1.Improving classification of low-resource COVID-19 literature by using Named Entity Recognition
Oscar LITHGOW-SERRANO ; Joseph CORNELIUS ; Vani KANJIRANGAT ; Carlos-Francisco MÉNDEZ-CRUZ ; Fabio RINALDI
Genomics & Informatics 2021;19(3):e22-
Automatic document classification for highly interrelated classes is a demanding task that becomes more challenging when there is little labeled data for training. Such is the case of the coronavirus disease 2019 (COVID-19) Clinical repository—a repository of classified and translated academic articles related to COVID-19 and relevant to the clinical practice—where a 3-way classification scheme is being applied to COVID-19 literature. During the 7th Biomedical Linked Annotation Hackathon (BLAH7) hackathon, we performed experiments to explore the use of named-entity-recognition (NER) to improve the classification. We processed the literature with OntoGene’s Biomedical Entity Recogniser (OGER) and used the resulting identified Named Entities (NE) and their links to major biological databases as extra input features for the classifier. We compared the results with a baseline model without the OGER extracted features. In these proof-of-concept experiments, we observed a clear gain on COVID-19 literature classification. In particular, NE’s origin was useful to classify document types and NE’s type for clinical specialties. Due to the limitations of the small dataset, we can only conclude that our results suggests that NER would benefit this classification task. In order to accurately estimate this benefit, further experiments with a larger dataset would be needed.
2.Evidence-based clinical practice guidelines on seeking referral for preoperative cardiac evaluation for elective noncardiac surgery.
Laudico Adriano V ; Roxas Manuel Francisco T ; Cruz Ma. Concepcion L ; Valera Benjamin Daniel S ; Dans Antonio L ; Gutierrez Romeo R
Philippine Journal of Surgical Specialties 1999;54(4):171-223
The Philippine Council for Health Research and Development-Department of Science and Technology (PCHRD-DOST), and the Philippine College of Surgeons (PCS) signed a Memorandum of Agreement on 1 June 1999, whereby both agreed to support the formation of Evidence-Based Clinical Practice Guidelines (EBCPGs) on specific areas of surgical care in the Philippines. The areas were to be specified by the PCS, and those areas should have a reasonably large potential of improving the quality of patient care throughout the country, and can be implemented nationwide in both government and private health facilities The first clinical area selected was on when to refer for preoperative cardiac evaluation for elective noncardiac surgery, and when would the intraoperative presence of a cardiologist be beneficial. A Technical Working Group (TWG) was appointed, which: 1) searched and appraised the evidence; 2) prepared a first draft EBCPG; 3) presented the evidence to a Panel of Experts; 4) supervised the panel using the nominal group technique (6 November 1999 - PCS Building); and 5) prepared the second draft EBCPG based on the consensus recommendations of the panel. All processes strictly conformed to the methods of evidence-based guidelines formation specified by evidence-baesd medicine texts The second draft EBCPG was presented on 11 December 1999 during the 55th Clinical Congress of the PCS, and the final draft approved by the PCS Board of Regents on 29 January 2000 Literature search was conducted through the MEDLINE, COCHRANE Library an the HERDIN Database. A total of 2,156 titles, 427 abstracts and 77 full text articles were appraised. Data from 23 prospective cohort studies were encoded into the software COCHRANE Review Manager (RevMan), Version 3.0 for Windows (updated October 7, 1996). Tables were generated which contained authors, outcome rates, relative risks and the 95% confidence intervals of the relative risks. Three perioperative outcomes were identified-cardiac morbidity, cardiac death, and overall cardiac events
Human ; Risk ; Cardiologists ; Surgeons ; Research ; Publications ; Patient Care ; Health Facilities
3.Primary care services in the UHC: Cost identification study
Noel L. Espallardo ; Endrik Sy ; Annie A. Francisco ; Joseph Laceda ; Lyndon Patrick Dayrit ; Maria Victoria Concepcion P. Cruz ; Policarpio B. Joves Jr
The Filipino Family Physician 2022;60(2):260-267
Background:
In order to financially sustain the participation of the private sector in the UHC, there is a need to find reasonable balance of accountability in the costing of health services. The costing must be based on actual resources used from the perspective of the private health service provider.
Objective:
The objective of this paper was to determine the cost of primary care services from the framework of the UHC reform in the private sector.
Method:
This is a multi-method approach to cost-identification in establishing and providing primary care health service in the UHC. The approaches used by the authors included review of published literature, laws and policies from DOH and other regulatory agencies. From this review, they develop the minimum facility requirement for basic primary care facility and primary care facility with ancillary services. They used the actual expenditures of existing primary care clinics, 2021 quotations from equipment and supplies companies, published construction rates and consensus approach to establish the cost. Based on 2021 value of Philippine Peso, they estimated the cost of constructing and operating a primary care facility.
