1,720,995 research outputs found
The gut microbiome in intestinal diseases: and the infrastructure to investigate it
Get PDFThe gut microbiota – the collection of micro-organisms in the gut – can best be viewed as a newly discovered organ, defined as a group of adjacent cells with a function. The gut microbiota, in fact, fulfils a number of important functions: it digests our food, synthesizes amino acids, trains our immune system, and helps resist gastrointestinal infections. The composition and functions of the gut microbiota can therefore have a large impact on our health. In this thesis the role of the gut microbiota in intestinal disorders is systematically analysed using DNA sequencing techniques. The intestinal disease we focus on most is inflammatory bowel disease (IBD), a recurrent remittent inflammatory disease of the gut that comprises Crohn’s disease and ulcerative colitis. However, irritable bowel syndrome (IBS), traditionally characterized as a functional disorder consisting of a combination of gut complaints, and bacterial gastroenteritis, a bacterial infection often leading to diarrhoea, were also investigated. One of the most important discoveries of this thesis is the relationship between use of proton pump inhibitors (PPIs), one of most prescribed drugs in Europe and the United States, and the gut microbiota. PPIs work by reducing stomach acid, normally an important barrier to bacteria entering the intestinal tract, and we observed that bacteria normally found in the mouth were now present in the gut of PPI users. PPI users also have a more pro-inflammatory gut microbiota, showing a decrease in favourable butyrate-producing bacteria and an increase in the Enterobacteriaceae that can produce toxin. As a consequence, PPI users are more susceptible to both bacterial gastroenteritis, e.g. that caused by Salmonella spp, and to Clostridium difficile infections. After these results were published in 2016, government officials began to question whether PPIs should remain available as over-the-counter drugs in grocery stores, and this debate was still ongoing as of the writing of this thesis. This discovery received a lot of media attention in the written press: De Telegraaf, Reuters and Scientific American, on the radio: RTV Noord and BNR Nieuwsradio and on the television show Kassa. Another important discovery, the gut metagenomes of IBD and IBS are compared to those of population controls and are described in great detail using the metagenomic sequencing technique. With this technique, we were able to both determine the composition of the gut microbiome and infer its function, strain diversity, the level of virulence and the level of antibiotic resistance, leading to thousands of new results. We also present a computer algorithm that uses gut metagenomes to reliably distinguish IBD from IBS (AUC=0.93), performing much better than faecal calprotectin, which is currently used as a marker to distinguish between the two conditions. In the future, a gut microbiome-based test could reduce the number of painful and costly colonoscopies. This discovery was published in the renowned journal Science Translation Medicine and the Dutch television programme Editie NL on RTL4 discussed its importance for patients with irritable bowel syndrome. The results of this thesis allow us to better understand intestinal disesases and to work towards microbiota-based diagnostics and therapeutics
The gut microbiome in intestinal diseases:and the infrastructure to investigate it
Get PDFThe gut microbiota – the collection of micro-organisms in the gut – can best be viewed as a newly discovered organ, defined as a group of adjacent cells with a function. The gut microbiota, in fact, fulfils a number of important functions: it digests our food, synthesizes amino acids, trains our immune system, and helps resist gastrointestinal infections. The composition and functions of the gut microbiota can therefore have a large impact on our health. In this thesis the role of the gut microbiota in intestinal disorders is systematically analysed using DNA sequencing techniques. The intestinal disease we focus on most is inflammatory bowel disease (IBD), a recurrent remittent inflammatory disease of the gut that comprises Crohn’s disease and ulcerative colitis. However, irritable bowel syndrome (IBS), traditionally characterized as a functional disorder consisting of a combination of gut complaints, and bacterial gastroenteritis, a bacterial infection often leading to diarrhoea, were also investigated. One of the most important discoveries of this thesis is the relationship between use of proton pump inhibitors (PPIs), one of most prescribed drugs in Europe and the United States, and the gut microbiota. PPIs work by reducing stomach acid, normally an important barrier to bacteria entering the intestinal tract, and we observed that bacteria normally found in the mouth were now present in the gut of PPI users. PPI users also have a more pro-inflammatory gut microbiota, showing a decrease in favourable butyrate-producing bacteria and an increase in the Enterobacteriaceae that can produce toxin. As a consequence, PPI users are more susceptible to both bacterial gastroenteritis, e.g. that caused by Salmonella spp, and to Clostridium difficile infections. After these results were published in 2016, government officials began to question whether PPIs should remain available as over-the-counter drugs in grocery stores, and this debate was still ongoing as of the writing of this thesis. This discovery received a lot of media attention in the written press: De Telegraaf, Reuters and Scientific American, on the radio: RTV Noord and BNR Nieuwsradio and on the television show Kassa.Another important discovery, the gut metagenomes of IBD and IBS are compared to those of population controls and are described in great detail using the metagenomic sequencing technique. With this technique, we were able to both determine the composition of the gut microbiome and infer its function, strain diversity, the level of virulence and the level of antibiotic resistance, leading to thousands of new results. We also present a computer algorithm that uses gut metagenomes to reliably distinguish IBD from IBS (AUC=0.93), performing much better than faecal calprotectin, which is currently used as a marker to distinguish between the two conditions. In the future, a gut microbiome-based test could reduce the number of painful and costly colonoscopies. This discovery was published in the renowned journal Science Translation Medicine and the Dutch television programme Editie NL on RTL4 discussed its importance for patients with irritable bowel syndrome. The results of this thesis allow us to better understand intestinal disesases and to work towards microbiota-based diagnostics and therapeutics
