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Hossain SF, Huang M, Ono N, Morita A, Kanaya S, Altaf-Ul-Amin M. Development of a biomarker database toward performing disease classification and finding disease interrelations. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6168336. [PMID: 33705530 PMCID: PMC7951048 DOI: 10.1093/database/baab011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 02/19/2021] [Accepted: 02/25/2021] [Indexed: 12/11/2022]
Abstract
A biomarker is a measurable indicator of a disease or abnormal state of a body that plays an important role in disease diagnosis, prognosis and treatment. The biomarker has become a significant topic due to its versatile usage in the medical field and in rapid detection of the presence or severity of some diseases. The volume of biomarker data is rapidly increasing and the identified data are scattered. To provide comprehensive information, the explosively growing data need to be recorded in a single platform. There is no open-source freely available comprehensive online biomarker database. To fulfill this purpose, we have developed a human biomarker database as part of the KNApSAcK family databases which contain a vast quantity of information on the relationships between biomarkers and diseases. We have classified the diseases into 18 disease classes, mostly according to the National Center for Biotechnology Information definitions. Apart from this database development, we also have performed disease classification by separately using protein and metabolite biomarkers based on the network clustering algorithm DPClusO and hierarchical clustering. Finally, we reached a conclusion about the relationships among the disease classes. The human biomarker database can be accessed online and the inter-disease relationships may be helpful in understanding the molecular mechanisms of diseases. To our knowledge, this is one of the first approaches to classify diseases based on biomarkers. Database URL: http://www.knapsackfamily.com/Biomarker/top.php.
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Affiliation(s)
- Shaikh Farhad Hossain
- Computational Systems Biology Lab, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Ming Huang
- Computational Systems Biology Lab, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Naoaki Ono
- Computational Systems Biology Lab, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Aki Morita
- Computational Systems Biology Lab, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Shigehiko Kanaya
- Computational Systems Biology Lab, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Md Altaf-Ul-Amin
- Computational Systems Biology Lab, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
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Marinheiro R, Parreira L, Amador P, Mesquita D, Farinha J, Fonseca M, Duarte T, Lopes C, Fernandes A, Caria R. Ventricular Arrhythmias in Patients with Obstructive Sleep Apnea. Curr Cardiol Rev 2019; 15:64-74. [PMID: 30338742 PMCID: PMC6367697 DOI: 10.2174/1573403x14666181012153252] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/05/2018] [Accepted: 10/09/2018] [Indexed: 12/15/2022] Open
Abstract
Obstructive Sleep Apnea (OSA) is a prevalent condition thought to increase in the future. Being mostly undiagnosed, the most serious complications are cardiovascular diseases, among which are arrhythmias. Controversy remains as to whether OSA is a primary etiologic factor for ventricular arrhythmias, because of the high incidence of cardiovascular comorbidities in OSA patients. Howev-er, there is mostly a strong evidence of a relation between OSA and ventricular arrhythmias. A few mechanisms have been proposed to be responsible for this association and some electrocardiographic changes have also been demonstrated to be more frequent in OSA patients. Treatment of OSA with Continuous Positive Airway Pressure (CPAP) has the potential to reduce arrhythmias and confer a mortality benefit.
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Affiliation(s)
- Rita Marinheiro
- Cardiology Department, Centro Hospitalar de Setubal, Setubal, Portugal
| | - Leonor Parreira
- Cardiology Department, Centro Hospitalar de Setubal, Setubal, Portugal
| | - Pedro Amador
- Cardiology Department, Centro Hospitalar de Setubal, Setubal, Portugal
| | - Dinis Mesquita
- Cardiology Department, Centro Hospitalar de Setubal, Setubal, Portugal
| | - José Farinha
- Cardiology Department, Centro Hospitalar de Setubal, Setubal, Portugal
| | - Marta Fonseca
- Cardiology Department, Centro Hospitalar de Setubal, Setubal, Portugal
| | - Tatiana Duarte
- Cardiology Department, Centro Hospitalar de Setubal, Setubal, Portugal
| | - Cláudia Lopes
- Cardiology Department, Centro Hospitalar de Setubal, Setubal, Portugal
| | - Andreia Fernandes
- Cardiology Department, Centro Hospitalar de Setubal, Setubal, Portugal
| | - Rui Caria
- Cardiology Department, Centro Hospitalar de Setubal, Setubal, Portugal
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Abstract
INTRODUCTION LTOT is a well-established treatment option for hypoxemic patients. Scientific evidence for its benefits of LTOT dates back to the 1980s, when two randomized controlled trials showed prolonged survival in COPD-patients undergoing LTOT for at least 15 hours/day. In contrast, the potential benefits of LTOT in non-COPD-patients has not been well researched and the recommendations for its application are primarily extrapolated from trials on COPD-patients. Recently, a large trial confirmed that COPD-patients who don't meet classic indication criteria, and have moderate desaturation at rest or during exercise, do not benefit from oxygen therapy. Also the significant technical evolution of LTOT devices has improved its application. Areas covered: A literature research was performed in pubmed regarding home oxygen therapy (terms: LTOT, ambulatory oxygen therapy, short burst oxygen therapy, nocturnal oxygen therapy). Expert commentary: LTOT proved a survival benefit for COPD patients about 30 years ago. Whether the results of these trials are still valid for patients under modern treatment guidelines remains unknown. Nevertheless, the classic indication criteria for LTOT still persist in guidelines, since there is a lack of updated evidence for the effects of LTOT in more severe hypoxemic patients.
