1
|
Ampadi Ramachandran R, Tell LA, Rai S, Millagaha Gedara NI, Xu X, Riviere JE, Jaberi-Douraki M. An Automated Customizable Live Web Crawler for Curation of Comparative Pharmacokinetic Data: An Intelligent Compilation of Research-Based Comprehensive Article Repository. Pharmaceutics 2023; 15:pharmaceutics15051384. [PMID: 37242626 DOI: 10.3390/pharmaceutics15051384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/17/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Data curation has significant research implications irrespective of application areas. As most curated studies rely on databases for data extraction, the availability of data resources is extremely important. Taking a perspective from pharmacology, extracted data contribute to improved drug treatment outcomes and well-being but with some challenges. Considering available pharmacology literature, it is necessary to review articles and other scientific documents carefully. A typical method of accessing articles on journal websites is through long-established searches. In addition to being labor-intensive, this conventional approach often leads to incomplete-content downloads. This paper presents a new methodology with user-friendly models to accept search keywords according to the investigators' research fields for metadata and full-text articles. To accomplish this, scientifically published records on the pharmacokinetics of drugs were extracted from several sources using our navigating tool called the Web Crawler for Pharmacokinetics (WCPK). The results of metadata extraction provided 74,867 publications for four drug classes. Full-text extractions performed with WCPK revealed that the system is highly competent, extracting over 97% of records. This model helps establish keyword-based article repositories, contributing to comprehensive databases for article curation projects. This paper also explains the procedures adopted to build the proposed customizable-live WCPK, from system design and development to deployment phases.
Collapse
Affiliation(s)
- Remya Ampadi Ramachandran
- 1DATA Consortium, Kansas State University Olathe, Olathe, KS 66061, USA
- Food Animal Residue Avoidance and Databank Program (FARAD), Kansas State University Olathe, Olathe, KS 66061, USA
- Department of Mathematics, Kansas State University, Manhattan, KS 66502, USA
| | - Lisa A Tell
- FARAD, Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA
| | - Sidharth Rai
- 1DATA Consortium, Kansas State University Olathe, Olathe, KS 66061, USA
- Food Animal Residue Avoidance and Databank Program (FARAD), Kansas State University Olathe, Olathe, KS 66061, USA
- Department of Mathematics, Kansas State University, Manhattan, KS 66502, USA
| | - Nuwan Indika Millagaha Gedara
- 1DATA Consortium, Kansas State University Olathe, Olathe, KS 66061, USA
- Food Animal Residue Avoidance and Databank Program (FARAD), Kansas State University Olathe, Olathe, KS 66061, USA
- Department of Mathematics, Kansas State University, Manhattan, KS 66502, USA
| | - Xuan Xu
- 1DATA Consortium, Kansas State University Olathe, Olathe, KS 66061, USA
- Food Animal Residue Avoidance and Databank Program (FARAD), Kansas State University Olathe, Olathe, KS 66061, USA
- Department of Mathematics, Kansas State University, Manhattan, KS 66502, USA
| | - Jim E Riviere
- 1DATA Consortium, Kansas State University Olathe, Olathe, KS 66061, USA
- Food Animal Residue Avoidance and Databank Program (FARAD), Kansas State University Olathe, Olathe, KS 66061, USA
| | - Majid Jaberi-Douraki
- 1DATA Consortium, Kansas State University Olathe, Olathe, KS 66061, USA
- Food Animal Residue Avoidance and Databank Program (FARAD), Kansas State University Olathe, Olathe, KS 66061, USA
- Department of Mathematics, Kansas State University, Manhattan, KS 66502, USA
| |
Collapse
|
2
|
Therapeutic Drug Monitoring of Antifungal Agents in Critically Ill Patients: Is There a Need for Dose Optimisation? Antibiotics (Basel) 2022; 11:antibiotics11050645. [PMID: 35625289 PMCID: PMC9137962 DOI: 10.3390/antibiotics11050645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/06/2022] [Accepted: 05/07/2022] [Indexed: 02/01/2023] Open
Abstract
Invasive fungal infections are an important cause of morbidity and mortality, especially in critically ill patients. Increasing resistance rates and inadequate antifungal exposure have been documented in these patients, due to clinically relevant pharmacokinetic (PK) and pharmacodynamic (PD) alterations, leading to treatment failure. Physiological changes such as third spacing (movement of fluid from the intravascular compartment to the interstitial space), hypoalbuminemia, renal failure and hepatic failure, as well as common interventions in the intensive care unit, such as renal replacement therapy and extracorporeal membrane oxygenation, can lead to these PK and PD alterations. Consequently, a therapeutic target concentration that may be useful for one patient may not be appropriate for another. Regular doses do not take into account the important PK variations in the critically ill, and the need to select an effective dose while minimising toxicity advocates for the use of therapeutic drug monitoring (TDM). This review aims to describe the current evidence regarding optimal PK/PD indices associated with the clinical efficacy of the most commonly used antifungal agents in critically ill patients (azoles, echinocandins, lipid complexes of amphotericin B, and flucytosine), provide a comprehensive understanding of the factors affecting the PK of each agent, document the PK parameters of critically ill patients compared to healthy volunteers, and, finally, make recommendations for therapeutic drug monitoring (TDM) of antifungals in critically ill patients.
Collapse
|
3
|
Species Distribution of Candidemia and Their Susceptibility in a Single Japanese University Hospital: Prior Micafungin Use Affects the Appearance of Candida parapsilosis and Elevation of Micafungin MICs in Non- parapsilosis Candida Species. J Fungi (Basel) 2021; 7:jof7080596. [PMID: 34436135 PMCID: PMC8397203 DOI: 10.3390/jof7080596] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/14/2021] [Accepted: 07/21/2021] [Indexed: 12/26/2022] Open
Abstract
Introduction: Micafungin is a recommended echinocandin antifungal agent for candidemia treatment and prophylaxis. However, overuse of echinocandin antifungals may cause resistance. There is currently no information available regarding the low susceptibility associated with using micafungin. This study investigated the effect of micafungin use on changes in the detected Candida species and low susceptibility. Methods: We conducted a retrospective survey and included records of Candida spp. detected in blood cultures from January 2010 to December 2018 in our hospital. Survey items included clinical outcomes at 30 days after positive cultures, patient characteristics, and drug prescription status. Patient background information included gender, previous hospitalization, stay in the intensive care unit, comorbidities, and history of surgery (within 90 days before candidemia onset) and drug exposure. Species detected and their minimum inhibitory concentrations (MICs) and amount of antifungal prescriptions by department were investigated. Risk factors for detecting C. parapsilosis and for low susceptibility to micafungin were evaluated using multivariate analysis. Results: A total of 153 Candida clinical blood isolates were collected and C. albicans was the most prevalent species, followed by C. parapsilosis and C. glabrata. In the analysis by department, antifungal use and non-albicans Candida species were most frequently detected in the hematology department. Multivariate analysis showed that prior micafungin use increased the risk of C. parapsilosis (odds ratio (OR) 4.22; 95% confidence interval (CI) 1.39–12.79; p = 0.011). MIC90 of micafungin on C. glabrata and C. parapsilosis was 1.0 μg/mL. Prior micafungin use was clarified as a risk factor resulting in MIC > 0.06 μg/mL for micafungin in non-parapsilosis Candida species (OR 13.2; 95% CI 3.23–54.2; p < 0.01). Conclusion: Prior micafungin use increased the risk of C. parapsilosis and the MIC > 0.06 μg/mL of micafungin in non-parapsilosis Candida species. Since there are only a few antifungal options, further antifungal stewardship considering azole antifungal agents use is required.
Collapse
|