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DOAJ Open Access 2025
Plant-derived extracts or compounds for Helicobacter-associated gastritis: a systematic review of their anti-Helicobacter activity and anti-inflammatory effect in animal experiments

Danni Chen, Wenlai Wang, Xiangyun Chen et al.

Abstract Background Helicobacter infection, which is the leading cause of gastritis and stomach cancer, has become common worldwide. Almost all Helicobacter-infected patients have chronic active gastritis, also known as Helicobacter-associated gastritis (HAG). However, the eradication rate of Helicobacter is decreasing due to the poor efficacy of current medications, which causes infection to recur, inflammation to persist, and stomach cancer to develop. Natural components have robust antibacterial activity and anti-inflammatory capacity, as confirmed by many studies of alternative natural medicines. Purpose This article aimed to conduct a comprehensive search and meta-analysis to evaluate the efficacy of anti-Helicobacter and anti-inflammatory activities of plant-derived extracts or compounds that can treat HAG in animal experiments. We intended to provide detailed preclinical-research foundation including plant and compound information, as well as the mechanisms by which these plant-derived substances inhibit the progression of Helicobacter infection, gastritis and neoplasms for future study. Methods The systematic review is aligned with the guidelines outlined in the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement, and the protocol was registered in PROSPERO (CRD42024527889). An extensive search was performed across multiple databases, including PubMed, Scopus, Web of Science, Embase, China National Knowledge Infrastructure (CNKI), the Chinese Scientific Journal database (VIP), the Wanfang database, and the China biomedical literature service system (SinoMed), up until November 2023. Meta-analysis on Review Manager software (RevMan 5.4) estimating anti-Helicobacter and anti-inflammatory activity was performed. We used the Systematic Review Center for Laboratory Animal Experimentation (SYRCLE) risk of bias tool to evaluate the risk of bias of each study included. Results Our study encompassed 61 researches, comprised 36 extracts and 37 compounds improving HAG by inhibiting Helicobacter infection, the inflammatory response, oxidative stress, and regulating apoptosis and proliferation. Sixteen families especially Asteraceae, Fabaceae and Rosaceae and nine classes including Terpenoids, Alkaloids, Phenols, and Flavonoids may be promising directions for valuable new drugs. The Meta-analyse demonstrated the plant-base substance treatments possess significant anti-Helicobacter and anti-inflammation activity comparing to control groups. The included plants and compounds confirmed that signaling pathways NF-κB, JAK2/STAT3, MAPK, TLR4/MyD88, PI3K/AKT, NLRP3/Caspase-1 and NRF2/HO-1 play a key role in the progression of HAG. Conclusion Plant-derived extracts or compounds actively improve HAG by modulating relevant mechanisms and signaling pathways, particularly through the anti-Helicobacter and inflammatory regulation ways. Further researches to apply these treatments in humans are needed, which will provide direction for the future development of therapeutic drugs to increase eradication rate and alleviate gastritis.

Other systems of medicine
DOAJ Open Access 2025
Antidepressant effect of Radix bupleuri - Radix paeoniae alba herb pair on chronic unpredictable mild stress rats based on cortical metabolomics

Kanglin Cai, Xinyu Chen, Yongkai Cao et al.

Abstract Objective Depression is a serious mental disorder, and its incidence rate has increased rapidly. Radix Bupleuri (root of Bupleurum chinensis DC. BR)-Radix Paeoniae Alba (root of Paeonia lactiflora Pall. PRA) herb pair has been historically used for treating depression in Traditional Chinese Medicine (TCM) while the mechanisms need to be fully revealed. Methods The effects of the BR-PRA herb pair were investigated using a rat model of chronic unpredictable mild stress (CUMS). First, the depressive-like behavior of rats was evaluated by open field test (OFT), elevated plus-maze test (EMP), and forced swimming test (FST). Secondly, histomorphological changes in the CA1 and CA3 regions of the hippocampus were analyzed by hematoxylin-eosin, nissl, and Golgi staining. Ultra high-performance liquid chromatograph tandem quadrupole mass spectrometry (UHPLC-QTRAP-MS/MS) was performed to reveal potential antidepressant mechanisms. Results Following CUMS exposure, rats displayed depressive-like behavior, and neuronal death in the hippocampal region was observed. Consequently, these abnormal changes were reversed by BR-PRA herb-pair intervention. A total of 26 different metabolites related to depression were identified by metabolomics, mainly involving eleven metabolic pathways of pentose phosphate pathway, purine metabolism, and amino sugar and nucleotide sugar metabolism. BR-PRA herb-pair improved four metabolites, including homocitrulline, N-acetyllysine, corticosterone, and N-acetylglutamate. It also may affect the development of depression by interfering with the hypothalamus-pituitary-adrenal axis (HPA axis), amino acid metabolism related to lysine and glutamate, and modulation of oxidative stress. Conclusion BR-PRA herb-pair alleviated depressive-like behavior in CUMS rats, recovered hippocampus damage, and regulated cerebral cortex metabolism, which may be related to the HPA axis, amino acid metabolism related to lysine and glutamate, and modulation of oxidative stress. Clinical trial number Not applicable.