The gut microbiome in intestinal diseases:and the infrastructure to investigate it
Get PDFThe gut microbiota – the collection of micro-organisms in the gut – can best be viewed as a newly discovered organ, defined as a group of adjacent cells with a function. The gut microbiota, in fact, fulfils a number of important functions: it digests our food, synthesizes amino acids, trains our immune system, and helps resist gastrointestinal infections. The composition and functions of the gut microbiota can therefore have a large impact on our health. In this thesis the role of the gut microbiota in intestinal disorders is systematically analysed using DNA sequencing techniques. The intestinal disease we focus on most is inflammatory bowel disease (IBD), a recurrent remittent inflammatory disease of the gut that comprises Crohn’s disease and ulcerative colitis. However, irritable bowel syndrome (IBS), traditionally characterized as a functional disorder consisting of a combination of gut complaints, and bacterial gastroenteritis, a bacterial infection often leading to diarrhoea, were also investigated. One of the most important discoveries of this thesis is the relationship between use of proton pump inhibitors (PPIs), one of most prescribed drugs in Europe and the United States, and the gut microbiota. PPIs work by reducing stomach acid, normally an important barrier to bacteria entering the intestinal tract, and we observed that bacteria normally found in the mouth were now present in the gut of PPI users. PPI users also have a more pro-inflammatory gut microbiota, showing a decrease in favourable butyrate-producing bacteria and an increase in the Enterobacteriaceae that can produce toxin. As a consequence, PPI users are more susceptible to both bacterial gastroenteritis, e.g. that caused by Salmonella spp, and to Clostridium difficile infections. After these results were published in 2016, government officials began to question whether PPIs should remain available as over-the-counter drugs in grocery stores, and this debate was still ongoing as of the writing of this thesis. This discovery received a lot of media attention in the written press: De Telegraaf, Reuters and Scientific American, on the radio: RTV Noord and BNR Nieuwsradio and on the television show Kassa.Another important discovery, the gut metagenomes of IBD and IBS are compared to those of population controls and are described in great detail using the metagenomic sequencing technique. With this technique, we were able to both determine the composition of the gut microbiome and infer its function, strain diversity, the level of virulence and the level of antibiotic resistance, leading to thousands of new results. We also present a computer algorithm that uses gut metagenomes to reliably distinguish IBD from IBS (AUC=0.93), performing much better than faecal calprotectin, which is currently used as a marker to distinguish between the two conditions. In the future, a gut microbiome-based test could reduce the number of painful and costly colonoscopies. This discovery was published in the renowned journal Science Translation Medicine and the Dutch television programme Editie NL on RTL4 discussed its importance for patients with irritable bowel syndrome. The results of this thesis allow us to better understand intestinal disesases and to work towards microbiota-based diagnostics and therapeutics
The gut microbiome in intestinal diseases:and the infrastructure to investigate it
Get PDFThe gut microbiota – the collection of micro-organisms in the gut – can best be viewed as a newly discovered organ, defined as a group of adjacent cells with a function. The gut microbiota, in fact, fulfils a number of important functions: it digests our food, synthesizes amino acids, trains our immune system, and helps resist gastrointestinal infections. The composition and functions of the gut microbiota can therefore have a large impact on our health. In this thesis the role of the gut microbiota in intestinal disorders is systematically analysed using DNA sequencing techniques. The intestinal disease we focus on most is inflammatory bowel disease (IBD), a recurrent remittent inflammatory disease of the gut that comprises Crohn’s disease and ulcerative colitis. However, irritable bowel syndrome (IBS), traditionally characterized as a functional disorder consisting of a combination of gut complaints, and bacterial gastroenteritis, a bacterial infection often leading to diarrhoea, were also investigated. One of the most important discoveries of this thesis is the relationship between use of proton pump inhibitors (PPIs), one of most prescribed drugs in Europe and the United States, and the gut microbiota. PPIs work by reducing stomach acid, normally an important barrier to bacteria entering the intestinal tract, and we observed that bacteria normally found in the mouth were now present in the gut of PPI users. PPI users also have a more pro-inflammatory gut microbiota, showing a decrease in favourable butyrate-producing bacteria and an increase in the Enterobacteriaceae that can produce toxin. As a consequence, PPI users are more susceptible to both bacterial gastroenteritis, e.g. that caused by Salmonella spp, and to Clostridium difficile infections. After these results were published in 2016, government officials began to question whether PPIs should remain available as over-the-counter drugs in grocery stores, and this debate was still ongoing as of the writing of this thesis. This discovery received a lot of media attention in the written press: De Telegraaf, Reuters and Scientific American, on the radio: RTV Noord and BNR Nieuwsradio and on the television show Kassa.Another important discovery, the gut metagenomes of IBD and IBS are compared to those of population controls and are described in great detail using the metagenomic sequencing technique. With this technique, we were able to both determine the composition of the gut microbiome and infer its function, strain diversity, the level of virulence and the level of antibiotic resistance, leading to thousands of new results. We also present a computer algorithm that uses gut metagenomes to reliably distinguish IBD from IBS (AUC=0.93), performing much better than faecal calprotectin, which is currently used as a marker to distinguish between the two conditions. In the future, a gut microbiome-based test could reduce the number of painful and costly colonoscopies. This discovery was published in the renowned journal Science Translation Medicine and the Dutch television programme Editie NL on RTL4 discussed its importance for patients with irritable bowel syndrome. The results of this thesis allow us to better understand intestinal disesases and to work towards microbiota-based diagnostics and therapeutics
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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