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Find video protocols related to scientific articles indexed in Pubmed.
Comparison of 26 sphingomonad genomes reveals diverse environmental adaptations and biodegradative capabilities.
Appl. Environ. Microbiol.
PUBLISHED: 04-05-2013
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Sphingomonads comprise a physiologically versatile group within the Alphaproteobacteria that includes strains of interest for biotechnology, human health, and environmental nutrient cycling. In this study, we compared 26 sphingomonad genome sequences to gain insight into their ecology, metabolic versatility, and environmental adaptations. Our multilocus phylogenetic and average amino acid identity (AAI) analyses confirm that Sphingomonas, Sphingobium, Sphingopyxis, and Novosphingobium are well-resolved monophyletic groups with the exception of Sphingomonas sp. strain SKA58, which we propose belongs to the genus Sphingobium. Our pan-genomic analysis of sphingomonads reveals numerous species-specific open reading frames (ORFs) but few signatures of genus-specific cores. The organization and coding potential of the sphingomonad genomes appear to be highly variable, and plasmid-mediated gene transfer and chromosome-plasmid recombination, together with prophage- and transposon-mediated rearrangements, appear to play prominent roles in the genome evolution of this group. We find that many of the sphingomonad genomes encode numerous oxygenases and glycoside hydrolases, which are likely responsible for their ability to degrade various recalcitrant aromatic compounds and polysaccharides, respectively. Many of these enzymes are encoded on megaplasmids, suggesting that they may be readily transferred between species. We also identified enzymes putatively used for the catabolism of sulfonate and nitroaromatic compounds in many of the genomes, suggesting that plant-based compounds or chemical contaminants may be sources of nitrogen and sulfur. Many of these sphingomonads appear to be adapted to oligotrophic environments, but several contain genomic features indicative of host associations. Our work provides a basis for understanding the ecological strategies employed by sphingomonads and their role in environmental nutrient cycling.
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A phylogenetic analysis of the phylum Fibrobacteres.
Syst. Appl. Microbiol.
PUBLISHED: 04-03-2013
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Members of the phylum Fibrobacteres are highly efficient cellulolytic bacteria, best known for their role in rumen function and as potential sources of novel enzymes for bioenergy applications. Despite being key members of ruminants and other digestive microbial communities, our knowledge of this phylum remains incomplete, as much of our understanding is focused on two recognized species, Fibrobacter succinogenes and F. intestinalis. As a result, we lack insights regarding the environmental niche, host range, and phylogenetic organization of this phylum. Here, we analyzed over 1000 16S rRNA Fibrobacteres sequences available from public databases to establish a phylogenetic framework for this phylum. We identify both species- and genus-level clades that are suggestive of previously unknown taxonomic relationships between Fibrobacteres in addition to their putative lifestyles as host-associated or free-living. Our results shed light on this poorly understood phylum and will be useful for elucidating the function, distribution, and diversity of these bacteria in their niches.
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Evolution of Sindbis virus with a low-methionine-resistant phenotype is dependent both on a pre-existing mutation and on the methionine concentration in the medium.
PLoS ONE
PUBLISHED: 02-27-2013
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SVlm21 is a mutant of Sindbis virus which was isolated by serial passage of virus in mosquito cells maintained in low-methionine medium; it therefore has a low-methionine-resistant (LMR) phenotype. This phenotype requires mutations at nts 319 and 321; these mutations result in Arg to Leu and Ser to Cys changes at positions 87 and 88 respectively in the viral methyl transferase, nsP1. To better understand the genesis of SVlm21, we carried out serial passages of viruses having only one of these amino acid changes, but in mosquito cells maintained in normal methionine-medium. Whether the passage was begun with SV319 or with SV321, the dominant virus population which emerged always acquired the second SVlm21 amino acid change. However, when the passage was begun with virus having neither the nt 319 or the nt321 mutation, even after many passages neither of these mutations was seen in the passaged virus population. Virus with the LMR phenotype emerged earlier when the virus encoded a wild-type RDRP (passage 4) rather than the mutant RDRP encoded by SVpzf (passage 7). When the methionine concentration in the medium of mosquito cells was increased to 250 µM, more than 20 passages were required until the LMR phenotype predominated. Competition experiments were carried out to compare the relative fitness of SVlm21, SVwt, SV319 and SV321 to each other. Our results indicated that SVlm21 was dominant to SVwt, as well as to both SV319 and SV321. However, SV319 and SV321 were able to co-exist with SVwt implying that in these mixed infection the presence of SVwt inhibited the emergence of SVlm21. Finally, our experiments highlight how a virus population by mutation and selection can adapt to the intracellular concentration of a simple metabolite, S-adenosylmethionine.
