during the early phase of T. cruzi infection, following microvascular damage in the context of a chronic murine model of Chagas disease. The effects of both schedules were assessed at 24 and 90 days postinfection by evaluating parasitemia, mortality, and cardiac histopathological changes as well as the expression of ICAM, VCAM, and E-selectin in cardiac tissue. Thromboxane A2, soluble ICAM, and E-selectin blood levels were also measured. While aspirin did not affect parasitemia or mortality in the infected mice, it decreased both cardiac inflammatory infiltrates and thromboxane levels. Additionally, at 90 days postinfection, aspirin normalized sICAM and sE-selectin levels. Considering the improved endothelial function induced by aspirin, we propose the possibility of including this drug in clinical therapy to treat chronic Chagas disease.
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Generation of high-fidelity few-cycle pulses at 2.1 ?m via cross-polarized wave generation.
Opt Express
PUBLISHED: 04-24-2013
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We demonstrate the generation of temporally clean few-cycle pulses at 2.1 ?m by shortening of 6-optical-cycle pulses via cross-polarized wave (XPW) generation in BaF(2), CaF(2) and CVD-Diamond crystals. By combining spectra and single-shot third-order intensity cross-correlation traces in a novel Bayesian pulse retrieval technique, we measured pulse durations of 20 fs, corresponding to 2.8 optical cycles. Our results show that XPW generation in the infrared could provide a high-fidelity source of few-cycle pulses for strong-field physics applications. It could also serve as an injector for high-peak power ultrafast mid-IR wavelength parametric amplifiers.
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Self-modulation of nonlinear Alfvén waves in a strongly magnetized relativistic electron-positron plasma.
Phys Rev E Stat Nonlin Soft Matter Phys
PUBLISHED: 04-19-2013
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We study the self-modulation of a circularly polarized Alfvén wave in a strongly magnetized relativistic electron-positron plasma with finite temperature. This nonlinear wave corresponds to an exact solution of the equations, with a dispersion relation that has two branches. For a large magnetic field, the Alfvén branch has two different zones, which we call the normal dispersion zone (where d?/dk>0) and the anomalous dispersion zone (where d?/dk<0). A nonlinear Schrödinger equation is derived in the normal dispersion zone of the Alfvén wave, where the wave envelope can evolve as a periodic wave train or as a solitary wave, depending on the initial condition. The maximum growth rate of the modulational instability decreases as the temperature is increased. We also study the Alfvén wave propagation in the anomalous dispersion zone, where a nonlinear wave equation is obtained. However, in this zone the wave envelope can evolve only as a periodic wave train.
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Periodontal disease epidemiology - learned and unlearned?
Periodontol. 2000
PUBLISHED: 04-12-2013
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The notion of periodontal disease being the major cause of tooth loss among adults was rooted in the focal infection paradigm that dominated the first half of the 20th century. This paradigm was established largely by personal opinions, and it was not until the development of periodontal indices in the mid-1950s that periodontal epidemiology gained momentum. Unfortunately, the indices used suffered from a number of flaws, whereby the interpretation of the research results took the form of circular reasoning. It was under this paradigm that therapeutic and preventive intervention for periodontal diseases became entirely devoted to oral hygiene, as poor oral hygiene and older age were understood to explain nearly all the variation in disease occurrence. In the early 1980s, studies appeared that contradicted the concepts of poor oral hygiene as the inevitable trigger of periodontitis and of linear and ubiquitous periodontitis progression, whereby periodontal epidemiology was led into a relatively short-lived high-risk era. At this time, it became evident that old scourges continue to haunt periodontology: the inability to agree in operational clinical criteria for a periodontitis diagnosis and the inability to devise both a meaningful and a useful classification of periodontal diseases based on nominalist principles. The meager outcome of the high-risk era led researchers to resurrect the focal infection paradigm, which is now dressed up as periodontal medicine. Unfortunately, these developments have left the core of periodontology somewhat disheveled and deserted.
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Protective role of acetylsalicylic acid in experimental Trypanosoma cruzi infection: evidence of a 15-epi-lipoxin A?-mediated effect.
PLoS Negl Trop Dis
PUBLISHED: 04-01-2013
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Chagas disease, produced by Trypanosoma cruzi, affects more than 8 million people, producing approximately 10,000 deaths each year in Latin America. Migration of people from endemic regions to developed countries has expanded the risk of infection, transforming this disease into a globally emerging problem. PGE? and other eicosanoids contribute to cardiac functional deficits after infection with T. cruzi. Thus, the inhibition of host cyclooxygenase (COX) enzyme emerges as a potential therapeutic target. In vivo studies about the effect of acetylsalicylic acid (ASA) upon T. cruzi infection are controversial, and always report the effect of ASA at a single dose. Therefore, we aimed to analyze the effect of ASA at different doses in an in vivo model of infection and correlate it with the production of arachidonic acid metabolites. ASA decreased mortality, parasitemia, and heart damage in T. cruzi (Dm28c) infected mice, at the low doses of 25 and 50 mg/Kg. However, this effect disappeared when the high ASA doses of 75 and 100 mg/Kg were used. We explored whether this observation was related to the metabolic shift toward the production of 5-lipoxygenase derivatives, and although we did not observe an increase in LTB4 production in infected RAW cells and mice infected, we did find an increase in 15-epi-LXA? (an ASA-triggered lipoxin). We also found high levels of 15-epi-LXA? in T. cruzi infected mice treated with the low doses of ASA, while the high ASA doses decreased 15-epi-LXA? levels. Importantly, 15-epi-LXA? prevented parasitemia, mortality, and cardiac changes in vivo and restored the protective role in the treatment with a high dose of ASA. This is the first report showing the production of ASA-triggered lipoxins in T. cruzi infected mice, which demonstrates the role of this lipid as an anti-inflammatory molecule in the acute phase of the disease.
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EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats.
Bioinformatics
PUBLISHED: 03-11-2013
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Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore required.
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Benznidazole prevents endothelial damage in an experimental model of Chagas disease.
Acta Trop.
PUBLISHED: 03-06-2013
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To evaluate the effect of benznidazole on endothelial activation in a murine model of Chagas disease.
