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FooDis : a food-disease relation mining pipeline
Gjorgjina Cenikj, Tome Eftimov, Barbara Koroušić-Seljak, 2023, izvirni znanstveni članek

Povzetek: Nowadays, it is really important and crucial to follow the new biomedical knowledge that is presented in scientific literature. To this end, Information Extraction pipelines can help to automatically extract meaningful relations from textual data that further require additional checks by domain experts. In the last two decades, a lot of work has been performed for extracting relations between phenotype and health concepts, however, the relations with food entities which are one of the most important environmental concepts have never been explored. In this study, we propose FooDis, a novel Information Extraction pipeline that employs state-of-the-art approaches in Natural Language Processing to mine abstracts of biomedical scientific papers and automatically suggests potential cause or treat relations between food and disease entities in different existing semantic resources. A comparison with already known relations indicates that the relations predicted by our pipeline match for 90% of the food-disease pairs that are common in our results and the NutriChem database, and 93% of the common pairs in the DietRx platform. The comparison also shows that the FooDis pipeline can suggest relations with high precision. The FooDis pipeline can be further used to dynamically discover new relations between food and diseases that should be checked by domain experts and further used to populate some of the existing resources used by NutriChem and DietRx.
Ključne besede: text mining, relation extraction, named entity recognition, named entity linking, food-disease relations
Objavljeno v DiRROS: 25.05.2023; Ogledov: 284; Prenosov: 137
.pdf Celotno besedilo (1,11 MB)
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SciFoodNER : food named entity recognition for scientific text
Gjorgjina Cenikj, Gašper Petelin, Barbara Koroušić-Seljak, Tome Eftimov, 2022, objavljeni znanstveni prispevek na konferenci

Ključne besede: food, named entity recognition, named entity linking, information extraction
Objavljeno v DiRROS: 09.03.2023; Ogledov: 386; Prenosov: 192
.pdf Celotno besedilo (551,39 KB)
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Immunological outcomes of allergen-specific immunotherapy in food allergy
Anne-Marie Malby Schoos, Dominique Bullens, Bo Lund Chawes, Joana Costa, Liselot De Vlieger, Audrey DunnGalvin, Michelle M. Epstein, Johan Garssen, Christiane Hilger, Karen Knipping, Mihaela Zidarn, 2020, izvirni znanstveni članek

Povzetek: IgE-mediated food allergies are caused by adverse immunologic responses to food proteins. Allergic reactions may present locally in different tissues such as skin, gastrointestinal and respiratory tract and may result is systemic life-threatening reactions. During the last decades, the prevalence of food allergies has significantly increased throughout the world, and considerable efforts have been made to develop curative therapies. Food allergen immunotherapy is a promising therapeutic approach for food allergies that is based on the administration of increasing doses of culprit food extracts, or purified, and sometime modified food allergens. Different routes of administration for food allergen immunotherapy including oral, sublingual, epicutaneous and subcutaneous regimens are being evaluated. Although a wealth of data from clinical food allergen immunotherapy trials has been obtained, a lack of consistency in assessed clinical and immunological outcome measures presents a major hurdle for evaluating these new treatments. Coordinated efforts are needed to establish standardized outcome measures to be applied in food allergy immunotherapy studies, allowing for better harmonization of data and setting the standards for the future research. Several immunological parameters have been measured in food allergen immunotherapy, including allergen-specific immunoglobulin levels, basophil activation, cytokines, and other soluble biomarkers, T cell and B cell responses and skin prick tests. In this review we discuss different immunological parameters and assess their applicability as potential outcome measures for food allergen immunotherapy that may be included in such a standardized set of outcome measures.
Ključne besede: food hypersensitivity, food intolerance, immunotherapy, immunology, food allergy, food allergens, oral immunotherapy
Objavljeno v DiRROS: 15.02.2021; Ogledov: 1163; Prenosov: 892
.pdf Celotno besedilo (1,45 MB)
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Nrf2-interacting nutrients and COVID-19 : time for research to develop adaptation strategies
Jean Bousquet, Jean-Paul Cristol, Wienczyslawa Czarlewski, Josep M. Antò i Boquè, Adrian Martineau, Tari Haahtela, Susana C. Fonseca, Guido Iaccarino, Hubert Blain, Alessandro Fiocchi, Nisera Bajrović, Natalija Edelbaher, Maja Jošt, Peter Kopač, Anja Koren, Mitja Košnik, Karmen Kramer Vrščaj, Samo Kreft, Nika Lalek, Bojan Madjar, Tonka Poplas-Susič, Irma Rozman Sinur, Tanja Soklič, Katja Triller Vadnal, Nadja Triller, Jure Urbančič, Mihaela Zidarn, 2020, pregledni znanstveni članek

