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Article ; Online: Virtual patient with temporal evolution for mechanical ventilation trial studies: A stochastic model approach.

Ang, Christopher Yew Shuen / Chiew, Yeong Shiong / Wang, Xin / Ooi, Ean Hin / Nor, Mohd Basri Mat / Cove, Matthew E / Chase, J Geoffrey

Computer methods and programs in biomedicine

2023 Volume 240, Page(s) 107728

Abstract: Background and objective: Healthcare datasets are plagued by issues of data scarcity and class imbalance. Clinically validated virtual patient (VP) models can provide accurate in-silico representations of real patients and thus a means for synthetic ... ...

Abstract	Background and objective: Healthcare datasets are plagued by issues of data scarcity and class imbalance. Clinically validated virtual patient (VP) models can provide accurate in-silico representations of real patients and thus a means for synthetic data generation in hospital critical care settings. This research presents a realistic, time-varying mechanically ventilated respiratory failure VP profile synthesised using a stochastic model. Methods: A stochastic model was developed using respiratory elastance (E Results: A total of 120,000 3-hour VPs for pressure control (PC) and volume control (VC) ventilation modes are generated using stochastic simulation. Optimisation of the stochastic simulation process yields an ideal noise percentage of 5-10% and simulation iteration of 200,000 iterations, allowing the simulation of a realistic and diverse set of E Conclusion: VPs capable of temporal evolution demonstrate feasibility for use in designing, developing, and optimising bedside MV guidance protocols through in-silico simulation and validation. Overall, the temporal VPs developed using stochastic simulation alleviate the need for lengthy, resource intensive, high cost clinical trials, while facilitating statistically robust virtual trials, ultimately leading to improved patient care and outcomes in mechanical ventilation.
MeSH term(s)	Humans ; Respiration, Artificial/methods ; Retrospective Studies ; Computer Simulation ; Critical Care/methods ; Research Design
Language	English
Publishing date	2023-07-21
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	632564-6
ISSN	1872-7565 ; 0169-2607
ISSN (online)	1872-7565
ISSN	0169-2607
DOI	10.1016/j.cmpb.2023.107728
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Article ; Online: Radial artery cardiac catheterization: changing the convincing data/work to change (CD/WC) ratio.

Cove, Christopher

Cardiology journal

2009 Volume 16, Issue 4, Page(s) 297–299

MeSH term(s)	Angioplasty, Balloon, Coronary/methods ; Cardiac Catheterization/methods ; Coronary Artery Disease/diagnosis ; Humans ; Radial Artery
Language	English
Publishing date	2009
Publishing country	Poland
Document type	Comment ; Editorial
ZDB-ID	2488680-4
ISSN	1897-5593 ; 1897-5593
ISSN (online)	1897-5593
ISSN	1897-5593
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Article ; Online: Quantification of respiratory effort magnitude in spontaneous breathing patients using Convolutional Autoencoders.

Ang, Christopher Yew Shuen / Chiew, Yeong Shiong / Vu, Lien Hong / Cove, Matthew E

Computer methods and programs in biomedicine

2021 Volume 215, Page(s) 106601

Abstract: Background: Spontaneous breathing (SB) effort during mechanical ventilation (MV) is an important metric of respiratory drive. However, SB effort varies due to a variety of factors, including evolving pathology and sedation levels. Therefore, assessment ... ...

Abstract	Background: Spontaneous breathing (SB) effort during mechanical ventilation (MV) is an important metric of respiratory drive. However, SB effort varies due to a variety of factors, including evolving pathology and sedation levels. Therefore, assessment of SB efforts needs to be continuous and non-invasive. This is important to prevent both over- and under-assistance with MV. In this study, a machine learning model, Convolutional Autoencoder (CAE) is developed to quantify the magnitude of SB effort using only bedside MV airway pressure and flow waveform. Method: The CAE model was trained using 12,170,655 simulated SB flow and normal flow data (NB). The paired SB and NB flow data were simulated using a Gaussian Effort Model (GEM) with 5 basis functions. When the CAE model is given a SB flow input, it is capable of predicting a corresponding NB flow for the SB flow input. The magnitude of SB effort (SBE Results: The CAE model was able to produce NB flows from the clinical SB flows with the median SBE Conclusion: A Convolutional Autoencoder model was developed with simulated SB and NB flow data and is capable of quantifying the magnitude of patient spontaneous breathing effort. This provides potential application for real-time monitoring of patient respiratory drive for better management of patient-ventilator interaction.
MeSH term(s)	Humans ; Normal Distribution ; Positive-Pressure Respiration ; Respiration, Artificial ; Respiratory Mechanics
Language	English
Publishing date	2021-12-22
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	632564-6
ISSN	1872-7565 ; 0169-2607
ISSN (online)	1872-7565
ISSN	0169-2607
DOI	10.1016/j.cmpb.2021.106601
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Article ; Online: Predicting mechanically ventilated patients future respiratory system elastance - A stochastic modelling approach.