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The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics.
BMC Bioinformatics
PUBLISHED: 02-08-2013
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User-centred design (UCD) is a type of user interface design in which the needs and desires of users are taken into account at each stage of the design process for a service or product; often for software applications and websites. Its goal is to facilitate the design of software that is both useful and easy to use. To achieve this, you must characterise users requirements, design suitable interactions to meet their needs, and test your designs using prototypes and real life scenarios.For bioinformatics, there is little practical information available regarding how to carry out UCD in practice. To address this we describe a complete, multi-stage UCD process used for creating a new bioinformatics resource for integrating enzyme information, called the Enzyme Portal (http://www.ebi.ac.uk/enzymeportal). This freely-available service mines and displays data about proteins with enzymatic activity from public repositories via a single search, and includes biochemical reactions, biological pathways, small molecule chemistry, disease information, 3D protein structures and relevant scientific literature.We employed several UCD techniques, including: persona development, interviews, canvas sort card sorting, user workflows, usability testing and others. Our hope is that this case study will motivate the reader to apply similar UCD approaches to their own software design for bioinformatics. Indeed, we found the benefits included more effective decision-making for design ideas and technologies; enhanced team-working and communication; cost effectiveness; and ultimately a service that more closely meets the needs of our target audience.
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[Bioethics and rationality. Personalism at the service of expanding the horizon of reason at the foundation of bioethics].
Cuad Bioet
PUBLISHED: 01-17-2013
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Personalism not only provides a valuable contribution to those interested in bioethics by allowing contrasts with other schools and currents of thought, but its ethical and anthropological features can serve to widen the horizon of reason. Bioethics today needs to expand the horizon of rationality in which it is animated through: 1) An ontologically ground personalism thanks to which the personal being emerges with all its evidence as being in the most proper sense of being. 2) The overcoming of subjectivism-objectivism antinomy through the claim that human subjectivity is an objective fact. 3) The recognition of the personalistic norm of action as a fundamental precept of natural law. When bioethics is built with openness to the objective datum of subjectivity it becomes easy to appreciate the human person as a real aim that should not be used as mere means. 4) The discovery of the normative basis of the moral life, because determining the ultimate end of human action is not the same as obtaining an ultimate justification of the norms of human action. When this distinction is deeply assimilated, it can show that the precepts of natural law must be respected regardless the acceptance of Gods existence.
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A fast-evolving human NPAS3 enhancer gained reporter expression in the developing forebrain of transgenic mice.
Philos. Trans. R. Soc. Lond., B, Biol. Sci.
PUBLISHED: 01-01-2013
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The developmental brain gene NPAS3 stands out as a hot spot in human evolution because it contains the largest number of human-specific, fast-evolving, conserved, non-coding elements. In this paper we studied 2xHAR142, one of these elements that is located in the fifth intron of NPAS3. Using transgenic mice, we show that the mouse and chimp 2xHAR142 orthologues behave as transcriptional enhancers driving expression of the reporter gene lacZ to a similar NPAS3 expression subdomain in the mouse central nervous system. Interestingly, the human 2xHAR142 orthologue drives lacZ expression to an extended expression pattern in the nervous system. Thus, molecular evolution of 2xHAR142 provides the first documented example of human-specific heterotopy in the forebrain promoted by a transcriptional enhancer and suggests that it may have contributed to assemble the unique properties of the human brain.
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Routine CSF analysis in coccidioidomycosis is not required.
PLoS ONE
PUBLISHED: 01-01-2013
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Although routinely done, there has been no evaluation of the utility of performing routine cerebrospinal fluid (CSF) examination in patients with active coccidioidomycosis and high complement fixation (IgG) antibody titers or other risk factors for disseminated infection. In our review 100% of patients diagnosed with coccidioidal meningitis had at least one sign or symptom consistent with infection of the central nervous system, headache was present in 100% of those with meningitis, while no patients without signs/symptoms of CNS infection were found to have coccidioidal meningitis, irrespective of antibody titers or other risk factors. Thus routine lumbar puncture may be unnecessary for patients with coccidioidomycosis who lack suggestive clinical symptoms.
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The annotation-enriched non-redundant patent sequence databases.
Database (Oxford)
PUBLISHED: 01-01-2013
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The EMBL-European Bioinformatics Institute (EMBL-EBI) offers public access to patent sequence data, providing a valuable service to the intellectual property and scientific communities. The non-redundant (NR) patent sequence databases comprise two-level nucleotide and protein sequence clusters (NRNL1, NRNL2, NRPL1 and NRPL2) based on sequence identity (level-1) and patent family (level-2). Annotation from the source entries in these databases is merged and enhanced with additional information from the patent literature and biological context. Corrections in patent publication numbers, kind-codes and patent equivalents significantly improve the data quality. Data are available through various user interfaces including web browser, downloads via FTP, SRS, Dbfetch and EBI-Search. Sequence similarity/homology searches against the databases are available using BLAST, FASTA and PSI-Search. In this article, we describe the data collection and annotation and also outline major changes and improvements introduced since 2009. Apart from data growth, these changes include additional annotation for singleton clusters, the identifier versioning for tracking entry change and the entry mappings between the two-level databases. Database URL: http://www.ebi.ac.uk/patentdata/nr/
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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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InterPro in 2011: new developments in the family and domain prediction database.
Nucleic Acids Res.
PUBLISHED: 11-16-2011
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InterPro (http://www.ebi.ac.uk/interpro/) is a database that integrates diverse information about protein families, domains and functional sites, and makes it freely available to the public via Web-based interfaces and services. Central to the database are diagnostic models, known as signatures, against which protein sequences can be searched to determine their potential function. InterPro has utility in the large-scale analysis of whole genomes and meta-genomes, as well as in characterizing individual protein sequences. Herein we give an overview of new developments in the database and its associated software since 2009, including updates to database content, curation processes and Web and programmatic interfaces.
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Functions of the pointing gesture in mothers and their 12 to 36-month-old children during everyday activities.