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Patients with COPD with higher levels of anxiety are more physically active.
Chest
PUBLISHED: 02-02-2013
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Physical activity (PA) has been found to be an excellent predictor of mortality beyond traditional measures in COPD. We aimed to determine the association between depression and anxiety with accelerometry-based PA in patients with COPD.
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Effect of black tea extract on herpes simplex virus-1 infection of cultured cells.
BMC Complement Altern Med
PUBLISHED: 01-16-2013
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The purpose of this investigation was to determine if black tea extract (BTE), consisting primarily of flavanol compounds called theaflavins, could inhibit herpes simplex virus type-1 (HSV-1) infection in cultured A549 (human epithelial) and Vero cells.
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Lung bullae with air-fluid levels: what is the appropriate therapeutic approach?
Respir Care
PUBLISHED: 10-13-2011
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Air-fluid levels within emphysematous lung bullae are a relatively uncommon occurrence in patients with preexisting bullous disease, and are not commonly reported. We report 2 cases of new onset air-fluid levels in patients with underlying bullous disease with substantially different clinical presentations but with clinical improvement after medical therapy only.
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Genome sequence of Streptomyces griseus strain XylebKG-1, an ambrosia beetle-associated actinomycete.
J. Bacteriol.
PUBLISHED: 04-01-2011
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Streptomyces griseus strain XylebKG-1 is an insect-associated strain of the well-studied actinobacterial species S. griseus. Here, we present the genome of XylebKG-1 and discuss its similarity to the genome of S. griseus subsp. griseus NBRC13350. XylebKG-1 was isolated from the fungus-cultivating Xyleborinus saxesenii system. Given its similarity to free-living S. griseus subsp. griseus NBRC13350, comparative genomics will elucidate critical components of bacterial interactions with insects.
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The role of anti-infectives in the treatment of refractory asthma.
Ther Adv Respir Dis
PUBLISHED: 04-01-2011
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Refractory asthma not only has a significant effect on quality of life, but also imposes an economic burden on society. Increasing evidence suggests that there is a pathophysiologic interaction between infection and allergic disease in patients with severe or refractory asthma. Therapeutic trials of macrolides and azoles are being utilized in some patients with refractory asthma who fail to respond to standard therapy. In this article we review the definition of refractory asthma and the potential pathophysiologic interactions between infection and allergic disease. Emerging data suggest that microorganisms and their byproducts may be a therapeutic target in the therapy of patients with severe or refractory asthma.
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Monitoring brain oxygen saturation during coronary bypass surgery improves outcomes in diabetic patients: a post hoc analysis.
Heart Surg Forum
PUBLISHED: 02-25-2011
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Having previously demonstrated in a prospective study of 200 coronary artery bypass (CAB) patients that by using the brain as an index organ, interventions to improve cerebral oxygenation would have systemic outcome benefits, we undertook a post hoc analysis of the diabetic subset (n = 57) of the overall study group to determine whether the outcomes of these patients were similarly improved.
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Integrated management strategies for chronic obstructive pulmonary disease.
J Multidiscip Healthc
PUBLISHED: 09-18-2010
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Chronic obstructive pulmonary disease (COPD) remains the fourth leading cause of death, is associated with significant morbidity and places a substantial time and cost burden on the health care system. Unfortunately, treatment for COPD remains underutilized and continues to focus on the acute care of complications. The chronic care model (CCM) shifts this focus from the acute management of symptoms and complications to the prevention and optimal management of the chronic disease. This model utilizes resources from the community and the health care system and emphasizes self-management, provides comprehensive clinic support, and implements evidence-based guidelines and technology into clinical practice to ensure delivery of the highest quality of care. The goal of this review is to use a case-based approach to provide practical information about how integrated care using the CCM can be applied to the clinical care of a complex patient with COPD, shifting the management goals for COPD from reactive to proactive and ultimately improving outcomes.