Other systems of medicine
DOAJ Open Access 2024
Ayurvedic Management of Vipadika (Palmoplantar Psoriasis)

Dinesh Kumar Kumawat, Anita Sharma

Introduction:Psoriasis is an immune-mediated illness, in which the skin develops persistent inflammatory abnormalities. Palmoplantar psoriasis (PPP) affects about 5% of all psoriasis patients, and it is difficult to treat this type of psoriasis.Main Clinical Finding:This was a case report of a 23-year-old female, who presented with complaints of painful cracks with intermittent bleeding over the palms of hand and soles of feet. Less scaly patches and other skin changes were found over the palms of hands surface and were also associated with intense itching and burning sensation for the past 3 years.Diagnosis:Condition was diagnosed as PPP (Ayurvedic diagnosis – Vata Kapha dominant Tridoshaja Vipadika).Interventions:The patient was treated with Avipattikara + pitantaka + Suddhagandaka yoga, Mahatikta Ghruta, Arogyavardhini vati, Khadiraristha, and local application of Jivantyadi yamaka daily for 42 days.Outcome:The patient had relief in all the symptoms after 15 days of treatment with no new eruptions. Complete remission of the disease was observed after 2 months of treatment with the improved skin condition.Conclusion:This case study demonstrates the potential and usefulness of Ayurveda in the management of PPP.

Other systems of medicine
DOAJ Open Access 2024
Co-design knowledge mobilization tools for universal accessibility in municipalities

Maëlle Corcuff, Maëlle Corcuff, Marie-Eve Lamontagne et al.

IntroductionModern research teams are re-evaluating conventional methods with the aim of improving the usefulness of knowledge for users, focusing on the role of knowledge users in shaping innovation. In disability field, encouraging participatory research inherently involves diverse perspectives and inclusion, which aligns with the principles of universal accessibility. By actively involving individuals with various backgrounds, abilities, and needs in the research process, we can better understand and address the challenges faced in adopting universal accessibility. This approach ensures that solutions are more comprehensive, inclusive, and effectively cater to the needs of all individuals, fostering a more equitable and accessible environment for everyone. Despite municipal organizations mandating universal accessibility action plans, they lack tools for efficient implementation. The aim of this study was to develop knowledge mobilization tools tailored to a specific municipal context in Quebec, Canada, to facilitate the implementation of universal accessibility measures by municipal employees.MethodsThe co-design process employed in this study was organized into four distinct stages, following the Morales model: (1) Exploration (2) Co-Design (3) Validation (4) Development.ResultsStages one and two highlighted the employees' lack of awareness about universal accessibility issues and their need to have more information and resources about how universal accessibility is encountered in their work. A steering committee co-designed three video vignettes about universal accessibility, the city's action plan and measures included in it.DiscussionThe co-design approach used in this study allowed us to observe the non-linear nature of partnership research with an organization as complex as a municipality. Our study shows significant advantages of collaboration between the municipal sector and research.

Other systems of medicine, Medical technology
DOAJ Open Access 2024
Enhancing hepatoprotective action: oxyberberine amorphous solid dispersion system targeting TLR4

Tingting Chen, Qingguo Li, Gaoxiang Ai et al.