Ang, Christopher Yew Shuen / Chiew, Yeong Shiong / Wang, Xin / Mat Nor, Mohd Basri / Cove, Matthew E / Chase, J Geoffrey

Computers in biology and medicine

2022 Volume 151, Issue Pt A, Page(s) 106275

Abstract: Background and objective: Respiratory mechanics of mechanically ventilated patients evolve significantly with time, disease state and mechanical ventilation (MV) treatment. Existing deterministic data prediction methods fail to comprehensively describe ... ...

Abstract	Background and objective: Respiratory mechanics of mechanically ventilated patients evolve significantly with time, disease state and mechanical ventilation (MV) treatment. Existing deterministic data prediction methods fail to comprehensively describe the multiple sources of heterogeneity of biological systems. This research presents two respiratory mechanics stochastic models with increased prediction accuracy and range, offering improved clinical utility in MV treatment. Methods: Two stochastic models (SM2 and SM3) were developed using retrospective patient respiratory elastance (E Results: Clinical validation shows all three models captured more than 98% (median) of future E Conclusion: The new stochastic models significantly improve prediction, clinical utility, and thus feasibility for synchronisation with clinical interventions. Paired with other MV protocols, the stochastic models developed can potentially form part of decision support systems, providing guided, personalised, and safe MV treatment.
MeSH term(s)	Humans ; Respiration, Artificial/methods ; Positive-Pressure Respiration/methods ; Retrospective Studies ; Respiratory Mechanics ; Respiratory System
Language	English
Publishing date	2022-11-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2022.106275
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Article ; Online: Assessing the role of habitat and species interactions in the population decline and detection bias of Neotropical leaf litter frogs in and around La Selva Biological Station, Costa Rica

Maria D. Vera Alvarez / Christopher Fernandez / Michael V. Cove

Neotropical Biology and Conservation, Vol 14, Iss 2, Pp 143-

2019 Volume 156

Abstract: Worldwide, amphibian populations have been declining rapidly. This decline can be attributed to many factors including climate change, pesticide exposure, and emerging infectious diseases, among other important factors, but few studies have examined the ... ...

Abstract	Worldwide, amphibian populations have been declining rapidly. This decline can be attributed to many factors including climate change, pesticide exposure, and emerging infectious diseases, among other important factors, but few studies have examined the influence of species interactions. In this study, we examined how habitat factors and co-occurring avian and mammalian species, as well as humans, exert direct and indirect effects on Neotropical amphibian population dynamics. We further examined how these habitat and species interactions could affect our ability to reliably detect amphibian presence to robustly estimate population trends. We conducted amphibian visual encounter surveys at 26 randomly selected sites in the La Selva Biological Station, in northeastern Costa Rica, as well as 26 sites across five additional forest fragments in the region. Furthermore, we used camera traps to collect data on avian and mammalian communities and human visitation at those amphibian survey plots. From these data, we were able to estimate species occupancy probabilities for leaf litter frogs across sites and their relationships to habitat and interspecific species interaction covariates. We also conducted an experiment with plastic model frogs to estimate detection probabilities when a population is known to occur at a site with certainty. Our results suggested that strawberry poison dart frog (Oophaga pumilio) occupancy was positively related to secondary forest and their detection was negatively related to increasing air temperatures at the times of the surveys. Leaf litter frog occupancy was negatively related to core La Selva sites and human detections at sites, yet their detection was positively related to human trail presence, which might be related to reduced leaf litter cover due to heavy trampling. Our experimental surveys suggested that Neotropical leaf litter frog communities are difficult to detect when present and future studies should explicitly account for this detection bias to effectively monitor ...
Keywords	Biology (General) ; QH301-705.5
Subject code	590
Language	English
Publishing date	2019-07-01T00:00:00Z
Publisher	Pensoft Publishers
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Virtual patient framework for the testing of mechanical ventilation airway pressure and flow settings protocol.

Ang, Christopher Yew Shuen / Lee, Jay Wing Wai / Chiew, Yeong Shiong / Wang, Xin / Tan, Chee Pin / Cove, Matthew E / Nor, Mohd Basri Mat / Zhou, Cong / Desaive, Thomas / Chase, J Geoffrey

Computer methods and programs in biomedicine

2022 Volume 226, Page(s) 107146

Abstract: Background and objective: Model-based and personalised decision support systems are emerging to guide mechanical ventilation (MV) treatment for respiratory failure patients. However, model-based treatments require resource-intensive clinical trials ... ...

