An automated identification and analysis of ontological terms in gastrointestinal diseases and nutrition-related literature provides useful insights

With an unprecedented growth in the biomedical literature, keeping up to date with the new developments presents an immense challenge. Publications are often studied in isolation of the established literature, with interpretation being subjective and often introducing human bias. With ontology-driven annotation of biomedical data gaining popularity in recent years and online databases offering metatags with rich textual information, it is now possible to automatically text-mine ontological terms and complement the laborious task of manual management, interpretation, and analysis of the accumulated literature with downstream statistical analysis. In this paper, we have formulated an automated workflow through which we have identified ontological information, including nutrition-related terms in PubMed abstracts (from 1991 to 2016) for two main types of Inflammatory Bowel Diseases: Crohn’s Disease and Ulcerative Colitis; and two other gastrointestinal (GI) diseases, namely, Coeliac Disease and Irritable Bowel Syndrome. Our analysis reveals unique clustering patterns as well as spatial and temporal trends inherent to the considered GI diseases in terms of literature that has been accumulated so far. Although automated interpretation cannot replace human judgement, the developed workflow shows promising results and can be a useful tool in systematic literature reviews. The workflow is available at https://github.com/KociOrges/pytag.

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An automated identification and analysis of ontological terms in gastrointestinal diseases and nutrition-related literature provides useful insights

10.7287/peerj.preprints.26869 ◽

2018 ◽

Author(s):

Orges Koci ◽

Michael Logan ◽

Vaios Svolos ◽

Richard K. Russell ◽

Konstantinos Gerasimidis ◽

...

Keyword(s):

Temporal Trends ◽

Gastrointestinal Diseases ◽

Biomedical Literature ◽

Biomedical Data ◽

Automated Identification ◽

Online Databases ◽

Bowel Diseases ◽

Inflammatory Bowel ◽

Irritable Bowel ◽

Spatial And Temporal Trends

With an unprecedented growth in the biomedical literature, keeping up to date with the new developments presents an immense challenge. Publications are often studied in isolation of the established literature, with interpretation being subjective and often introducing human bias. With ontology-driven annotation of biomedical data gaining popularity in recent years and online databases offering metatags with rich textual information, it is now possible to automatically text-mine ontological terms and complement the laborious task of manual management, interpretation, and analysis of the accumulated literature with downstream statistical analysis. In this paper, we have formulated an automated workflow through which we have identified ontological information, including nutrition-related terms in PubMed abstracts (from 1991 until 2016) for two main types of Inflammatory Bowel Diseases: Crohn's Disease and Ulcerative Colitis; and two other gastrointestinal diseases, namely, Coeliac Disease and Irritable Bowel Syndrome. Our analysis reveals unique clustering patterns as well as spatial and temporal trends inherent to the considered gastrointestinal diseases in terms of literature that has been accumulated so far. Although automated interpretation cannot replace human judgement, the developed workflow shows promising results and can be a useful tool in systematic literature reviews. The workflow is available at https://github.com/KociOrges/pytag .

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An automated identification and analysis of ontological terms in gastrointestinal diseases and nutrition-related literature provides useful insights

10.7287/peerj.preprints.26869v1 ◽

2018 ◽

Author(s):

Orges Koci ◽

Michael Logan ◽

Vaios Svolos ◽

Richard K. Russell ◽

Konstantinos Gerasimidis ◽

...

Keyword(s):

Temporal Trends ◽

Gastrointestinal Diseases ◽

Biomedical Literature ◽

Biomedical Data ◽

Automated Identification ◽

Online Databases ◽

Bowel Diseases ◽

Inflammatory Bowel ◽

Irritable Bowel ◽

Spatial And Temporal Trends

With an unprecedented growth in the biomedical literature, keeping up to date with the new developments presents an immense challenge. Publications are often studied in isolation of the established literature, with interpretation being subjective and often introducing human bias. With ontology-driven annotation of biomedical data gaining popularity in recent years and online databases offering metatags with rich textual information, it is now possible to automatically text-mine ontological terms and complement the laborious task of manual management, interpretation, and analysis of the accumulated literature with downstream statistical analysis. In this paper, we have formulated an automated workflow through which we have identified ontological information, including nutrition-related terms in PubMed abstracts (from 1991 until 2016) for two main types of Inflammatory Bowel Diseases: Crohn's Disease and Ulcerative Colitis; and two other gastrointestinal diseases, namely, Coeliac Disease and Irritable Bowel Syndrome. Our analysis reveals unique clustering patterns as well as spatial and temporal trends inherent to the considered gastrointestinal diseases in terms of literature that has been accumulated so far. Although automated interpretation cannot replace human judgement, the developed workflow shows promising results and can be a useful tool in systematic literature reviews. The workflow is available at https://github.com/KociOrges/pytag .

