{"cells":[{"metadata":{},"cell_type":"markdown","source":"Interleukins are a group of naturally occurring proteins that mediate communication between cells. Interleukins manage cell growth and differentiation. Interleukins are also important in regulating immune responses, such as inflammation.\n\nInterleukins are part of a bigger group of messenger molecules called cytokines. They are a part of the “inflammatory cascade” that involves the coordinated, sequential activation of immune response pathways.\n\nCytokines are produced by a broad range of cells, including immune cells like macrophages, B lymphocytes, T lymphocytes and mast cells, as well as endothelial cells, fibroblasts, and various stromal cells.https://blog.healthmatters.io/2018/08/23/what-is-interleukin-6/\n\n#Interleukin-6 (IL-6) is an endogenous chemical which is active in inflammation, and in B cell maturation. Besides being an immune protein, it is also a pyrogen, and is responsible for fever in autoimmune, infectious or non-infectious disease","execution_count":null},{"metadata":{"_kg_hide-input":true,"trusted":true},"cell_type":"code","source":"#codes from Rodrigo Lima  @rodrigolima82\nfrom IPython.display import Image\nImage(url = 'https://encrypted-tbn0.gstatic.com/images?q=tbn%3AANd9GcQxItufa3tAIZtMvf4JqJU7hlGGpVtz8Ti-JDF83tQ1HSvRMUFT&usqp=CAU',width=400,height=400)","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"youtube.com","execution_count":null},{"metadata":{"_uuid":"8f2839f25d086af736a60e9eeb907d3b93b6e0e5","_cell_guid":"b1076dfc-b9ad-4769-8c92-a6c4dae69d19","trusted":true,"collapsed":true,"_kg_hide-output":true},"cell_type":"code","source":"# This Python 3 environment comes with many helpful analytics libraries installed\n# It is defined by the kaggle/python Docker image: https://github.com/kaggle/docker-python\n# For example, here's several helpful packages to load\n\nimport numpy as np # linear algebra\nimport pandas as pd # data processing, CSV file I/O (e.g. pd.read_csv)\nimport json\nimport matplotlib.pyplot as plt\nimport seaborn as sns\nimport plotly.offline as py\nimport plotly.graph_objs as go\nimport plotly.offline as py\nimport plotly.express as px\n\n# Input data files are available in the read-only \"../input/\" directory\n# For example, running this (by clicking run or pressing Shift+Enter) will list all files under the input directory\n\nimport os\nfor dirname, _, filenames in os.walk('/kaggle/input'):\n    for filename in filenames:\n        print(os.path.join(dirname, filename))\n\n# You can write up to 5GB to the current directory (/kaggle/working/) that gets preserved as output when you create a version using \"Save & Run All\" \n# You can also write temporary files to /kaggle/temp/, but they won't be saved outside of the current session","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"#Interleukin-6 as a potential biomarker of COVID-19 progression. By Zulvikar Syambani Ulhaqa,1, and Gita Vita Soraya\nMed Mal Infect. 2020 Apr 4 - doi: 10.1016/j.medmal.2020.04.002\n\nPrevious retrospective studies indicated that an elevated level of interleukin-6 (IL-6) was associated with a high case fatality of COVID-19 infection. Thus, a meta-analysis of the current scientific literature was performed to investigate whether the measurement of serum IL-6 may predict disease progression of COVID-19 patients.\n\nHedge's standardized mean difference (SMD) with 95% confidence interval (CI) was used to assess the IL-6 level in non-severe and severe patients. Heterogeneity was evaluated with Q-test and I2 statistics. Begg's funnel plot and Egger's regression test were applied to determine publication bias if the pooled effect size consisted of 10 or more studies. A sensitivity test was performed by sequentially omitting one study each time to evaluate the stability of the results. Data that was not expressed as mean and standard deviation was extrapolated from the sample size, median, and interquartile range (IQR). The meta-analysis was performed using RevMan version 5.3 and the value of 0.05 was indicative of statistical significance. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7129451/","execution_count":null},{"metadata":{"trusted":true},"cell_type":"code","source":"df = pd.read_csv('/kaggle/input/trec-covid-information-retrieval/CORD-19/CORD-19/metadata.csv')\ndf.shape","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"Although the heterogeneity was considerably high (I2 = 89%; P < 0.00001), they observed that IL-6 levels were significantly increased in COVID-19-infected patients with severe condition compared with those with non-severe condition (SMD = 0.71, 95%CI −0.31–1.12, P = 0.0005). Begg's funnel plot (data not shown) and Egger's test were performed, and no publication bias was observed (P Egger's test = 0.117). A sensitivity analysis was conducted by eliminating one individual study each time. However, the results remained unchanged, suggesting that the findings were statistically stable and robust.