Span J Psychol
PUBLISHED: 11-09-2011
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This study longitudinally examined the production of pointing in four Spanish 1-year-old and four Spanish 2-year-old children in interactive situations with their mothers at home over the course of one year. Three aspects were analyzed: a) the functions of the pointing gesture, their accurate comprehension by the interlocutor (mother or child), and their order of emergence in the child; b) whether or not there were differences in the production of pointing according to who initiated the interaction; and c) whether maternal and child speech were related to maternal and child pointing production. The results showed that the pointing function of showing is the most frequent for both children and mothers from groups 1 and 2, and the first to emerge followed by the informing, requesting object, requesting action, and requesting cooperation functions. The accuracy with which these intentions were comprehended was found to be very high for both mother and child. Pointing production was greater when the speaker initiated the interaction than when the other person did, indicating that gestures follow the turn-taking system. Finally, the production of pointing to showing in children and mothers was found to be related to maternal and child speech, while pointing to request cooperation triggered the process of joint activity between mother and child.
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Subgingival microbial consortia and the clinical features of periodontitis in adolescents.
Eur. J. Oral Sci.
PUBLISHED: 10-11-2011
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This study aimed to investigate the association between microbial consortia and the clinical features of periodontitis using a multilevel modeling approach. A total of 958 sites in 87 adolescents with periodontitis (cases) and 73 controls were microbiologically sampled and clinically examined. Associations between each of the clinical parameters clinical attachment, probing depth, supragingival plaque, calculus, bleeding on probing, and each of 18 bacterial species; and between the same clinical parameters and each of two microbial consortia identified, were investigated using mixed-effects regression modeling. Higher counts of Tannerella forsythia, Campylobacter rectus, and Porphyromonas gingivalis were all statistically significantly associated with higher values of clinical attachment level, probing depth, and bleeding on probing in the sampled site, when both case status and between-subject variance were accounted for. Higher counts for the consortium comprising the putative periodontopathogens were statistically significantly associated in a dose-response manner with both higher clinical attachment levels and with increased pocket depth. The counts for the consortium predominantly comprising the early-colonizer species were statistically significantly negatively associated with the presence of supragingival calculus, but positively associated with the presence of supragingival plaque. The study demonstrates a relationship between the counts of putative periodontopathogens and clinical attachment levels and probing pocket depths, even for low levels of these clinical parameters.
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Defining a periodontitis case: analysis of a never-treated adult population.
J. Clin. Periodontol.
PUBLISHED: 09-28-2011
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The purpose of the present study was to assess the extent to which the three periodontitis case definition systems proposed by van der Velden, Tonetti & Claffey and Page & Eke identify the same cases in a population of never-treated adults with limited tradition for oral hygiene procedures.
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Effect of mechanical debridement on distal periodontal aspects of second molars after the extraction of third molars: a systematic review.
J. Periodontol.
PUBLISHED: 09-26-2011
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The risk of periodontal defects after the extraction of third molars continues to challenge clinicians.
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[Coronary stents and non-cardiac surgery: current management strategies].
Rev Med Chil
PUBLISHED: 09-14-2011
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The care of patients with coronary stents in the perioperative period of non-cardiac surgery requires anesthesiologists, surgeons and cardiologists. The management of dual antiplatelet therapy should be handled depending on type and urgency of the surgery, the risk of bleeding, type of coronary stent implanted, time from placement and the risk of stent thrombosis. For patients identified as high risk of stent thrombosis, surgery should be planned at hospitals with cardiac catheterization facilities. These patients require postoperative monitoring and antiplatelet therapy should be restarted immediately. Stent thrombosis should be recognized early and treated aggressively with percutaneous coronary intervention.
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Convergent evolution of two mammalian neuronal enhancers by sequential exaptation of unrelated retroposons.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 08-29-2011
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The proopiomelanocortin gene (POMC) is expressed in a group of neurons present in the arcuate nucleus of the hypothalamus. Neuron-specific POMC expression in mammals is conveyed by two distal enhancers, named nPE1 and nPE2. Previous transgenic mouse studies showed that nPE1 and nPE2 independently drive reporter gene expression to POMC neurons. Here, we investigated the evolutionary mechanisms that shaped not one but two neuron-specific POMC enhancers and tested whether nPE1 and nPE2 drive identical or complementary spatiotemporal expression patterns. Sequence comparison among representative genomes of most vertebrate classes and mammalian orders showed that nPE1 is a placental novelty. Using in silico paleogenomics we found that nPE1 originated from the exaptation of a mammalian-apparent LTR retrotransposon sometime between the metatherian/eutherian split (147 Mya) and the placental mammal radiation (? 90 Mya). Thus, the evolutionary origin of nPE1 differs, in kind and time, from that previously demonstrated for nPE2, which was exapted from a CORE-short interspersed nucleotide element (SINE) retroposon before the origin of prototherians, 166 Mya. Transgenic mice expressing the fluorescent markers tomato and EGFP driven by nPE1 or nPE2, respectively, demonstrated coexpression of both reporter genes along the entire arcuate nucleus. The onset of reporter gene expression guided by nPE1 and nPE2 was also identical and coincidental with the onset of Pomc expression in the presumptive mouse diencephalon. Thus, the independent exaptation of two unrelated retroposons into functional analogs regulating neuronal POMC expression constitutes an authentic example of convergent molecular evolution of cell-specific enhancers.
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Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.
Mol. Syst. Biol.
PUBLISHED: 07-23-2011
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Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets of the size of many thousands of sequences. Some methods allow computation of larger data sets while sacrificing quality, and others produce high-quality alignments, but scale badly with the number of sequences. In this paper, we describe a new program called Clustal Omega, which can align virtually any number of protein sequences quickly and that delivers accurate alignments. The accuracy of the package on smaller test cases is similar to that of the high-quality aligners. On larger data sets, Clustal Omega outperforms other packages in terms of execution time and quality. Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam.
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Effects of periodontal therapy on systemic markers of inflammation in patients with metabolic syndrome: a controlled clinical trial.
J. Periodontol.
PUBLISHED: 07-12-2011
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The systemic inflammation in both metabolic syndrome (MetS) and periodontitis is a common denominator of the association of these conditions with higher risk of atherosclerosis. The current study investigates whether periodontal therapy may reduce systemic inflammation in patients with MetS and reduce cardiovascular risk.