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The Placebo and Nocebo Responses in Clinical Trials in Inflammatory Bowel Diseases

Frontiers in Pharmacology ◽

10.3389/fphar.2021.641436 ◽

2021 ◽

Vol 12 ◽

Author(s):

Paul Enck ◽

Sibylle Klosterhalfen

Keyword(s):

Clinical Trials ◽

Inflammatory Bowel Diseases ◽

Placebo Response ◽

Gastrointestinal Diseases ◽

Nocebo Effect ◽

Bowel Diseases ◽

Inflammatory Bowel ◽

Maintenance Of Remission ◽

Irritable Bowel ◽

Meta Analyses

Placebo and nocebo responses are mostly discussed in clinical trials with functional bowel disorders. Much less has been investigated and is known in gastrointestinal diseases beyond irritable bowel syndrome (IBS), especially in inflammatory bowel diseases (IBD). For the purpose of this review, we screened the Journal of Interdisciplinary Placebo Studies (JIPS) database with approximately 4,500 genuine placebo research articles and identified nine meta-analyses covering more than 135 randomized and placebo-controlled trials (RCTs) with more than 10,000 patients with Crohn´s disease (CD) and another five meta-analyses with 150 RCTs and more than 10,000 patients with ulcerative colitis (UC). Only three discussed nocebo effects, especially in the context of clinical use of biosimilars to treat inflammation. The articles were critically analyzed with respect to the size of the placebo response in CD and UC, its effects on clinical improvement versus maintenance of remission, and mediators and moderators of the response identified. Finally, we discussed and compared the differences and similarities of the placebo responses in IBD and IBS and the nocebo effect in switching from biologics to biosimilars in IBD management.

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Biogenic amines in the colon

Postępy Higieny i Medycyny Doświadczalnej ◽

10.5604/01.3001.0014.7954 ◽

2021 ◽

Vol 75 ◽

pp. 183-190

Author(s):

Miłosz Jastrzębski ◽

Adam Przybyłkowski

Keyword(s):

Nervous System ◽

Biogenic Amines ◽

Human Body ◽

Human Colon ◽

Gi Tract ◽

Histaminergic System ◽

Inflammatory Agent ◽

Bowel Diseases ◽

Inflammatory Bowel ◽

Irritable Bowel

The gastrointestinal (GI) tract contains the highest concentration of biogenic amines in the human body. Neurons located in the GI tract, modulated by biogenic amines and various peptide and non-peptide transmitters, are called Enteric Nervous System (ENS). That explains why many medications used in neurology and psychiatry present side effects from the gut. Serotonin (5-hyroxytrypatamine, 5-HT), 95% of which is synthesized in the gut, is the most important amine (beside epinephrine and norepinephrine) colon functionality but another substances such as histamine, dopamine and melatonin are also potent in modulating intestine’s actions. Over 30 receptors for 5-HT were described in the human body, and 5-HT3, 5-HT4 and 5-HT7 are known to have the highest influence on motility and are a potent target for the drugs for treatment GI disorders, such as Irritable Bowel Syndrome (IBS) and Inflammatory Bowel Diseases (IBD). Histamine is a key biogenic amine for pathogenesis of allergy also in the colon. Alteration in histaminergic system is found in patients with diarrhea and allergic enteropathy. Dopamine affects functions of the large intestine but its modulating actions are more presented in the upper part of GI tract. Melatonin is best known for regulating circadian circle, but may also be a potent anti-inflammatory agent within the gut. Despite many years of research, it seems that more studies are needed to fully understand human colon neurochemistry.

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FECAL CALPROTECTIN: levels for the ethiological diagnosis in Brazilian patients with gastrointestinal symptoms

Arquivos de Gastroenterologia ◽

10.1590/s0004-28032015000100011 ◽

2015 ◽

Vol 52 (1) ◽

pp. 50-54 ◽

Cited By ~ 8

Author(s):

Lorete Maria da Silva KOTZE ◽

Renato Mitsunori NISIHARA ◽

Sandra Beatriz MARION ◽

Murilo Franco CAVASSANI ◽

Paulo Gustavo KOTZE

Keyword(s):