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7129451/","execution_count":null},{"metadata":{"trusted":true,"_kg_hide-input":true},"cell_type":"code","source":"df.head()","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"#Codes from Salman Chen https://www.kaggle.com/salmanhiro/covids-incubation-transmission-related-articles/comments","execution_count":null},{"metadata":{"_uuid":"d629ff2d2480ee46fbb7e2d37f6b5fab8052498a","_cell_guid":"79c7e3d0-c299-4dcb-8224-4455121ee9b0","trusted":true},"cell_type":"code","source":"title = df.copy()","execution_count":null,"outputs":[]},{"metadata":{"_kg_hide-input":true,"trusted":true},"cell_type":"code","source":"#codes from Rodrigo Lima  @rodrigolima82\nfrom IPython.display import Image\nImage(url = 'https://encrypted-tbn0.gstatic.com/images?q=tbn%3AANd9GcRRtwq7VwNmlnYqOSU_DM-5N6XTMai8Vx93YnBy1lpP6m43FurP&usqp=CAU',width=400,height=400)","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"What is the Difference Between Cytokines and Interleukins - pinterest.com","execution_count":null},{"metadata":{"trusted":true},"cell_type":"code","source":"title = title.dropna(subset=['title'])","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"title.head()","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"title['title'] = title['title'].str.replace('[^a-zA-Z]', ' ', regex=True)\ntitle['title'] = title['title'].str.lower()","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"title.tail()","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"Cytokines are vital in regulating immunological and inflammatory responses. Among them, IL-6 is of major importance because of its pleiotropic effects. The authors presented the evidence that circulating IL-6 levels are closely linked to the severity of COVID-19 infection. An increase in IL-6 levels has previously been observed in patients with respiratory dysfunction, implying a possible shared mechanism of cytokine-mediated lung damage caused by COVID-9 infection. Furthermore, it seems that the highly pathogenic SARS-CoV-2 is associated with rapid virus replication and a tendency to infect the lower respiratory tract, resulting in an elevated response of IL-6-induced severe respiratory distress. Thus, their results suggest that serial measurement of circulating IL-6 levels may be important in identifying disease progression among COVID-19-infected patients. In line with Their findings, an elevated level of IL-6 has been proven to be a good biomarker for severity of hepatitis B virus (HBV) infection. Therefore, it is reasonable that immediate initial evaluation of IL-6 level be performed upon hospital admission of COVID-19 patients, due to its potential benefits to assess worsening clinical features and disease progression in COVID-19. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7129451/","execution_count":null},{"metadata":{"trusted":true},"cell_type":"code","source":"title['keyword_interleukin'] = title['title'].str.find('interleukin')","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"If the result prompt -1, then the title doesn't contained the keyword. ","execution_count":null},{"metadata":{"trusted":true},"cell_type":"code","source":"title.head()","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"included_interleukin = title.loc[title['keyword_interleukin'] != -1]\nincluded_interleukin","execution_count":null,"outputs":[]},{"metadata":{"_kg_hide-output":true,"trusted":true},"cell_type":"code","source":"import json\nfile_path = '/kaggle/input/trec-covid-information-retrieval/CORD-19/CORD-19/document_parses/pdf_json/5726297380b86a67cf694c0483d546051d1e8be6.json'\nwith open(file_path) as json_file:\n     json_file = json.load(json_file)\njson_file","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"\"Abstract: In Pakistan, Plasmodium vivax is endemic causing approximately 70% of the malaria cases. A number of haematological changes, especially thrombocytopaenia have been reported for P. vivax. Several host factors including cell-mediated immune cells, such as IL-1, IL-6 and IL-10 have been documented for P. vivax-induced thrombocytopaenia. However, study on correlation of cytokines and thrombocytopaenia in P. vivax, particularly in patients with severe signs and symptoms has not been reported from Pakistan. Methods: A case control study to correlate TNF, IL-6 and IL-10 in healthy controls and thrombocytopaenic P. vivax-infected patients (both uncomplicated and complicated cases) from southern Pakistan was carried out during January 2009 to December 2011. Enzyme-linked immunosorbent assay (ELISA) was performed for determination of TNF, IL-6 and IL-10 levels. Results: Out of 182 cases, mild thrombocytopaenia (platelet count 100,000-150,000 mm 3 ) was observed in ten (5.5%), moderate (50,000-100,000 mm 3 ) in 93 (51.1%), and profound thrombocytopaenia (<50,000 mm 3 ) was detected in 79 (43.4%) patients. IL-6 and IL-10 levels were found approximately three-fold higher in the mild cases compared to healthy controls. Two-fold increase in TNF and IL-10 (p < 0.0001) was observed in profound thrombocytopaenic when compared with moderate cases, while IL-6 was not found to be significantly elevated.