Povzetek: There are large between- and within-country variations in COVID-19 death rates. Some very low death rate settings such as Eastern Asia, Central Europe, the Balkans and Africa have a common feature of eating large quantities of fermented foods whose intake is associated with the activation of the Nrf2 (Nuclear factor (erythroid-derived 2)-like 2) anti-oxidant transcription factor. There are many Nrf2-interacting nutrients (berberine, curcumin, epigallocatechin gallate, genistein, quercetin, resveratrol, sulforaphane) that all act similarly to reduce insulin resistance, endothelial damage, lung injury and cytokine storm. They also act on the same mechanisms (mTOR: Mammalian target of rapamycin, PPAR[gamma]:Peroxisome proliferator-activated receptor, NF[kappa]B: Nuclear factor kappa B, ERK: Extracellular signal-regulated kinases and eIF2[alpha]:Elongation initiation factor 2[alpha]). They may as a result be important in mitigating the severity of COVID-19, acting through the endoplasmic reticulum stress or ACE-Angiotensin-II-AT1R axis (AT1R) pathway. Many Nrf2-interacting nutrients are also interacting with TRPA1 and/or TRPV1. Interestingly, geographical areas with very low COVID-19 mortality are those with the lowest prevalence of obesity (Sub-Saharan Africa and Asia). It is tempting to propose that Nrf2-interacting foods and nutrients can re-balance insulin resistance and have a significant effect on COVID-19 severity. It is therefore possible that the intake of these foods may restore an optimal natural balance for the Nrf2 pathway and may be of interest in the mitigation of COVID-19 severity.
Ključne besede: Covid-19, SARS-CoV-2, food, insulin resistance, obesity, Nrf2, nutrients, TRPA1
Objavljeno v DiRROS: 25.01.2021; Ogledov: 1560; Prenosov: 603
.pdf Celotno besedilo (1,61 MB)

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Mast cell activation test in the diagnosis of allergic disease and anaphylaxis
Rajia Bahri, Adnan Custovic, Peter Korošec, Marina Tsoumani, Martin Barron, Jiakai Wu, Rebekah Sayers, Alf Weimann, Monica Ruiz-Garcia, Nandinee Patel, Mira Šilar, 2018, izvirni znanstveni članek

Povzetek: Background. Food allergy is an increasing public health issue and the commonest cause of life-threatening anaphylactic reactions. Conventional allergy tests assess for the presence of allergen-specific IgE, significantly overestimating the rate of true clinical allergy resulting in over-diagnosis and adverse impact on health-related quality of life. Objective. To undertake initial validation and assessment of a novel diagnostic tool, the mast cell activation test (MAT). Methods. Primary human mast cells (hMCs) were generated from peripheral blood precursors, and sensitized using patient sera and then incubated with allergen. Mast cell degranulation was assessed by flow cytometry and mediator release. We compared the diagnostic performance of MAT to existing diagnostic tools to assess in a cohort of peanut-sensitized individuals undergoing double-blind, placebo-controlled challenge. Results. hMCs sensitized with sera from peanut, grass pollen and hymenoptera- (wasp venom) allergic patients demonstrated allergen-specific and dose-dependent degranulation by both expression of surface activation markers (CD63 and CD107a) and functional assays (prostaglandins D2 and ß-hexosaminidase release). In this cohort of peanut-sensitized individuals, MAT was found to have superior discrimination performance compared to other testing modalities including component-resolved diagnostics and basophil activation test. Using functional principle component analysis, we identified 5 clusters or patterns of reactivity in the resulting dose-response curves, which at preliminary analysis corresponded to the reaction phenotypes seen at challenge. Conclusion. MAT is a robust tool which may confer superior diagnostic performance compared to existing allergy diagnostics, and may be useful to explore differences in effector cell function between basophils and mast cells during allergic reactions.
Ključne besede: allergy and immunology -- diagnosis, anaphylaxis, immunologic tests, mast cells, food hypersensitivity, basophil activation test, BAT, mast cell activation test
Objavljeno v DiRROS: 30.11.2020; Ogledov: 1550; Prenosov: 961
.pdf Celotno besedilo (3,30 MB)
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8.
Anaesthetic management of patients with pre-existing allergic conditions : a narrative review
Pascale Dewachter, Peter Kopač, Jose Julio Laguna, Paul Michel Mertes, Vito Sabato, Gerald W. Volcheck, Peter J. Cooke, 2019, pregledni znanstveni članek