Abstract Oxyberberine (OBB) is a significant natural compound, with excellent hepatoprotective properties. However, the poor water solubility of OBB hinders its release and absorption thus resulting in low bioavailability. To overcome these drawbacks of OBB, amorphous spray-dried powders (ASDs) of OBB were formulated. The dissolution, characterizations, and pharmacokinetics of OBB-ASDs formulation were investigated, and its hepatoprotective action was disquisitive in the D-GalN/LPS-induced acute liver injury (ALI) mouse model. The characterizations of OBB-ASDs indicated that the crystalline form of OBB active pharmaceutical ingredients (API) was changed into an amorphous form in OBB-ASDs. More importantly, OBB-ASDs showed a higher bioavailability than OBB API. In addition, OBB-ASDs treatment restored abnormal histopathological changes, improved liver functions, and relieved hepatic inflammatory mediators and oxidative stress in ALI mice. The spray drying techniques produced an amorphous form of OBB, which could significantly enhance the bioavailability and exhibit excellent hepatoprotective effects, indicating that the OBB-ASDs can exhibit further potential in hepatoprotective drug delivery systems. Our results provide guidance for improving the bioavailability and pharmacological activities of other compounds, especially insoluble natural compounds. Meanwhile, the successful development of OBB-ASDs could shed new light on the research process of poorly soluble medicine.

Medicine, Science
DOAJ Open Access 2023
Network pharmacology-based strategy to investigate the effect and mechanism of α-solanine against glioma

ChunPeng Wang, XiaoHui Liu, ShiWen Guo

Abstract Background An anti-tumour activity has been demonstrated for α-solanine, a bioactive compound extracted from the traditional Chinese herb Solanum nigrum L. However, its efficacy in the treatment of gliomas and the underlying mechanisms remain unclear. The aim of this study was to investigate the inhibitory effects of α-solanine on glioma and elucidate its mechanisms and targets using network pharmacology, molecular docking, and molecular biology experiments. Methods Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) was utilized to predict the potential targets of α-solanine. GeneCards was used to gather glioma-related targets, and the STRING online database was used to analyze protein–protein interaction (PPI) networks for the shared targets. Hub genes were identified from the resulting PPI network and further investigated using Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Additionally, prognostic and gene set enrichment analyses (GSEA) were carried out to identify potential therapeutic targets and their underlying mechanisms of action in relation to the prognosis of gliomas. In vitro experiments were conducted to verify the findings from the network pharmacology analysis. Results A total of 289 α-solanine targets and 1149 glioma-related targets were screened, of which 78 were common targets. 11 hub genes were obtained, including SRC, HRAS, HSP90AA1, IGF1, MAPK1, MAPK14, KDR, STAT1, JAK2, MAP2K1, and IGF1R. The GO and KEGG pathway analyses unveiled that α-solanine was strongly associated with several signaling pathways, including positive regulation of MAP kinase activity and PI3K-Akt. Moreover, α-solanine (10 µM and 15 µM) inhibited the proliferation and migration but promoted the apoptosis of glioma cells. Finally, STAT1 was identified as a potential mediator of the effect of α-solanine on glioma prognosis. Conclusion α-Solanine can inhibit the proliferation and migration of gliomas by regulating multiple targets and signalling pathways. These findings lay the foundation for the creation of innovative clinical anti-glioma agents.

Other systems of medicine
DOAJ Open Access 2023
LONGITUDINALIDADE NA ATENÇÃO PRIMÁRIA À SAÚDE: EXPLORANDO A CONTINUIDADE DO CUIDADO AO LONGO DO TEMPO

Larayne Gallo Farias Oliveira, Lislaine Aparecida Fracolli, Denise Maria Campos de Lima Castro et al.

A longitudinalidade do cuidado possibilita a criação de uma conexão de confiança entre usuários e profissionais, o que facilita a comunicação efetiva e uma compreensão mais completa das necessidades e do histórico de saúde de cada pessoa. Este estudo tem como objetivo refletir sobre a importância da longitudinalidade na APS, discutindo seus benefícios, desafios e perspectivas. Trata-se de um estudo reflexivo, realizado entre março e maio de 2023, fundamentado na formulação discursiva da importância da longitudinalidade na APS que visou explorar as tendências, desafios e perspectivas associados a esse aspecto crucial do cuidado ao longo do tempo. O texto está apresentado em três partes de acordo com os pontos de reflexão. Uma revisão da literatura foi realizada para reunir evidências e análises relacionadas à longitudinalidade na APS, abordando seus benefícios, obstáculos e possíveis soluções. Os resultados apontam para a longitudinalidade, como aspecto crucial da APS na promoção da saúde e prevenção de doenças ao longo do tempo. Estes destacam a necessidade de fortalecer a longitudinalidade na APS, considerando o impacto positivo que isso pode ter na saúde da população uma vez que essa relação fortalece a qualidade do cuidado, a adesão ao tratamento e a satisfação do usuário.