Results:
The total estimated cost of building a primary health care facility based on the DOH licensing standard was estimated to be around PhP2,490,000. The cost of furniture and equipment as required in the DOH AO was PhP474,685. Thus, the total cost of the construction and equipment for a basic primary care facility setup is PhP2,964,685. We estimated the annual operating cost with the building estimated to depreciate in 20 years and the furniture and equipment in 5 years, the annualized cost for the building is PhP124,500 and for the furniture and equipment PhP94,937. The total annual salary of the staff based on government standards was PhP2,381,962. The maintenance, operating and overhead expenses (MOOE) which included water and electricity, repair and maintenance, waste disposal, supplies and other fees was PhP451,190. The total annual operating cost of a basic primary care facility is PhP3,052,590. This facility can provide basic services such as outpatient consultation and minor surgeries. Using the same approach for the basic facility, the total annual operating cost of a basic primary care facility with ancillary service is PhP11,023,670. This facility can provide outpatient consultation, minor surgeries and primary care services such as health education and preventive care plus the ancillary services like pharmacy, clinical laboratory and x-ray. For patients with diabetes, the total annual cost is PhP8,986. The significant cost driver is the clinical assessment and non-pharmacologic intervention. The researchers found the same cost pattern for the annual cost care of patients with hypertension but with a slightly higher annual total with PhP9,963. Their sensitivity analysis based on inflation, construction, equipment and operating expense may increase these cost estimates by 20% in the next 5 years.
Conclusion
Based on their findings, the current per capita support from PHIC Konsulta package is not adequate in the private sector both for wellness and care of patients with chronic condition. PHIC needs to consider adjusting per capita rates and consider case rate payment as it is currently doing for hospital care. Without this proposed adjustment, only those patients in the higher socioeconomic status will be capable of consulting the private sector. This scenario defeats the equity issue that is a primary concern in the UHC.
Universal Health Care
4.Detrusor Overactivity After Partial Bladder Outlet Obstruction Is Associated With High Urinary Adenosine Triphosphate Levels in Female Wistar Rats
Luís VALE ; Francisco CRUZ ; Ana CHARRUA
International Neurourology Journal 2024;28(Suppl 1):34-39
Purpose:
Bladder outlet obstruction (BOO) commonly causes detrusor overactivity (DO). In this study, a post hoc analysis of previous obtained data, we investigate if DO occurring in initial phases of BOO is associated with changes in urinary adenosine triphosphate (ATP) levels.
Methods:
Adult female Wistar rats were submitted to partial BOO (pBOO) or to sham obstruction. Cystometry was performed at 3 or 15 days after pBOO and saline voided was collected for ATP determination. Normality was tested using Shapiro-Wilk test. The mean frequency of voiding contractions (VCs) of the sham-operated animals at 15 days after surgery, plus or minus 3 standard deviations, was used to represent the normal range. Statistical analyses were performed using the chi-square and Mann-Whitney tests.
Results:
DO was indicated by a VC frequency greater than or equal to 0.9 VCs/min. DO was observed in 63% of animals at 3 days and in 33% at 15 days following pBOO. ATP levels were significantly higher in rats with DO compared to those without DO.
Conclusions
The DO phenotype, occurring in the initial phases of BOO, is associated with comparatively high urinary ATP levels.
5.Clinical practice guidelines for the diagnosis and management of Dyspnea in primary care and outpatient setting
Noel L. Espallardo ; Haydee Danganan ; Jessica Mae C. Cruz ; Kriziaoumo P. Orpia ; Irene Veron Chico ; John Michael Deblois ; Peter Julian Francisco ; Jonathan Babsa-ay ; Ma Golda Catigbe ; Jobelle Bernabe
The Filipino Family Physician 2023;61(2):263-286
Background:
Dyspnea also referred to as shortness of breath or breathlessness is defined as “a subjective experience of breathing discomfort that consists of qualitatively distinct sensations that vary in intensity.” Dyspnea is a symptom of the disease, rather than a disease itself. Its etiology can be designated as arising from four primary categories: respiratory, cardiac, neuromuscular, psychogenic, systemic illness, or a combination of these.
Objective:
The general objective in developing this guideline is to improve the quality and outcomes of care to adult patients with dyspnea or shortness of breath in primary care and outpatient setting.