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Hematological features in adolescents with periodontitis.
Clin Oral Investig
PUBLISHED: 05-09-2011
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The aim of this study was to assess whether adolescent cases of periodontitis present with different hemogram findings than control subjects. This case-control study comprised 87 adolescent cases presenting with clinical attachment loss ?3 mm in at least two teeth and 73 control subjects. Blood samples were obtained by venipuncture and analyzed in an Abbott Cell-Dyn 3,500 hematology analyzer for values of white blood cells and red blood cells, hemoglobin, mean corpuscular volume, mean corpuscular hemoglobin, mean corpuscular hemoglobin concentration, red-cell distribution width, platelets, and mean platelet volume. Hematocrit values were obtained using volume fractions read from capillary tubes. The associations between log-transformed hemogram variables with each of the three exposure variables "case status" (yes/no), a "high percent sites with PD ?4 mm" (yes/no), and a "high percent sites with BOP" (yes/no) were investigated using multivariate linear regression analyses. Periodontitis cases presented with 5% higher values for the mean platelet volume than did controls. Subjects with a high percent sites with probing depth ?4 mm had eosinophil counts that were on average 27% lower than among subjects with fewer deepened pockets. They also had 7% higher values for the mean platelet volume than did persons with less pocketing. Eosinophil counts and mean platelet volumes may be associated with the parameters of periodontitis in adolescents. While standard hematological testing did not show abnormalities in adolescents with periodontitis compared to healthy controls, eosinophil counts and mean platelet volumes may reflect periodontal inflammation.
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Progesterone and 17?-estradiol increase differentiation of mouse embryonic stem cells to motor neurons.
IUBMB Life
PUBLISHED: 04-26-2011
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Embryonic stem (ES) cells have the capacity to differentiate into endodermal, mesodermal, and ectodermal lineages. Motor neuron (MN) differentiation of mouse ES cells involves embryoid bodies formation with addition of Sonic hedgehog and retinoic acid. In this work, using immunocytochemistry, flow cytometry, and quantitative RT-PCR, we investigated whether progesterone or 17?-estradiol have inductive effects on ES cell-derived MN, as it has been demonstrated that these hormones modify proliferation and neural differentiation of pluripotent cells. When 100 nM progesterone was added during differentiation, we found higher proportions of MN, compared to the control condition; coincubation of progesterone with the progesterone receptor (PR) antagonist RU-486 caused a decrease in the number of MN to a percentage even lower than controls. The addition of nanomolar concentrations of 17?-estradiol also significantly induced MN differentiation. This effect of estradiol was completely antagonized by addition of the general estrogen receptor (ER) antagonist ICI 182,780. To identify the ER subtype mediating the increase on MN differentiation, we incubated estradiol with the ER-? antagonist MPP or with the ER-? blocker PHTPP. When we coincubated 17?-estradiol with MPP, we found a significant decrease in the percentage of MN. In contrast, the coincubation of 17?-estradiol with PHTPP had no effect on the induction of MN differentiation. All these effects on cell number were confirmed by significant changes in the expression of the MN markers Islet-1 and Choline acetyl transferase, assessed by real-time RT-PCR. Cell proliferation in embryoid bodies was significantly enhanced by progesterone treatment. No changes in apoptotic cell death were found in differentiating cells after progesterone or 17?-estradiol addition. Our findings indicate that progesterone and 17?-estradiol induce a higher proportion of MN derived from mouse ES cells through intracellular PR and ER, respectively. Furthermore, the effect of estradiol was mediated by specific activation of ER-?.
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High-harmonic generation from plasma mirrors at kilohertz repetition rate.
Opt Lett
PUBLISHED: 04-19-2011
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We report the first demonstration of high-harmonic generation from plasma mirrors at a 1 kHz repetition rate. Harmonics up to nineteenth order are generated at peak intensities close to 10¹? W/cm² by focusing 1 mJ, 25 fs laser pulses down to 1.7 ?m FWHM spot size without any prior wavefront correction onto a moving target. We minimize target surface motion with respect to the laser focus using online interferometry to ensure reproducible interaction conditions for every shot and record data at 1 kHz with unprecedented statistics. This allows us to unambiguously identify coherent wake emission as the main generation mechanism.
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Clustering of subgingival microbial species in adolescents with periodontitis.
Eur. J. Oral Sci.
PUBLISHED: 03-03-2011
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It has become increasingly recognized that groups of microorganisms interact within the subgingival plaque of adult subjects with periodontitis. It is much less clear, however, whether the consortia of microorganisms associated with periodontitis are different in early and more advanced cases of periodontitis. To investigate this point further, subgingival plaque was collected from six sites in 87 adolescents with periodontitis and 73 controls and the samples were analyzed for the detection of 18 microbial species using the DNA-DNA hybridization technique. Actinomyces oris accounted for the highest proportion of the flora and was more predominant among controls. Prevotella nigrescens, Prevotella intermedia, Porphyromonas gingivalis, and Tannerella forsythia were present at higher levels among the subjects with periodontitis. Factor analyses identified one factor characterized by highly positive loadings for T. forsythia, Campylobacter rectus, P. gingivalis, P. intermedia, P. nigrescens, Parvimonas micra, and Treponema denticola, and another factor characterized by highly positive loadings of A. oris, Capnocytophaga ochracea, Eikenella corrodens, Streptococcus intermedius, Selenomonas noxia, Streptococcus oralis, Streptococcus sanguinis, and Veillonella parvula. Aggregatibacter actinomycetemcomitans and Streptococcus mutans did not load on any of the two factors, while Fusobacterium nucleatum loaded on both. These findings confirm the occurrence of clustering of subgingival bacteria according to case status also among young individuals.
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Efficacy and safety of an intraoral electrostimulation device for xerostomia relief: a multicenter, randomized trial.
Arthritis Rheum.
PUBLISHED: 02-01-2011
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To evaluate the efficacy and safety of an intraoral electrostimulation device, consisting of stimulating electrodes, an electronic circuit, and a power source, in treating xerostomia. The device delivers electrostimulation through the oral mucosa to the lingual nerve in order to enhance the salivary reflex.