Medicine (General), Other systems of medicine
DOAJ Open Access 2023
Ayurvedic management of vitiligo: An experience

Amit Kataria, Sunaina, Monica Dhiman

Vitiligo is a kind of skin disease characterized by white hypopigmented patches. Although this disorder is not life-threatening, but has a serious cosmetic problem that affects the individual's emotional, psychological, and social well-being. A nine-year-old female child was diagnosed with Shvitra (~vitiligo) two years back who was presented with complaints of increasing area and number of depigmented patches of skin. She has taken PUVA (~Psoralen Plus Ultraviolet A), a type of radiation treatment, and corticosteroids but found no result. Then, an Ayurvedic treatment protocol was designed based on the signs and symptoms. The protocol includes Samshodhana (~eliminative) and Prashamana (~palliative) therapies with a combination of powdered herbal drugs having Raktaprasadaka (~improves the quality of blood), Raktashodhana (~blood purification), and Tridoshahara (~balances three regulatory functional factors of the body) action along with Bakuchi taila (~Psoralea corylifolia L.) for local application. The treatment protocol was found to be effective in the restoration of skin color.

Other systems of medicine
DOAJ Open Access 2022
Mesenteric Lymphadenitis Presenting as Acute Abdomen in a Child with Multisystem Inflammatory Syndrome

Evangelos Blevrakis, Eleni Vergadi, Maria Stefanaki et al.

Multisystem inflammatory syndrome in children (MIS-C) may develop as a rare complication following COVID-19. MIS-C presentation varies substantially, but fever and gastrointestinal symptoms are the most prominent. Indeed, gastrointestinal involvement may be severe enough to present as acute abdomen, posing challenges to clinicians. We present herein the case of a healthy five-year-old male who presented with fever, vomiting, and abdominal pain, resembling acute abdomen. The patient had no history of SARS-CoV-2 infection or exposure, and MIS-C diagnosis was initially surpassed unnoticed. The patient underwent exploratory laparotomy that only revealed mesenteric lymphadenitis. Postoperatively, the patient met the clinical and laboratory diagnostic criteria of MIS-C. SARS-CoV-2 exposure was serologically confirmed and MIS-C treatment was commenced, resulting in defervescence and a satisfactory outcome. In young patients presenting with acute abdomen, surgeons should be aware of MIS-C, so that earlier diagnosis and appropriate treatment are made prior to surgical interventions.

Other systems of medicine
DOAJ Open Access 2022
Fundamental signaling pathways for glioblastoma drug resistance and developing robust organoid models for drug discovery

Athira Pratap, Eun-Jung Lim, Ihn-Sil Kwak et al.

This article presents a review of the current literature on the molecular mechanisms of treatment resistance in glioblastoma. As mounting research continues to explore novel methods of treating glioblastoma, from using organoid models for drug screening to developing novel cellular therapies, it is critical to understand the fundamental molecular landscape that makes glioblastoma difficult to treat. This review explores the means of chemoresistance to the conventional chemotherapy temozolomide. Consideration of DNA repair pathways, p53-mediated apoptosis and autophagy, convergent proliferation pathways, and epigenetic mechanisms demonstrate avenues for the development of sophisticated drug targets and combination treatments. Ultimately, this article highlights each of these mechanisms and presents referential material for future endeavors in organoid-based drug screening.

Biotechnology, Miscellaneous systems and treatments
DOAJ Open Access 2022
DIRETRIZES PARA EDUCAÇÃO PERMANENTE EM SAÚDE MENTAL NA ATENÇÃO PRIMÁRIA

Jaqueline Naibert, Camila Giugliani

Trata-se de um produto técnico, em formato de Guia ou Manual, desenvolvido a partir dos diálogos realizados na pesquisa da Dissertação do Mestrado Profissional em Ensino na Saúde, com diferentes atores envolvidos na gestão, controle social, universidade e profissionais da saúde no cuidado em saúde mental na Atenção Primária em Saúde (APS). Serão apresentados um conjunto de diretrizes, abordando os temas e processos relativos à Educação Permanente em Saúde (EPS), sistematizados a partir da análise dos diálogos entre a pesquisadora e os participantes da pesquisa. O objetivo é propor diretrizes para a Educação Permanente em Saúde Mental na APS. Estudo exploratório, de abordagem qualitativa.  A coleta de dados se deu por meio de diálogos baseados nas categorias freireanas do diálogo e problematização.  Os diálogos ocorreram em encontros virtuais individuais, por vídeo chamada, cumprindo com as recomendações para enfrentamento da pandemia por COVID-19. Foram evidenciadas cinco grandes categorias temáticas: assistência, gestão, saúde do trabalhador, trabalho em rede e pandemia COVID-19. Dentro de cada uma, surgiram subcategorias. Os participantes identificam que a EPS é uma grande chave para qualificar os atendimentos e o acompanhamento em saúde mental, bem como a importância de serem abordados, nas capacitações e seminários, temas que sejam praticados no cotidiano do trabalho. Como produto, foram elaboradas diretrizes para educação permanente em saúde mental na APS, que poderão ser usadas como guia para qualificar o cuidado em saúde mental. Palavras-chave: Educação Continuada. Saúde Mental. Atenção Primária à Saúde.