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hnRNP A1 interacts with the genomic and subgenomic RNA promoters of Sindbis virus and is required for the synthesis of G and SG RNA.
J. Biomed. Sci.
PUBLISHED: 04-29-2010
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Sindbis virus (SV) is the prototype of alphaviruses which are a group of widely distributed human and animal pathogens. Heterogeneous nuclear ribonucleoprotein (hnRNP) A1 is an RNA-binding protein that shuttles between the nucleus and the cytoplasm. Our recent studies found that hnRNP A1 relocates from nucleus to cytoplasm in Sindbis virus (SV)-infected cells. hnRNP A1 binds to the 5 UTR of SV RNA and facilitates the viral RNA replication and translation.
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An insect herbivore microbiome with high plant biomass-degrading capacity.
PLoS Genet.
PUBLISHED: 04-13-2010
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Herbivores can gain indirect access to recalcitrant carbon present in plant cell walls through symbiotic associations with lignocellulolytic microbes. A paradigmatic example is the leaf-cutter ant (Tribe: Attini), which uses fresh leaves to cultivate a fungus for food in specialized gardens. Using a combination of sugar composition analyses, metagenomics, and whole-genome sequencing, we reveal that the fungus garden microbiome of leaf-cutter ants is composed of a diverse community of bacteria with high plant biomass-degrading capacity. Comparison of this microbiomes predicted carbohydrate-degrading enzyme profile with other metagenomes shows closest similarity to the bovine rumen, indicating evolutionary convergence of plant biomass degrading potential between two important herbivorous animals. Genomic and physiological characterization of two dominant bacteria in the fungus garden microbiome provides evidence of their capacity to degrade cellulose. Given the recent interest in cellulosic biofuels, understanding how large-scale and rapid plant biomass degradation occurs in a highly evolved insect herbivore is of particular relevance for bioenergy.
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Glycemic control among older adult hematopoietic cell transplant recipients.
J Gerontol Nurs
PUBLISHED: 02-05-2010
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Adults age 55 and older with hematological malignancies who require hematopoietic cell transplantation (HCT) for survival are at risk for a number of nonmalignancy-related, potentially life-threatening outcomes, often due to suboptimal immune function. Evidence is emerging regarding how abnormal glycemic levels-newly termed malglycemia-impair cells of the immune system. Further, older adult HCT recipients appear highly susceptible to malglycemic states, particularly hyperglycemia, due to treatment regimens, nutritional imbalances, states of immobility, and stress, all coupled with the natural aging process. Patients with preexisting diabetes may be at further risk for malglycemic states. The growing number of older adults receiving HCT will substantially increase the likelihood nurses will have to provide care to HCT survivors. Therefore, it is important nurses in all practice settings have an understanding of the short-and long-term effects of glycemic status on immune function.
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The graduate record examination: help or hindrance in nursing graduate school admissions?
J Prof Nurs
PUBLISHED: 11-28-2009
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Do graduate record examination (GRE) scores serve as strong predictors of student success in graduate school in nursing, and if so, is the extent to which they may indicate success outweighed by their perceived role as a barrier to application to graduate school in nursing? Academic ability, defined as cumulative grade point average (GPA), was used as the outcome indicator for success in graduate school and was compared with admission GRE scores for 217 students admitted to graduate programs at the University of Washington School of Nursing over a 1-year period. The GRE presented a large barrier to application that far outweighed the limited benefit of predicting 5% to 8% of explained variance in GPA.
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Tri-trophic linkages in disease: pathogen transmission to rainbow trout through stonefly prey.
Environ. Entomol.
PUBLISHED: 08-20-2009
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Relationships between macroinvertebrates and microorganisms in aquatic environments are only poorly understood despite the fact that many aquatic macroinvertebrates feed on microbial biofilms during some life stage. Better understanding of trophic interactions between microbial biofilms, macroinvertebrates, and fish may also help control fish diseases and loss of natural resources. It has also been suggested that pollution, habitat fragmentation, and poor water quality may contribute to increased pathogenesis and mortality in fish. Increased disease incidence is difficult to assess, however, in part because of the complexity of pathogen transmission dynamics. Several environmental pathogens exist whose reservoir(s) and means of transmission remain poorly understood, highlighting the need to study pathogen ecology and interactions with organisms other than susceptible hosts. Aeromonas salmonicida is rarely isolated from freshwater sediments. However, stonefly nymphs were found to frequently harbor A. salmonicida and were shown to preferentially feed on the bacterium. Rainbow trout juveniles were presented with different feeding regimes to determine the transmission capacity of nymphs, and all fish fed stoneflies harboring A. salmonicida expressed symptoms of disease. Although current rates of furunculosis in freshwater ecosystems are unknown, trout primarily feed on stoneflies when water oxygen levels are high and temperatures are low (winter months), which is presumed to correspond to high resistance to the pathogen. Given that furunculosis is associated with physiological stress and higher water temperatures, its natural incidence may change in response to global or regional climatological effects.