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The estrogen receptor ? colocalizes with proopiomelanocortin in hypothalamic neurons and binds to a conserved motif present in the neuron-specific enhancer nPE2.
Eur. J. Pharmacol.
PUBLISHED: 01-03-2011
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The gene encoding the prohormone proopiomelanocortin (POMC) is mainly expressed in two regions in vertebrates, namely corticotrophs and melanotrophs in the pituitary and a small population of neurons in the arcuate nucleus of the hypothalamus. In this latter region, POMC-derived peptides participate in the control of energy balance and sensitivity to pain. Neuronal expression of POMC is conferred by two enhancers, nPE1 and nPE2, which are conserved in most mammals, but no transcription factors are yet known to bind to these enhancers. In this work, by means of a one-hybrid screening, we identify that nPE2 possesses an element recognized by transcription factors of the nuclear receptor superfamily. This element, named NRBE, is conserved in all known nPE2 enhancers and is necessary to confer full enhancer strength to nPE2-driven reporter gene expression in transgenic mice assays, indicating that the phylogenetic conservation of the element is indicative of its functional importance. In a search for candidate nuclear receptors that might control POMC we observed that estrogen receptor alpha (ESR1) - a known regulator of energy balance at the hypothalamic level - can bind to the NRBE element in vitro. In addition we observed by immunofluorescence that ESR1 is coexpressed with POMC in around 25-30% of hypothalamic neurons of males and females during late embryonic stages and adulthood. Thus, our results indicate that hypothalamic expression of POMC is controlled by nuclear receptors and establish ESR1 as a candidate regulator of POMC.
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Aortic stenosis and acquired von Willebrand disease: lack of association.
J. Cardiothorac. Vasc. Anesth.
PUBLISHED: 01-01-2011
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The association between aortic stenosis (AS) and acquired von Willebrand disease type 2A has been described. It may be present in up to 90% of patients with AS. Shear stress has been proposed as the underlying mechanism; however, the physiopathology of this condition is not completely understood. No specific treatment has been studied in this specific population besides aortic valve replacement (AVR). As a coadjuvant therapy, some cardiac surgery centers use desmopressin routinely. The authors report the first stage of an ongoing study designed to compare the effects of desmopressin versus placebo in patients with severe AS scheduled for AVR. Because of the different incidences of the acquired von Willebrand type 2A reported in the literature, the first stage was conducted to describe the incidence of this clinical association in the present population, allowing the sample size for the second stage of the study to be obtained.
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Chagas disease: Present status of pathogenic mechanisms and chemotherapy.
Biol. Res.
PUBLISHED: 11-30-2010
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There are approximately 7.8 million people in Latin America, including Chile, who suffer from Chagas disease and another 28 million who are at risk of contracting it. Chagas is caused by the flagellate protozoan Trypanosoma cruzi. It is a chronic disease, where 20%-30% of infected individuals develop severe cardiopathy, with heart failure and potentially fatal arrhythmias. Currently, Chagas disease treatment is more effective in the acute phase, but does not always produce complete parasite eradication during indeterminate and chronic phases. At present, only nifurtimox or benznidazole have been proven to be superior to new drugs being tested. Therefore, it is necessary to find alternative approaches to treatment of chronic Chagas. The current treatment may be rendered more effective by increasing the activity of anti-Chagasic drugs or by modifying the hosts immune response. We have previously shown that glutathione synthesis inhibition increases nifurtimox and benznidazole activity. In addition, there is increasing evidence that cyclooxygenase inhibitors present an important effect on T. cruzi infection. Therefore, we found that aspirin reduced the intracellular infection in RAW 264.7 cells and, decreased myocarditis extension and mortality rates in mice. However, the long-term benefit of prostaglandin inhibition for Chagasic patients is still unknown.
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Genetic characterization of indigenous peoples from Oaxaca, Mexico, and its relation to linguistic and geographic isolation.
Hum. Biol.
PUBLISHED: 11-19-2010
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We used 15 short tandem repeat (STR) loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818, and FGA) to genetically characterize 361 individuals from 11 indigenous populations (Amuzgo, Chinanteco, Chontal, Huave, Mazateco, Mixe, Mixteco, Triqui, Zapoteco del Istmo, Zapoteco del Valle, and Zoque) from Oaxaca, Mexico. We also used previously published data from other Mexican peoples (Maya, Chol, Tepehua, Otomí, and Mestizos from northern and central Mexico) to delineate genetic relations, for a total of 541 individuals. Average heterozygosity (H) was lower in most populations from Oaxaca (range 0.687 in Zoque to 0.756 in Chontal) than values observed in Mestizo populations from Mexico (0.758 and 0.793 in central and northern Mestizo, respectively) but higher than values observed in other Amerindian populations from South America; the same relation was true for the number of alleles (n(a) ). We tested (using the software Structure) whether major geographic or linguistic barriers to gene flow existed among the populations of Oaxaca and found that the populations appeared to constitute one or two genetic groups, suggesting that neither geographic location nor linguistics had an effect on the genetic structure of these culturally and linguistically highly diverse indigenous peoples. Moreover, we found a low but statistically significant between-population differentiation. In addition, the genetic structure of Oaxacan populations did not fit an isolation-by-distance model. Finally, using AMOVA and a Bayesian clustering approach, we did not detect significant geographic or linguistic barriers to gene flow within Oaxaca. These results suggest that the indigenous communities of Oaxaca, although culturally isolated, can be genetically defined as a large, nearly panmictic population in which migration could be a more important population mechanism than genetic drift. Finally, compared with outgroups in Mexico (both indigenous peoples and Mestizos), three groups were apparent. Among them, only the Otomí population from Hidalgo has a different culture and language.
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The IMGT/HLA database.
Nucleic Acids Res.
PUBLISHED: 11-11-2010
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It is 12 years since the IMGT/HLA database was first released, providing the HLA community with a searchable repository of highly curated HLA sequences. The HLA complex is located within the 6p21.3 region of human chromosome 6 and contains more than 220 genes of diverse function. Many of the genes encode proteins of the immune system and are highly polymorphic. The naming of these HLA genes and alleles and their quality control is the responsibility of the WHO Nomenclature Committee for Factors of the HLA System. Through the work of the HLA Informatics Group and in collaboration with the European Bioinformatics Institute, we are able to provide public access to this data through the web site http://www.ebi.ac.uk/imgt/hla/. Regular updates to the web site ensure that new and confirmatory sequences are dispersed to the HLA community, and the wider research and clinical communities.