Miscellaneous systems and treatments, Public aspects of medicine
DOAJ Open Access 2021
The Association of Physical Function Measures With Frailty, Falls History, and Metabolic Syndrome in a Population With Complex Obesity

Amanda Rhynehart, Colin Dunlevy, Katie Hayes et al.

Background: Frailty, falls and metabolic syndrome are known to be associated with poorer physical function. This study builds on available research by further investigating the relationship between physical function measures, including those comprising frailty, with metabolic syndrome (MetS) and falls, in the context of complex obesity.Methods: Participants were recruited from the national Level 3 weight management service in Ireland. A retrospective audit of data gathered at initial assessment was performed. Data included past medical history, blood tests, blood pressure measurement, anthropometrics, falls history, self-reported physical activity levels (PALs) and physical function measures, including hand grip strength (HGS), “timed up and go” (TUG), functional reach (FR), sit to stand (STS) and gait speed. A modified version of the Fried Frailty Index was employed.Results: Of the 713 participants, 65.1% (n = 464) were female and 34.9% (n = 249) were male with a mean age of 44.2 (±11.7) years and body mass index (BMI) of 50.6 kg/m2 (±8.2). Frailty was identified in 3.4% (n = 24), falls in 28.8% (n = 205) and MetS in 55.1% (n = 393). Frailty was associated with older age (53.8 ± 14.3 vs. 43.9 ± 11.5 years), poorer PALs (27.29 ± 46.3 vs. 101.1 ± 147.4 min/wk), reduced grip strength (17.7 ± 4.6 vs. 34.2 ± 11.0 Kg) longer STS (21.7 ± 6.6 vs. 13.7 ± 5.7 s), shorter functional reach (29.7 ± 7.9 vs. 37.9 ± 8.2 cm) and slower gait speed (0.6 ± 0.2 vs. 1.1 ± 0.5 m/s). Those reporting a falls history had a reduced FR (35.8 ± 8.9 vs. 38.3 ± 7.8 cm) and slower STS (15.4 ± 8.0 vs. 13.3 ± 4.7 s). Participants with MetS had lower PALs (83.2 ± 128.2 vs. 119.2 ± 157.6) and gait speed (1.1 ± 0.3 vs. 1.2 ± 0.7 m/s). There was no difference in BMI between fallers and non-fallers (51.34 ± 8.44 vs. 50.33 ± 8.13 Kg/m2, p = 0.138), nor between those with or without MetS. Significant associations were found between BMI and all physical function measures except the TUAG.Conclusion: The associations between frailty, falls and MetS and their combined impact on physical function in people living with obesity demonstrates the need for appropriate screening. Utilising grip strength and gait speed to identify frailty in those with obesity and metabolic syndrome could help target therapies aimed at improving strength, physical function and ultimately quality of life.

Other systems of medicine, Medical technology
DOAJ Open Access 2020
Posições verticalizadas no parto e a prevenção de lacerações perineais: revisão sistemática e metanálise

Bruna Dedavid da Rocha, Cláudia Zamberlan, Hedioneia Maria Foletto Pivetta et al.

RESUMO Objetivo Investigar se a adoção de posições verticalizadas pela mulher, no parto, comparada à posição litotômica, previne lacerações perineais. Método Revisão sistemática com metanálise. As buscas foram realizada nas bases de dados: LILACS, Medline/PubMed, CINAHL, Cochrane Library, Web of Science, Science Direct e Scopus. As buscas na literatura cinzenta foram conduzidas nas bases Google Scholar e OpenGrey. Também foram consideradas as listas de referências dos artigos incluídos. Para análise da qualidade metodológica dos artigos, utilizou-se a ferramenta da colaboração Cochrane e a ACROBAT-NRSI. Resultados Foram elencados 26 estudos e 8 foram selecionados para a metanálise. O nível de evidência científica foi classificado pelo Sistema GRADE e considerado alto. Não houve diferença estatística significativa entre posições verticalizadas em relação as posições horizontais. Apesar dessa constatação, as posições verticalizadas apresentaram índices reduzidos de lacerações perineais graves. Conclusão A adoção de posições verticalizadas, no parto normal, pode ser encorajada pelos profissionais, pois pode evitar lacerações perineais graves, porém, não é possível afirmar com precisão a eficácia destas em detrimento das posições horizontais para o desfecho períneo íntegro.