Methods
The ADAPTE process was utilized in the development of the initial guideline recommendations where the following steps were followed: 1) definition of clinical questions, 2) searching, screening and appraisal of guidelines, 3) decision and selection of evidence and 4) iterative drafting of guideline recommendation was done. The retrieved guidelines were systematically evaluated for their quality and validity using the Appraisal of Guidelines for Research & Evaluation (AGREE) II Instrument, which is a tool developed to assess the methodological quality of practice guidelines. If the adopted guideline did not have recommendations for our clinical question, we developed the recommendations de novo using the GRADE approach. We prioritized retrieving systematic reviews and meta-analysis articles that are relevant to our clinical questions. In the development of recommendations, the guideline development team prioritized the interventions that address the following outcomes i.e., decrease in severity of dyspnea, resolution of dyspnea, improved quality of life and decrease mortality. Data from the articles were extracted and the evidence was then summarized and appraised based on the type of study. The recommendations were then developed by the team as the initial draft that was subjected to external review and consensus panel discussion for finalization.
Outpatients
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Dyspnea
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Primary Health Care
6.Association Between Functional Dyspepsia and Binge Eating Disorder: A Frequent, Often Overlooked Overlap Clinical Presentation
Francisco A FÉLIX-TÉLLEZ ; Alejandra X CRUZ-SALGADO ; José M REMES-TROCHE ; Ángel R FLORES-RENDON ; Héctor R ORDAZ-ÁLVAREZ ; José A VELARDE-RUIZ VELASCO ; Marco A O FLORES-LIZÁRRAGA ; José I SOTO-GONZÁLEZ ; Nadia S ABIZAID-HERRERA
Journal of Neurogastroenterology and Motility 2025;31(1):95-101
Background/Aims:
This study aims to investigate the association between Binge Eating Disorder and functional dyspepsia in a Mexican population, focusing on symptomatology and demographic characteristics.
Methods:
We conducted a cross-sectional study on 1016 subjects, evaluating binge eating disorder (BED) and functional dyspepsia based on the Rome IV criteria. Data collection included sociodemographic information, gastrointestinal symptom severity, and anxiety/depression screening using validated tools. A multivariate logistic regression analysis with the 2 test was conducted for comparison analysis.
Results:
The prevalence of dyspepsia in BED was 53.6% (95% CI, 46-56). Postprandial fullness (OR, 1.52; 95% CI, 1.06-2.17; P = 0.021) and overlap syndrome (OR, 1.80; 95% CI, 1.25-2.60; P = 0.002) were significantly associated with BED. Patients with BED also presented more severe postprandial distress syndrome (P = 0.027). Anxiety was prevalent in BED patients, while depression was more prominent in patients with BED and dyspepsia overlap.
Conclusions
BED patients have a high prevalence of dyspepsia with an association between postprandial fullness and this eating disorder. BED appears to be more prevalent in younger individuals and males. These findings underscore the importance of considering dyspepsia in the management of BED and highlight the need for further research on this association.
7.Effect of Eugenol on Detrusor Muscle: Potential for Overactive Bladder Treatment
Marília Cavalcante ARAÚJO ; Átila PEREIRA-GONÇALVES ; André Nogueira CARDEAL DOS SANTOS ; José Ednésio da Cruz FREIRE ; Luís PEIREIRA-DE-MORAIS ; Francisco Sydney HENRIQUE-FÉLIX ; Nicoly Câmara Castro SOUSA-JÚLIO ; José Henrique LEAL-CARDOSO ; Andrelina Noronha COELHO-DE-SOUZA
International Neurourology Journal 2024;28(4):253-263
Purpose:
This investigation was conducted to elucidate the effects of eugenol on bladder contractility through experimental and in silico approaches.
Methods:
To assess the impact of eugenol on muscular contractility, longitudinal strips of bladder tissue, measuring 2 mm by 6 mm, were mounted in perfusion chambers connected to an isometric force transducer. Furthermore, molecular docking studies were conducted to explore the potential of eugenol to target the M3 muscarinic acetylcholine receptor (M3R) and voltage-operated calcium channels (VOCCs) in muscle cells, utilizing in silico techniques.
Results:
Eugenol exhibited a concentration-dependent inhibitory effect on both the phasic and tonic components of the contraction induced by 60mM K+ and carbachol, completely suppressing this contraction at a concentration of 3mM. Additionally, eugenol inhibited the concentration-contraction curve elicited by Ba2+.
Conclusions
The in vitro and in silico results suggest that the mechanism of eugenol likely involves blockade of VOCCs and/or M3R, implicating eugenol as a promising molecule for the treatment of overactive bladder.
8.Effect of Eugenol on Detrusor Muscle: Potential for Overactive Bladder Treatment
Marília Cavalcante ARAÚJO ; Átila PEREIRA-GONÇALVES ; André Nogueira CARDEAL DOS SANTOS ; José Ednésio da Cruz FREIRE ; Luís PEIREIRA-DE-MORAIS ; Francisco Sydney HENRIQUE-FÉLIX ; Nicoly Câmara Castro SOUSA-JÚLIO ; José Henrique LEAL-CARDOSO ; Andrelina Noronha COELHO-DE-SOUZA
International Neurourology Journal 2024;28(4):253-263
Purpose:
This investigation was conducted to elucidate the effects of eugenol on bladder contractility through experimental and in silico approaches.