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Serum levels of C-reactive protein in adolescents with periodontitis.
J. Periodontol.
PUBLISHED: 11-02-2010
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The results of several cross-sectional studies suggested a relationship between periodontitis and higher serum levels of C-reactive protein (CRP). Most of these studies were restricted to adult study groups with severe periodontal inflammation, and the potential effects of confounding factors were frequently overlooked.
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Efficacy and safety of entecavir and/or tenofovir for prophylaxis and treatment of hepatitis B recurrence post-liver transplant.
Transplant. Proc.
PUBLISHED: 10-26-2010
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To establish the efficacy and safety of entecavir (ETV) and/or tenofovir (TDF) in the treatment and prevention of hepatitis B virus (HBV) recurrence after liver transplantation.
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Root resorption in the furcation area: a differential diagnostic consideration.
J. Periodontol.
PUBLISHED: 07-14-2010
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This report describes the case of a 51-year-old female who was referred to a periodontist with a tentative diagnosis of complicated furcation defect in the facial aspect of the second permanent molar in the mandibular right quadrant.
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ESR, electrochemical, molecular modeling and biological evaluation of 4-substituted and 1,4-disubstituted 7-nitroquinoxalin-2-ones as potential anti-Trypanosoma cruzi agents.
Spectrochim Acta A Mol Biomol Spectrosc
PUBLISHED: 07-07-2010
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Electrochemical and ESR studies were carried out in this work with the aim of characterizing the reduction mechanisms of 4-substituted and 1,4-disubstituted 7-nitroquinoxalin-2-ones by means of cyclic voltammetry in DMSO as aprotic solvent. Two reduction mechanisms were found for these compounds: the first, for compounds bearing a labile hydrogen by following a self-protonation mechanism (ECE steps), and the second, for compounds without labile hydrogen, based on a purely electrochemical reduction mechanism (typical of nitroheterocycles). The electrochemical results were corroborated using ESR spectroscopy allowing us to propose the hyperfine splitting pattern of the nitro-radical, which was later corroborated by the ESR simulation spectra. All these compounds were assayed as growth inhibitors against Trypanosoma cruzi: first, on the non-proliferative (and infective) form of the parasite (trypomastigote stage), and then, the ones that displayed activity, were assayed on the non-infective form (epimastigote stage). Thus, we found four new compounds highly active against T. cruzi. Finally, molecular modeling studies suggest the inhibition of the trypanothione reductase like one of the possible mechanisms involved in the trypanocidal action.
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Bioinformatics training: selecting an appropriate learning content management system--an example from the European Bioinformatics Institute.
Brief. Bioinformatics
PUBLISHED: 07-02-2010
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Todays molecular life scientists are well educated in the emerging experimental tools of their trade, but when it comes to training on the myriad of resources and tools for dealing with biological data, a less ideal situation emerges. Often bioinformatics users receive no formal training on how to make the most of the bioinformatics resources and tools available in the public domain. The European Bioinformatics Institute, which is part of the European Molecular Biology Laboratory (EMBL-EBI), holds the worlds most comprehensive collection of molecular data, and training the research community to exploit this information is embedded in the EBIs mission. We have evaluated eLearning, in parallel with face-to-face courses, as a means of training users of our data resources and tools. We anticipate that eLearning will become an increasingly important vehicle for delivering training to our growing user base, so we have undertaken an extensive review of Learning Content Management Systems (LCMSs). Here, we describe the process that we used, which considered the requirements of trainees, trainers and systems administrators, as well as taking into account our organizational values and needs. This review describes the literature survey, user discussions and scripted platform testing that we performed to narrow down our choice of platform from 36 to a single platform. We hope that it will serve as guidance for others who are seeking to incorporate eLearning into their bioinformatics training programmes.
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[Current management strategies for pulmonary hypertension in surgical patients].
Rev Med Chil
PUBLISHED: 06-30-2010
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Pulmonary hypertension is a clinical condition with a low prevalence, but carries high morbidity and mortality. Important advances in the understanding of this disease and in its therapy have occurred. A particular scenario is pulmonary hypertension in patients undergoing non-cardiac as well as cardiac surgery. The aim of this review is to present information that may allow diagnostic and therapeutic approaches of this clinical condition in patients undergoing surgery.
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Identification of Plasmodium relictum causing mortality in penguins (Spheniscus magellanicus) from São Paulo Zoo, Brazil.
Vet. Parasitol.
PUBLISHED: 05-27-2010
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This study reports avian malaria caused by Plasmodium relictum in Magellanic Penguins (Spheniscus magellanicus) from São Paulo Zoo. The disease was highly infective among the birds and was clinically characterized by its acute course and high mortality. The penguins of São Paulo Zoo were housed for at least 2 years without malaria; however, they had always been maintained in an enclosure protected from mosquito exposure during the night period. When they presented pododermatitis, they were freed at night for a short period. São Paulo Zoo is located in one of the last forest remnants of the city, an area of original Atlantic forest. In the winter, the space destined for Zoo birds is shared with migratory species. Hence the possibility exists that the disease was transmitted to the penguins by mosquitoes that had previously bitten infected wild birds. Avian malaria parasites are transmitted mainly by mosquitoes of the genera Aedes and Culex, common vectors in the Atlantic forest. In this study, one Culex (Cux.) sp. was found, infected with P. relictum. There are diverse problems in housing distinct species of animals in captivity, principally when occupying the same enclosure, since it facilitates the transmission of diseases with indirect cycles, as is the case of Plasmodium spp., because certain species that cause discrete infections in some bird species can become a serious danger for others, especially penguins, which do not possess natural resistance. Thus, serious implications exist for periodically testing and administrating malaria therapy in captive penguins potentially exposed to mosquitoes during the night period, as well as other captive birds from São Paulo Zoo.