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The effects of a computer-tailored message on secondary prevention in type 2 diabetes: a randomized trial.
Popul Health Manag
PUBLISHED: 08-12-2009
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The purpose of this study was to test the effect of computer-generated, tailored feedback on the quality of chronic disease management for type 2 diabetes when provided to a patient prior to a scheduled physician visit. A stand-alone computer application was developed to provide tailored feedback aimed at empowering patients to engage more actively in their diabetes management. Adults with type 2 diabetes (n = 203) were randomly assigned to groups receiving either efficacy (positive) messages (n = 68), risk (negative) messages (n = 67), or to a delayed treatment control group (n = 68). The intervention was delivered prior to a patients visit with his or her physician so that patients would have the opportunity to discuss the messages at the clinical appointment. Although there were no significant differences in the percentage of participants who received intensified care or routine tests between the control and intervention groups, we learned that more directive messaging may be needed to help patients effectively manage their diabetes. Patients may benefit from directive feedback, providing them with specific questions to ask their physician that can lead to improved care, rather than receiving general and educational informational messages.
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Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana flood-plain sediment and forest soil.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 06-19-2009
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Three Gram-negative, rod-shaped, non-spore-forming eubacterial strains were isolated in western Montana, USA, and subjected to taxonomic studies. Strains NWG-II14(T) and NWER-II11(T) were isolated from hyporheic sediments of a large alluvial flood plain, whereas strain G-1(T) was isolated from a conifer forest soil. On the basis of 16S rRNA gene sequence similarity, strains NWG-II14(T), NWER-II11(T) and G-1(T) were shown to belong to the family Sphingobacteriaceae and are most closely related to various species of the genus Pedobacter. The results of molecular, physiological and biochemical tests allowed genotypic and phenotypic differentiation of these three strains from 23 Pedobacter species with validly published names. The three isolates therefore represent novel species, for which the names Pedobacter nyackensis sp. nov. (type strain NWG-II14(T) =DSM 19625(T) =LMG 24260(T)), Pedobacter alluvionis sp. nov. (type strain NWER-II11(T) =DSM 19624(T) =LMG 24258(T)) and Pedobacter borealis sp. nov. (type strain G-1(T) =DSM 19626(T) =LMG 24259(T)) are proposed.
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Evaluation of withdrawal of maintenance tiotropium in COPD.
Respir Med
PUBLISHED: 05-14-2009
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In chronic diseases such as chronic obstructive pulmonary disease (COPD), patients may not perceive all of the benefits of drug therapy until withdrawal. Thus, we evaluated the effect of tiotropium withdrawal on clinical variables.
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Inhibition of herpes simplex virus type 1 with the modified green tea polyphenol palmitoyl-epigallocatechin gallate.
Food Chem. Toxicol.
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Green tea polyphenol epigallocatechin gallate (EGCG) is a strong antioxidant that has previously been shown to reduce the number of plaques in HIV-infected cultured cells. Modified EGCG, palmitoyl-EGCG (p-EGCG), is of interest as a topical antiviral agent for herpes simplex virus (HSV-1) infections. This study evaluated the effect of p-EGCG on HSV-infected Vero cells. Results of cell viability and cell proliferation assays indicate that p-EGCG is not toxic to cultured Vero cells and show that modification of the green tea polyphenol epigallocatechin gallate (EGCG) with palmitate increases the effectiveness of EGCG as an antiviral agent. Furthermore, p-EGCG is a more potent inhibitor of herpes simplex virus 1 (HSV-1) than EGCG and can be topically applied to skin, one of the primary tissues infected by HSV. Viral binding assay, plaque forming assay, PCR, real-time PCR, and fluorescence microscopy were used to demonstrate that p-EGCG concentrations of 50 ?M and higher block the production of infectious HSV-1 particles. p-EGCG was found to inhibit HSV-1 adsorption to Vero cells. Thus, p-EGCG may provide a novel treatment for HSV-1 infections.