Public aspects of medicine, Nursing
DOAJ Open Access 2019
Oxidative stress mediated by gyrophoric acid from the lichen Umbilicaria hirsuta affected apoptosis and stress/survival pathways in HeLa cells

Michal Goga, Martin Kello, Maria Vilkova et al.

Abstract Background Lichens produce a huge diversity of bioactive compounds with several biological effects. Gyrophoric acid (GA) is found in high concentrations in the common lichen Umbilicaria hirsuta, however evidence for biological activity was limited to anti-proliferative activity described on several cancer cell lines. Methods We developed and validated a new protocol for GA isolation, resulting in a high yield of highly pure GA (validated by HPLC and NMR) in an easy and time saving manner. Anti-proliferative and pro-apoptotic activity, oxygen radicals formation and stress/survival proteins activity changes was study by flow cytometry. Results The highly purified GA showed anti-proliferative activity against HeLa (human cervix carcinoma) and other tumor cells. Moreover, GA threated cells showed a significant increase in caspase-3 activation followed by PARP cleavage, PS externalization and cell cycle changes mediated by oxidative stress. Production of oxygen radicals led to DNA damage and changes in stress/survival pathways activation. Conclusions GA treatment on HeLa cells clearly indicates ROS production and apoptosis as form of occurred cell death. Moreover, DNA damage and changing activity of stress/survival proteins as p38MAPK, Erk1/2 and Akt mediated by GA treatment confirm pro-apoptotic potential. The pharmacological potential of U. hirsuta derived GA is discussed.

Other systems of medicine
S2 Open Access 1961
DEMONSTRATION OF MOUSE ISOANTIGENS AT THE CELLULAR LEVEL BY THE FLUORESCENT ANTIBODY TECHNIQUE

G. Möller

The fluorescent antibody technique has been applied for the demonstration of mouse isoantigens at the cellular level. Specific reactions were obtained by the indirect or "sandwich" technique with a variety of living normal and neoplastic cells. Isoantigens of the H-2 system and of other systems could be demonstrated as well and appeared to be localized at the cell membrane. As far as the H-2 system was concerned, the membrane localization could be confirmed on histological sections. Different types of non-specific staining reactions have been identified and described. Pinocytosis and cell injury led to such reactions that were morphologically distinguishable from the specific "ring" reaction and as far as pinocytosis is concerned, could be easily avoided by reducing the incubation time. In addition, a non-specific staining reaction morphologically indistinguishable from the specific "ring" reaction could be seen in a small proportion of bone marrow and lymph node cells but in no other cell type studied. The possible nature of this reaction is discussed.

388 sitasi en Medicine, Biology
S2 Open Access 2015
ANDSystem: an Associative Network Discovery System for automated literature mining in the field of biology

V. Ivanisenko, O. Saik, N. Ivanisenko et al.

BackgroundSufficient knowledge of molecular and genetic interactions, which comprise the entire basis of the functioning of living systems, is one of the necessary requirements for successfully answering almost any research question in the field of biology and medicine. To date, more than 24 million scientific papers can be found in PubMed, with many of them containing descriptions of a wide range of biological processes. The analysis of such tremendous amounts of data requires the use of automated text-mining approaches. Although a handful of tools have recently been developed to meet this need, none of them provide error-free extraction of highly detailed information.ResultsThe ANDSystem package was developed for the reconstruction and analysis of molecular genetic networks based on an automated text-mining technique. It provides a detailed description of the various types of interactions between genes, proteins, microRNA's, metabolites, cellular components, pathways and diseases, taking into account the specificity of cell lines and organisms. Although the accuracy of ANDSystem is comparable to other well known text-mining tools, such as Pathway Studio and STRING, it outperforms them in having the ability to identify an increased number of interaction types.ConclusionThe use of ANDSystem, in combination with Pathway Studio and STRING, can improve the quality of the automated reconstruction of molecular and genetic networks. ANDSystem should provide a useful tool for researchers working in a number of different fields, including biology, biotechnology, pharmacology and medicine.

81 sitasi en Computer Science, Medicine

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