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BioCatalogue: a universal catalogue of web services for the life sciences.
Nucleic Acids Res.
PUBLISHED: 05-19-2010
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The use of Web Services to enable programmatic access to on-line bioinformatics is becoming increasingly important in the Life Sciences. However, their number, distribution and the variable quality of their documentation can make their discovery and subsequent use difficult. A Web Services registry with information on available services will help to bring together service providers and their users. The BioCatalogue (http://www.biocatalogue.org/) provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Services in the BioCatalogue can be described and searched in multiple ways based upon their technical types, bioinformatics categories, user tags, service providers or data inputs and outputs. They are also subject to constant monitoring, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. The system is accessible via a human-readable Web 2.0-style interface and a programmatic Web Service interface. The BioCatalogue follows a community approach in which all services can be registered, browsed and incrementally documented with annotations by any member of the scientific community.
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A new bioinformatics analysis tools framework at EMBL-EBI.
Nucleic Acids Res.
PUBLISHED: 05-03-2010
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The EMBL-EBI provides access to various mainstream sequence analysis applications. These include sequence similarity search services such as BLAST, FASTA, InterProScan and multiple sequence alignment tools such as ClustalW, T-Coffee and MUSCLE. Through the sequence similarity search services, the users can search mainstream sequence databases such as EMBL-Bank and UniProt, and more than 2000 completed genomes and proteomes. We present here a new framework aimed at both novice as well as expert users that exposes novel methods of obtaining annotations and visualizing sequence analysis results through one uniform and consistent interface. These services are available over the web and via Web Services interfaces for users who require systematic access or want to interface with customized pipe-lines and workflows using common programming languages. The framework features novel result visualizations and integration of domain and functional predictions for protein database searches. It is available at http://www.ebi.ac.uk/Tools/sss for sequence similarity searches and at http://www.ebi.ac.uk/Tools/msa for multiple sequence alignments.
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Hepatitis C virus recurrence after liver transplantation: analysis of factors related to sustained viral response.
Transplant. Proc.
PUBLISHED: 03-23-2010
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To determine the efficacy and safety of pegylated interferon (peg-IFN) plus ribavirin to treat hepatitis C virus (HCV) recurrence, analyzing possible factors associated with sustained viral responses (SVR).
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Fast and efficient searching of biological data resources--using EB-eye.
Brief. Bioinformatics
PUBLISHED: 02-11-2010
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The EB-eye is a fast and efficient search engine that provides easy and uniform access to the biological data resources hosted at the EMBL-EBI. Currently, users can access information from more than 62 distinct datasets covering some 400 million entries. The data resources represented in the EB-eye include: nucleotide and protein sequences at both the genomic and proteomic levels, structures ranging from chemicals to macro-molecular complexes, gene-expression experiments, binary level molecular interactions as well as reaction maps and pathway models, functional classifications, biological ontologies, and comprehensive literature libraries covering the biomedical sciences and related intellectual property. The EB-eye can be accessed over the web or programmatically using a SOAP Web Services interface. This allows its search and retrieval capabilities to be exploited in workflows and analytical pipe-lines. The EB-eye is a novel alternative to existing biological search and retrieval engines. In this article we describe in detail how to exploit its powerful capabilities.
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Periodontal treatment during pregnancy did not reduce the occurrence of poor pregnancy outcomes.
Evid Based Dent
PUBLISHED: 12-22-2009
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This was a randomised controlled trial (RCT).
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Improvements to services at the European Nucleotide Archive.
Nucleic Acids Res.
PUBLISHED: 11-11-2009
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The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is Europes primary nucleotide sequence archival resource, safeguarding open nucleotide data access, engaging in worldwide collaborative data exchange and integrating with the scientific publication process. ENA has made significant contributions to the collaborative nucleotide archival arena as an active proponent of extending the traditional collaboration to cover capillary and next-generation sequencing information. We have continued to co-develop data and metadata representation formats with our collaborators for both data exchange and public data dissemination. In addition to the DDBJ/EMBL/GenBank feature table format, we share metadata formats for capillary and next-generation sequencing traces and are using and contributing to the NCBI SRA Toolkit for the long-term storage of the next-generation sequence traces. During the course of 2009, ENA has significantly improved sequence submission, search and access functionalities provided at EMBL-EBI. In this article, we briefly describe the content and scope of our archive and introduce major improvements to our services.
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Non-redundant patent sequence databases with value-added annotations at two levels.
Nucleic Acids Res.
PUBLISHED: 11-01-2009
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The European Bioinformatics Institute (EMBL-EBI) provides public access to patent data, including abstracts, chemical compounds and sequences. Sequences can appear multiple times due to the filing of the same invention with multiple patent offices, or the use of the same sequence by different inventors in different contexts. Information relating to the source invention may be incomplete, and biological information available in patent documents elsewhere may not be reflected in the annotation of the sequence. Search and analysis of these data have become increasingly challenging for both the scientific and intellectual-property communities. Here, we report a collection of non-redundant patent sequence databases, which cover the EMBL-Bank nucleotides patent class and the patent protein databases and contain value-added annotations from patent documents. The databases were created at two levels by the use of sequence MD5 checksums. Sequences within a level-1 cluster are 100% identical over their whole length. Level-2 clusters were defined by sub-grouping level-1 clusters based on patent family information. Value-added annotations, such as publication number corrections, earliest publication dates and feature collations, significantly enhance the quality of the data, allowing for better tracking and cross-referencing. The databases are available format: http://www.ebi.ac.uk/patentdata/nr/.
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IPD--the Immuno Polymorphism Database.
Nucleic Acids Res.
PUBLISHED: 10-29-2009
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The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) is a set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors, IPD-MHC, is a database of sequences of the Major Histocompatibility Complex of different species; IPD-human platelet antigens, alloantigens expressed only on platelets and IPD-ESTDAB, which provides access to the European Searchable Tumour cell-line database, a cell bank of immunologically characterised melanoma cell lines. The data is currently available online from the website and ftp directory.
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Contextual effects in the occurrence of periodontal attachment loss and necrotizing gingival lesions among adolescents.
Eur. J. Oral Sci.