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Affiliation(s)
- F S Magnet
- a Department of Pneumology, Faculty of Health/School of Medicine, Cologne Merheim Hospital , Kliniken der Stadt Köln gGmbH, Witten/Herdecke University , Köln , Germany
| | - J H Storre
- a Department of Pneumology, Faculty of Health/School of Medicine, Cologne Merheim Hospital , Kliniken der Stadt Köln gGmbH, Witten/Herdecke University , Köln , Germany.,b Department of Pneumology , University Medical Hospital , Freiburg , Germany
| | - W Windisch
- a Department of Pneumology, Faculty of Health/School of Medicine, Cologne Merheim Hospital , Kliniken der Stadt Köln gGmbH, Witten/Herdecke University , Köln , Germany
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Bordier P, Lataste A, Hofmann P, Robert F, Bourenane G. Nocturnal oxygen therapy in patients with chronic heart failure and sleep apnea: a systematic review. Sleep Med 2016; 17:149-57. [DOI: 10.1016/j.sleep.2015.10.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 10/12/2015] [Accepted: 10/13/2015] [Indexed: 11/16/2022]
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Hardinge M, Annandale J, Bourne S, Cooper B, Evans A, Freeman D, Green A, Hippolyte S, Knowles V, MacNee W, McDonnell L, Pye K, Suntharalingam J, Vora V, Wilkinson T. British Thoracic Society guidelines for home oxygen use in adults: accredited by NICE. Thorax 2015; 70 Suppl 1:i1-43. [DOI: 10.1136/thoraxjnl-2015-206865] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Effects of nocturnal oxygen therapy in patients with chronic heart failure and central sleep apnea: CHF-HOT study. Heart Vessels 2014; 31:165-72. [DOI: 10.1007/s00380-014-0592-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 10/10/2014] [Indexed: 11/30/2022]
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Suppressive effects of adaptive servo-ventilation on ventricular premature complexes with attenuation of sympathetic nervous activity in heart failure patients with sleep-disordered breathing. Heart Vessels 2013; 29:470-7. [DOI: 10.1007/s00380-013-0394-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 06/27/2013] [Indexed: 12/22/2022]
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Tomaello L, Zanolla L, Vassanelli C, LoCascio V, Ferrari M. Sleep disordered breathing is associated with appropriate implantable cardioverter defibrillator therapy in congestive heart failure patients. Clin Cardiol 2010; 33:E27-30. [PMID: 20043344 DOI: 10.1002/clc.20602] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Implantable cardioverter defibrillators (ICDs) are increasingly employed in patients affected by congestive heart failure (CHF) and sleep disordered breathing (SDB) is frequent in this population. HYPOTHESIS To investigate SDB prevalence and influence on appropriate ICD discharges in CHF patients. METHODS A total of 22 consecutive ICD patients with systolic CHF (left ventricular ejection fraction [LVEF]< 45%) were studied by polysomnography. RESULTS A total of 17 (77.2%) showed SDB (apnea-hypopnea index [AHI]_ 10 events/hour). After controlling for LVEF and New York Heart Association (NYHA) class, AHI and severity of hypoxia during sleep results correlated to appropriate ICD discharges (r = 0.718; P < .001, r = - 0.619; P = .003, respectively). CONCLUSIONS Sleep disordered breathing is frequent in ICD recipients due to left systolic ventricular dysfunction and may increase the risk of ventricular arrhythmia and appropriate ICD discharges.
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Affiliation(s)
- Luca Tomaello
- Department of Biomedical and Surgical Sciences, University of Verona, Italy.
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Suzuki JI. [Sleep apnea syndrome-related cardiovascular diseases]. Nihon Yakurigaku Zasshi 2007; 129:427-31. [PMID: 17575419 DOI: 10.1254/fpj.129.427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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