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Management of asthma during pregnancy.
Ther Adv Respir Dis
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Asthma is an inflammatory lung condition that is the most common chronic disease affecting pregnancy. The changes in pulmonary physiology during pregnancy include increased minute ventilation, decreased functional residual capacity, increased mucus production, and airway mucosa hyperemia and edema. Pregnancy is also associated with a physiological suppression of the immune system. Many studies have described the heterogeneous immune system response in women with asthma during pregnancy, which partly explains why asthma has been shown to worsen, improve, or remain stable in equal proportions of women during pregnancy. Asthma may be associated with poor maternal and fetal outcomes. However, better maternal and fetal outcomes are observed with better asthma control. Asthma controller medications are generally thought to be safe during pregnancy, but limited data are available for some of the medicines. Newer medications like omalizumab open avenues for the treatment of asthma, but also pose a challenge, as there is limited experience with their use. Therefore, a multidisciplinary approach, including obstetricians, asthma specialists, and pediatricians should collaborate with the patient to carefully weigh the risks and benefits to determine an optimal management plan for each individual patient. The aim of this review article is to summarize the most recent literature about the immunological changes that occur during pregnancy, physiological and clinical implications of asthma on pregnancy, and asthma management and medication use in pregnant women.
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Effect of a primary care continuing education program on clinical practice of chronic obstructive pulmonary disease: translating theory into practice.
Mayo Clin. Proc.
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To describe the development and implementation process and assess the effect on self-reported clinical practice changes of a multidisciplinary, collaborative, interactive continuing medical education (CME)/continuing education (CE) program on chronic obstructive pulmonary disease (COPD).
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Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens.
ISME J
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Herbivores gain access to nutrients stored in plant biomass largely by harnessing the metabolic activities of microbes. Leaf-cutter ants of the genus Atta are a hallmark example; these dominant neotropical herbivores cultivate symbiotic fungus gardens on large quantities of fresh plant forage. As the external digestive system of the ants, fungus gardens facilitate the production and sustenance of millions of workers. Using metagenomic and metaproteomic techniques, we characterize the bacterial diversity and physiological potential of fungus gardens from two species of Atta. Our analysis of over 1.2?Gbp of community metagenomic sequence and three 16S pyrotag libraries reveals that in addition to harboring the dominant fungal crop, these ecosystems contain abundant populations of Enterobacteriaceae, including the genera Enterobacter, Pantoea, Klebsiella, Citrobacter and Escherichia. We show that these bacterial communities possess genes associated with lignocellulose degradation and diverse biosynthetic pathways, suggesting that they play a role in nutrient cycling by converting the nitrogen-poor forage of the ants into B-vitamins, amino acids and other cellular components. Our metaproteomic analysis confirms that bacterial glycosyl hydrolases and proteins with putative biosynthetic functions are produced in both field-collected and laboratory-reared colonies. These results are consistent with the hypothesis that fungus gardens are specialized fungus-bacteria communities that convert plant material into energy for their ant hosts. Together with recent investigations into the microbial symbionts of vertebrates, our work underscores the importance of microbial communities in the ecology and evolution of herbivorous metazoans.
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Parents and Child Health Professionals Attitudes Towards Dietary Interventions for Children with Autism Spectrum Disorders.
J Autism Dev Disord
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Parents of children with autism spectrum disorders (ASD) use a wide range of interventions including poorly evidenced dietary interventions. To investigate parents and professionals experience of dietary interventions and attitudes towards a proposed trial to evaluate the gluten free casein free diet (GFCFD). Survey of UK parents of children with ASD, and professionals. 258 parents and 244 professionals participated. 83 % of children had received a range of dietary manipulations; three quarters of professionals have been asked for advice about GFCFD. Respondents identified an inadequate evidence base for dietary interventions in ASD and suggested modifications to a proposed trial design. Both parents and professionals supported the need for further evaluation of dietary interventions in ASD.
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What is Visualize?

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

How does it work?

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

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

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