PUBLISHED: 09-18-2009
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The aim of this study was to assess and quantify the random effects resulting from clustering in the following individual-level periodontal outcomes: presence of clinical attachment loss of > or = 1 mm (CAL1), presence of clinical attachment loss of > or = 3 mm (CAL3), and presence of necrotizing ulcerative gingivitis (NUG); or in the following class-level periodontal outcomes: number of students with CAL1, number of students with CAL3, and number of students with NUG. Mixed-effects logistic regression analysis was used to model these outcomes among 9,162 adolescents in 310 classes in 98 schools spread over 20 communes in the Province of Santiago, Chile, who had been examined for clinical attachment level and NUG, and had completed questionnaires on oral health-related behaviors. The results of all six analyses demonstrated statistically significant random effects, which in all analyses were particularly related to the schools, whereas the class effects were smaller and the commune random effects were almost negligible. The random effects were quantified using the median odds ratio (MOR), and the class-level MOR ranged between 1.05 and 1.51, whereas the school-level MOR values ranged from 2.07 to 2.39. The results of the study demonstrate the potential of the application of multilevel modeling to periodontal epidemiologic data, over and beyond the conventional use of the technique to account for the intrinsic sites-teeth-subject hierarchy in periodontal data.
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[Recombinant activated factor VII for perioperative bleeding].
Rev Med Chil
PUBLISHED: 09-04-2009
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Recombinant activated factor VII (rFVIIa) is a new haemostatic drug, originally used for the treatment of patients with hemophilia A and B. At the present time it is used for other bleeding conditions such as the perioperative period. When used prophylactically there is a reduction in the number of bleeding episodes but no changes in the need for blood transfusion or other blood products. The adverse effects are arterial or venous thromboembolic events that are mostly related to the severity of the underlying disease of the patient and the concurrent administration of other haemostatic agents, rather than the use of rFVIIa. Its use is recommended when there is a persistent bleeding after the reposition of blood products and when surgical causes of bleeding have been discarded. The cost of the medication should also be considered before its use.
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Transient recovery in a rat model of familial amyotrophic lateral sclerosis after transplantation of motor neurons derived from mouse embryonic stem cells.
Cell Transplant
PUBLISHED: 08-05-2009
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Embryonic stem (ES) cells can be induced to differentiate into motor neurons (MN). Animal models resembling MN degeneration and paralysis observed in familial amyotrophic lateral sclerosis (ALS) have been previously reported. In this work, we aimed to investigate whether transplanted MN could prevent motor deterioration in transgenic rats expressing a mutant form of human superoxide dismutase 1 (hSOD1(G93A)) associated with inherited ALS. Mouse ES cells were differentiated to neurons that express green fluorescent protein (GFP) under the promoter of the MN-specific gene hb9, as well as molecular markers indicative of MN identity. Cells were grafted into the lumbar spinal cord of adult wild-type (WT) or hSOD1(G93A) rats at 10 weeks of age, when transgenic animals are presymptomatic. Grafted cells with MN phenotype can survive for at least 1 week in hSOD1(G93A) animals. To quantitatively evaluate motor performance of WT and transgenic rats, we carried out weekly rotarod tests starting when the animals were 14 weeks old. Sham and grafted WT animals showed no decline in their ability to sustain themselves on the rotating rod. In contrast, sham hSOD1(G93A) rats decreased in motor performance from week 16 onwards, reaching paralysis by week 19 of age. In grafted transgenic animals, there was a significant improvement in rotarod competence at weeks 16 and 17 when compared to sham hSOD1(G93A). However, in the following weeks, transplanted hSOD1(G93A) rats showed motor deterioration and eventually exhibited paralysis by week 19. At end-stage, we found only a few endogenous MN in sham and grafted hSOD1(G93A) rats by cresyl violet staining; no choline acetyl transferase-positive nor GFP-positive MN were present in grafted transgenic subjects. In contrast, WT rats analyzed at the same age possessed grafted GFP-positive MN in their spinal cords. These results strongly suggest that the transgenic hSOD1(G93A) environment is detrimental to grafted MN in the long term.
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Mobile phone-based telemedicine system for the home follow-up of patients undergoing ambulatory surgery.
Telemed J E Health
PUBLISHED: 07-02-2009
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A pilot study was done to address the efficacy of a General Packet Radio Service mobile phone-based telemedicine system used to improve follow-up after ambulatory surgery. The method involves sending images of surgical wounds or other areas from the patients home, to assess local complications and avoid unnecessary hospital visits. Ninety-six (N = 96) patients were enrolled in the study. The phone used was a Nokia 6600, which provides images in Joint Photographic Experts Group format. These images were sent via e-mail and visualized on a standard 17-inch screen of a personal computer. After the follow-up period, self-reported patient satisfaction was assessed by analyzing the replies to a 9-item questionnaire. Thirty of the 96 patients (31.3%) reported local problems including: hematoma in 20 (66.7%) patients, surgical bandage blood-stained in 7 (23.3%), exudates in 1 (3.3%), allergic skin reactions in 1 (3.3%), and bandage too tight in 1 (3.3%). In total, 225 photographs were evaluated by 3 physicians. In all cases, it was possible to identify and assess the postoperative problem with consensus among the 3 physicians. Images served to resolve patients concerns in 20 individuals (66.7%). In 10 patients (33.3%), concerns were satisfied but it was suggested that follow-up images be sent in the following days. Only 1 patient (3.3%) was asked to visit the hospital. The telemedicine system proposed increases the efficiency of home follow-up to ambulatory surgery, avoids unnecessary hospital visits, and clearly improves patient satisfaction.
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Generation of 4.3 fs, 1 mJ laser pulses via compression of circularly polarized pulses in a gas-filled hollow-core fiber.
Opt Lett
PUBLISHED: 05-19-2009
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We report the generation of 4.3 fs, 1 mJ pulses at 1 kHz using a hollow-core fiber compressor seeded with circularly polarized laser pulses. We observe up to 30% more energy throughput compared to the case of linearly polarized laser input, together with significantly improved output spectral stability. Seeding with circularly polarized pulses proves to be an effective approach for high-energy operation of the hollow-fiber compression technique.
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JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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