Ulcerative Colitis ◽

Irritable Bowel Syndrome ◽

Crohn’S Disease ◽

Crohn's Disease ◽

Inflammatory Bowel Diseases ◽

Fecal Calprotectin ◽

Bowel Diseases ◽

Inflammatory Bowel ◽

Irritable Bowel ◽

Active Disease

Background Determination of fecal calprotectin can provide an important guidance for the physician, also in primary care, in the differential diagnosis of gastrointestinal disorders, meanly between inflammatory bowel diseases and irritable bowel syndrome. Objectives The aims of the present study were to prospectively investigate, in Brazilian adults with gastrointestinal complaints, the value of fecal calprotectin as a biomarker for the differential diagnosis between functional and organic disorders and to correlate the concentrations with the activity of inflammatory bowel diseases. Methods The study included consecutive patients who had gastrointestinal complaints in which the measurement levels of fecal calprotectin were recommended. Fecal calprotectin was measured using a Bühlmann (Basel, Switzerland) ELISA kit Results A total of 279 patients were included in the study, with median age of 39 years (range, 18 to 78 years). After clinical and laboratorial evaluation and considering the final diagnosis, patients were allocated into the following groups: a) Irritable Bowel Syndrome: 154 patients (102 female and 52 male subjects). b) Inflammatory Bowel Diseases group: 112 patients; 73 with Crohn’s disease; 38 female and 35 male patients; 52.1% (38/73) presented active disease, and 47.9% (35/73) had disease in remission and 39 patients with ulcerative colitis;19 female and 20 male patients; 48.7% (19/39) classified with active disease and 49.3% (20/39) with disease in remission. A significant difference (P<0.001) was observed between the median value of fecal calprotectin in Irritable Bowel Syndrome group that was 50.5 µg/g (IQR=16 - 294 µg/g); 405 µg/g (IQR=29 - 1980 µg/g) in Crohn’s disease patients and 457 µg/g (IQR=25 - 1430 µg/g) in ulcerative colitis patients. No difference was observed between the values found in the patients with Crohn’s disease and ulcerative colitis. Levels of fecal calprotectin were significantly lower in patients with inflammatory bowel diseases in remission when compared with active disease (P<0.001). Conclusions The present study showed that the determination of fecal calprotectin assists to differentiate between active and inactive inflammatory bowel diseases and between inflammatory bowel diseases and irritable bowel syndrome.

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Anhedonia in irritable bowel syndrome and in inflammatory bowel diseases and its relationship with abdominal pain

Neurogastroenterology & Motility ◽

10.1111/nmo.13531 ◽

2019 ◽

Vol 31 (3) ◽

pp. e13531 ◽

Cited By ~ 9

Author(s):

Luna Carpinelli ◽

Cristina Bucci ◽

Antonella Santonicola ◽

Fabiana Zingone ◽

Carolina Ciacci ◽

...

Keyword(s):

Irritable Bowel Syndrome ◽

Abdominal Pain ◽

Inflammatory Bowel Diseases ◽

Bowel Diseases ◽

Inflammatory Bowel ◽

Irritable Bowel

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Diet and Nutrients in Gastrointestinal Chronic Diseases

Nutrients ◽

10.3390/nu12092693 ◽

2020 ◽

Vol 12 (9) ◽

pp. 2693

Author(s):

Antonio Corsello ◽

Daniela Pugliese ◽

Antonio Gasbarrini ◽

Alessandro Armuzzi

Keyword(s):

Inflammatory Bowel Disease ◽

Irritable Bowel Syndrome ◽

Eating Habits ◽

Gastrointestinal Diseases ◽

Daily Amount ◽

Progression Of Disease ◽

Inflammatory Bowel ◽

Irritable Bowel ◽

The Impact ◽

Therapeutic Possibilities

Diet and nutrition are known to play key roles in many chronic gastrointestinal diseases, regarding both pathogenesis and therapeutic possibilities. A strong correlation between symptomatology, disease activity and eating habits has been observed in many common diseases, both organic and functional, such as inflammatory bowel disease and irritable bowel syndrome. New different dietary approaches have been evaluated in order improve patients’ symptoms, modulating the type of sugars ingested, the daily amount of fats or the kind of metabolites produced in gut. Even if many clinical studies have been conducted to fully understand the impact of nutrition on the progression of disease, more studies are needed to test the most promising approaches for different diseases, in order to define useful guidelines for patients.

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Modern Endoscopic Imaging in Diagnosis and Surveillance of Inflammatory Bowel Disease Patients

Gastroenterology Research and Practice ◽

10.1155/2018/5738068 ◽

2018 ◽

Vol 2018 ◽

pp. 1-10 ◽

Cited By ~ 3

Author(s):

Gheorghe Hundorfean ◽

Stephen P. Pereira ◽

John G. Karstensen ◽

Peter Vilmann ◽

Adrian Saftoiu

Keyword(s):

Inflammatory Bowel Disease ◽

Bowel Disease ◽

Relevant Literature ◽

Gastrointestinal Diseases ◽

High Definition ◽

Full Spectrum ◽

Endoscopic Techniques ◽

Bowel Diseases ◽

Inflammatory Bowel ◽

Monitoring Modality

Endoscopy remains the most important diagnostic and monitoring modality in the management of inflammatory bowel disease. Advances in imaging have progressively added new tools into the armamentarium of endoscopists with the goal of more accurate, sensitive, and accessible visual diagnoses for the benefit of patients with gastrointestinal diseases. Here, we review the relevant literature regarding commonly used endoscopic techniques (dye-based and digital chromoendoscopy, high-definition endoscopy, capsule endoscopy, and endosonography), as well as advanced and experimental technologies (full-spectrum endoscopy, endocytoscopy, autofluorescence, laser endoscopy, and endomicroscopy, including molecular imaging), applicable to inflammatory bowel diseases and emerging for implementation into everyday practice. Additionally, we discuss future directions and techniques as candidates for a superior inflammation imaging in the diagnosis and prediction of therapeutic response.

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