Povzetek: This narrative review seeks to distinguish the clinical patterns of pre-existing allergic conditions from other confounding non-allergic clinical entities, and to identify the potential related risks and facilitate their perioperative management. Follow-up investigation should be performed after a perioperative immediate hypersensitivity to establish a diagnosis and provide advice for subsequent anaesthetics, the main risk factor for perioperative immunoglobulin E (IgE)-mediated anaphylaxis being a previous uninvestigated perioperative immediate hypersensitivity reaction. The concept of cross-reactivity between drugs used in the perioperative setting and food is often quoted, but usually not supported by evidence. There is no reason to avoid propofol in egg, soy, or peanut allergy. The allergenic determinants have been characterised for fish, shellfish, and povidone iodine, but remain unknown for iodinated contrast agents. Iodinated drugs may be used in seafood allergy. Evidence supporting the risk for protamine allergy in fish allergy and in neutral protamine Hagedorn insulin use is lacking. Conversely, cross-reactivity to gelatin-based colloid may occur in agal syndrome. Atopy and allergic asthma along with other non-allergic conditions, such as NSAID-exacerbated respiratory disease, chronic urticaria, mastocytosis, and hereditary or acquired angioedema, are not risk factors for IgEmediated drug allergy, but there is a perioperative risk associated with the potential for exacerbation of the various conditions.
Ključne besede: allergy and immunology, drug hypersensitivity, food hypersensitivity, immediate hypersensitivity, anaphylaxis, anesthesia, drug-related side effects and adverse reactions, perioperative period, adverse effects
Objavljeno v DiRROS: 16.10.2020; Ogledov: 1304; Prenosov: 453
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Is diet partly responsible for differences in COVID-19 death rates between and within countries? : protocol for a systematic review
Jean Bousquet, Josep M. Antò i Boquè, Guido Laccarino, Wienczyslawa Czarlewski, Tari Haahtela, Aram Anto, Cezmi A. Akdis, Hubert Blain, Giorgio Walter Canonica, Karmen Kramer Vrščaj, Tari Haahtela, Mitja Košnik, Anja Koren, Peter Kopač, Maja Jošt, Samo Kreft, Klemen Jenko, Bojan Madjar, Davor Plavec, Tanja Soklič, Jure Urbančič, Mihaela Zidarn, 2020, pregledni znanstveni članek

Povzetek: Reported COVID-19 deaths in Germany are relatively low as compared to many European countries. Among the several explanations proposed, an early and large testing of the population was put forward. Most current debates on COVID-19 focus on the differences among countries, but little attention has been given to regional differences and diet. The low-death rate European countries (e.g. Austria, Baltic States, Czech Republic, Finland, Norway, Poland, Slovakia) have used different quarantine and/or confinement times and methods and none have performed as many early tests as Germany. Among other factors that may be significant are the dietary habits. It seems that some foods largely used in these countries may reduce angiotensin-converting enzyme activity or are anti-oxidants. Among the many possible areas of research, it might be important to understand diet and angiotensin-converting enzyme-2 (ACE2) levels in populations with different COVID-19 death rates since dietary interventions may be of great benefit.
Ključne besede: coronavirus, diet, angiotensin-converting enzyme, antioxidant, food
Objavljeno v DiRROS: 09.09.2020; Ogledov: 1421; Prenosov: 1133
.pdf Celotno besedilo (1,12 MB)
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