\"\nAuthors: Afsheen Raza, Muhammad Shahzeb Khan, Najia Karim Ghanchi, Ahmed Raheem, Mohammad Beg. Aga Khan University.  ","execution_count":null},{"metadata":{"trusted":true},"cell_type":"code","source":"IL = pd.read_csv('../input/cusersmarildownloadsinterleukincsv/interleukin.csv', sep=';')\nIL","execution_count":null,"outputs":[]},{"metadata":{"_kg_hide-input":true,"trusted":true},"cell_type":"code","source":"#codes from Rodrigo Lima  @rodrigolima82\nfrom IPython.display import Image\nImage(url = 'https://encrypted-tbn0.gstatic.com/images?q=tbn%3AANd9GcTO67Jx2Ys2OT7N7G5mNIqCp6xVenXoCZgt0_IozHN9cGW-Xqw8&usqp=CAU',width=400,height=400)","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"#The Role of Interleukin-6 in Oral Diseases\n\nIL-6, together with other cytokines and active-phase reactants, modulates the response to oral bacteria. An excessive IL-6 response may contribute to the development of a chronic inflammatory lesion, resulting in loss of periodontal ligament and alveolar bone. This might happen through IL-6’s tissue-degradation effects on connective tissue and bone—mediated by metalloproteinases and osteoclasts, activation of T cells, or amplification of the inflammatory cascade. Local IL-6 production is probably at the source of the inflammatory response, mainly through macrophages, neutrophils, endothelial cells, and fibroblasts. The role that IL-6 plays as a growth factor in oral cancers is becoming increasingly clear. Potential diagnostic chairside tests and IL-6-modulating strategies could become available in the future that may significantly improve the efficacy of oral disease management.https://dimensionsofdentalhygiene.com/article/the-role-of-interleukin-6-in-oral-diseases/","execution_count":null},{"metadata":{"trusted":true},"cell_type":"code","source":"IL.describe()","execution_count":null,"outputs":[]},{"metadata":{"trusted":true},"cell_type":"code","source":"IL['204252_at'].hist()\nplt.show()","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"#Codes from Taikutsu https://www.kaggle.com/ravels1991/simple-eda/notebook#Plotting","execution_count":null},{"metadata":{"_kg_hide-input":true,"trusted":true},"cell_type":"code","source":"ax = IL.groupby('Samples')['204252_at'].max().sort_values(ascending=True).plot(kind='barh', figsize=(12,8),\n                                                                                   title='Maximum Interleukin-6 Samples')\nplt.xlabel('204252_at')\nplt.ylabel('Samples')\nplt.show()","execution_count":null,"outputs":[]},{"metadata":{"_kg_hide-input":true,"trusted":true},"cell_type":"code","source":"ax = IL.groupby('Samples')['211804_s_at', '211803_at'].sum().plot(kind='bar', rot=45, figsize=(12,6), logy=True,\n                                                                 title='211804_s_at x 211803_at')\nplt.xlabel('Samples')\nplt.ylabel('Log Scale 211804_s_at')\nplt.show()","execution_count":null,"outputs":[]},{"metadata":{"_kg_hide-input":true,"trusted":true},"cell_type":"code","source":"ax = IL.groupby('Samples')['211804_s_at', '211803_at'].sum().plot(kind='barh', figsize=(14,8),\n                                                                 title='211804_s_at x 211803_at', logx=True, linewidth=3)\nplt.xlabel('Log Scale 211804_s_at')\nplt.ylabel('Samples')\nplt.show()","execution_count":null,"outputs":[]},{"metadata":{"_kg_hide-input":true,"trusted":true},"cell_type":"code","source":"#codes from Rodrigo Lima  @rodrigolima82\nfrom IPython.display import Image\nImage(url = 'https://encrypted-tbn0.gstatic.com/images?q=tbn%3AANd9GcSfKM9ny6lvxiXRkLxDps9NFRuWdpSy2Bt3THOwDJTWSSPoVoqy&usqp=CAU',width=400,height=400)","execution_count":null,"outputs":[]},{"metadata":{},"cell_type":"markdown","source":"#Elevated Interleukin-6:\n\nIL-6 can be elevated with inflammation, infection, autoimmune disorders, cardiovascular diseases, and some leukemias.\n\nElevated levels can specifically be due to:\n\nObesity; Too much food sugar/refined foods; Too much alcohol consumption; Chronic Stress;Not enough sleep; Smoking; Too much excercise; Infection, sepsis, and septicemia; Localized infections, such as prosthetic joint infections (PJI); Chronic inflammatory disorders, including rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), ankylosing spondylitis (AS), and inflammatory bowel disease (IBD)https://blog.healthmatters.io/2018/08/23/what-is-interleukin-6/","execution_count":null},{"metadata":{},"cell_type":"markdown","source":"Kaggle Notebook Runner: Marília Prata  @mpwolke","execution_count":null}],"metadata":{"kernelspec":{"language":"python","display_name":"Python 3","name":"python3"},"language_info":{"pygments_lexer":"ipython3","nbconvert_exporter":"python","version":"3.6.4","file_extension":".py","codemirror_mode":{"name":"ipython","version":3},"name":"python","mimetype":"text/x-python"}},"nbformat":4,"nbformat_minor":4}