Methods:
To assess the impact of eugenol on muscular contractility, longitudinal strips of bladder tissue, measuring 2 mm by 6 mm, were mounted in perfusion chambers connected to an isometric force transducer. Furthermore, molecular docking studies were conducted to explore the potential of eugenol to target the M3 muscarinic acetylcholine receptor (M3R) and voltage-operated calcium channels (VOCCs) in muscle cells, utilizing in silico techniques.
Results:
Eugenol exhibited a concentration-dependent inhibitory effect on both the phasic and tonic components of the contraction induced by 60mM K+ and carbachol, completely suppressing this contraction at a concentration of 3mM. Additionally, eugenol inhibited the concentration-contraction curve elicited by Ba2+.
Conclusions
The in vitro and in silico results suggest that the mechanism of eugenol likely involves blockade of VOCCs and/or M3R, implicating eugenol as a promising molecule for the treatment of overactive bladder.
9.Association Between Functional Dyspepsia and Binge Eating Disorder: A Frequent, Often Overlooked Overlap Clinical Presentation
Francisco A FÉLIX-TÉLLEZ ; Alejandra X CRUZ-SALGADO ; José M REMES-TROCHE ; Ángel R FLORES-RENDON ; Héctor R ORDAZ-ÁLVAREZ ; José A VELARDE-RUIZ VELASCO ; Marco A O FLORES-LIZÁRRAGA ; José I SOTO-GONZÁLEZ ; Nadia S ABIZAID-HERRERA
Journal of Neurogastroenterology and Motility 2025;31(1):95-101
Background/Aims:
This study aims to investigate the association between Binge Eating Disorder and functional dyspepsia in a Mexican population, focusing on symptomatology and demographic characteristics.
Methods:
We conducted a cross-sectional study on 1016 subjects, evaluating binge eating disorder (BED) and functional dyspepsia based on the Rome IV criteria. Data collection included sociodemographic information, gastrointestinal symptom severity, and anxiety/depression screening using validated tools. A multivariate logistic regression analysis with the 2 test was conducted for comparison analysis.
Results:
The prevalence of dyspepsia in BED was 53.6% (95% CI, 46-56). Postprandial fullness (OR, 1.52; 95% CI, 1.06-2.17; P = 0.021) and overlap syndrome (OR, 1.80; 95% CI, 1.25-2.60; P = 0.002) were significantly associated with BED. Patients with BED also presented more severe postprandial distress syndrome (P = 0.027). Anxiety was prevalent in BED patients, while depression was more prominent in patients with BED and dyspepsia overlap.
Conclusions
BED patients have a high prevalence of dyspepsia with an association between postprandial fullness and this eating disorder. BED appears to be more prevalent in younger individuals and males. These findings underscore the importance of considering dyspepsia in the management of BED and highlight the need for further research on this association.
10.Effect of Eugenol on Detrusor Muscle: Potential for Overactive Bladder Treatment
Marília Cavalcante ARAÚJO ; Átila PEREIRA-GONÇALVES ; André Nogueira CARDEAL DOS SANTOS ; José Ednésio da Cruz FREIRE ; Luís PEIREIRA-DE-MORAIS ; Francisco Sydney HENRIQUE-FÉLIX ; Nicoly Câmara Castro SOUSA-JÚLIO ; José Henrique LEAL-CARDOSO ; Andrelina Noronha COELHO-DE-SOUZA
International Neurourology Journal 2024;28(4):253-263
Purpose:
This investigation was conducted to elucidate the effects of eugenol on bladder contractility through experimental and in silico approaches.
Methods:
To assess the impact of eugenol on muscular contractility, longitudinal strips of bladder tissue, measuring 2 mm by 6 mm, were mounted in perfusion chambers connected to an isometric force transducer. Furthermore, molecular docking studies were conducted to explore the potential of eugenol to target the M3 muscarinic acetylcholine receptor (M3R) and voltage-operated calcium channels (VOCCs) in muscle cells, utilizing in silico techniques.
Results:
Eugenol exhibited a concentration-dependent inhibitory effect on both the phasic and tonic components of the contraction induced by 60mM K+ and carbachol, completely suppressing this contraction at a concentration of 3mM. Additionally, eugenol inhibited the concentration-contraction curve elicited by Ba2+.
Conclusions
The in vitro and in silico results suggest that the mechanism of eugenol likely involves blockade of VOCCs and/or M3R, implicating eugenol as a promising molecule for the treatment of overactive bladder.