Abstract	Background and objective: Model-based and personalised decision support systems are emerging to guide mechanical ventilation (MV) treatment for respiratory failure patients. However, model-based treatments require resource-intensive clinical trials prior to implementation. This research presents a framework for generating virtual patients for testing model-based decision support, and direct use in MV treatment. Methods: The virtual MV patient framework consists of 3 stages: 1) Virtual patient generation, 2) Patient-level validation, and 3) Virtual clinical trials. The virtual patients are generated from retrospective MV patient data using a clinically validated respiratory mechanics model whose respiratory parameters (respiratory elastance and resistance) capture patient-specific pulmonary conditions and responses to MV care over time. Patient-level validation compares the predicted responses from the virtual patient to their retrospective results for clinically implemented MV settings and changes to care. Patient-level validated virtual patients create a platform to conduct virtual trials, where the safety of closed-loop model-based protocols can be evaluated. Results: This research creates and presents a virtual patient platform of 100 virtual patients generated from retrospective data. Patient-level validation reported median errors of 3.26% for volume-control and 6.80% for pressure-control ventilation mode. A virtual trial on a model-based protocol demonstrates the potential efficacy of using virtual patients for prospective evaluation and testing of the protocol. Conclusion: The virtual patient framework shows the potential to safely and rapidly design, develop, and optimise new model-based MV decision support systems and protocols using clinically validated models and computer simulation, which could ultimately improve patient care and outcomes in MV.
MeSH term(s)	Humans ; Computer Simulation ; Respiration, Artificial/methods ; Respiratory Mechanics/physiology ; Retrospective Studies ; Clinical Trials as Topic
Language	English
Publishing date	2022-09-18
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	632564-6
ISSN	1872-7565 ; 0169-2607
ISSN (online)	1872-7565
ISSN	0169-2607
DOI	10.1016/j.cmpb.2022.107146
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Article: Squamates as prey: Predator diversity patterns and predator-prey size relationships

Schalk, Christopher M / Michael V. Cove

Food webs. 2018 Dec., v. 17

2018

Abstract: Understanding the relationships between prey and their predators can provide important insights into evolution of defenses, foraging ecology, and functional roles within their ecosystem. Squamates (lizards and snakes) exhibit a wide range of ... ...

Abstract	Understanding the relationships between prey and their predators can provide important insights into evolution of defenses, foraging ecology, and functional roles within their ecosystem. Squamates (lizards and snakes) exhibit a wide range of morphological, ecological and behavioral variation and are model organisms for the study of the evolution of anti-predator traits, making them an ideal group to search for general patterns in predator-prey relationships. We compiled a squamate predator database that consisted of 1152 squamate predation-prey interactions representing 396 lizard species from 30 families and 217 snake species from 13 families. We quantified the predator taxonomic diversity and explored the relationship between predator size and prey size. Both lizards and snakes were preyed upon by a greater diversity of squamate predators compared to avian and mammalian predators. Snakes appear to be more vulnerable to a broader size range of predators compared to lizards, which is likely attributed to differences in their body morphology. These results provide further support for the hypotheses that predation pressure may affect the evolutionary trajectory of squamate defenses.
Keywords	Squamata ; birds ; databases ; ecosystems ; food webs ; foraging ; lizards ; mammals ; models ; predation ; predator-prey relationships ; predators ; snakes ; species diversity
Language	English
Dates of publication	2018-12
Size	p. e00103.
Publishing place	Elsevier Inc.
Document type	Article
ISSN	2352-2496
DOI	10.1016/j.fooweb.2018.e00103
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Family Business of Aortopathies.

Fernandez, Genaro / Cameron, Scott / Nayda, John / Cove, Christopher / Waits, Bryan

The American journal of medicine

2015 Volume 128, Issue 11, Page(s) e13–5

MeSH term(s)	Aged, 80 and over ; Aneurysm, Dissecting/diagnosis ; Aneurysm, Dissecting/etiology ; Aortic Aneurysm/diagnosis ; Aortic Aneurysm/etiology ; Family ; Female ; Humans ; Syndrome
Language	English
Publishing date	2015-11
Publishing country	United States
Document type	Case Reports ; Journal Article
ZDB-ID	80015-6
ISSN	1555-7162 ; 1873-2178 ; 0002-9343 ; 1548-2766
ISSN (online)	1555-7162 ; 1873-2178
ISSN	0002-9343 ; 1548-2766
DOI	10.1016/j.amjmed.2015.06.018
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Article: Redo craniotomy or bevacizumab for symptomatic steroid-refractory true or pseudoprogression following IMRT for glioblastoma.

Cook, Theresa A / Jayamanne, Dasantha T / Wheeler, Helen R / Wong, Matthew H F / Parkinson, Jonathon F / Cook, Raymond J / Kastelan, Marina A / Cove, Nicola J / Brown, Christopher / Back, Michael F

Neuro-oncology practice

2021 Volume 8, Issue 5, Page(s) 601–608

Abstract: Background: There is minimal evidence to support decision making for symptomatic steroid-refractory pseudoprogression or true progression occurring after intensity-modulated radiation therapy (IMRT) for glioblastoma (GBM). This study audited the ... ...

Abstract	Background: There is minimal evidence to support decision making for symptomatic steroid-refractory pseudoprogression or true progression occurring after intensity-modulated radiation therapy (IMRT) for glioblastoma (GBM). This study audited the survival outcome of patients managed with redo craniotomy (RedoSx) or bevacizumab (BEV) for steroid-refractory mass effect after IMRT for GBM. Methods: Patients with GBM managed between 2008 and 2019 with the EORTC-NCIC Protocol were entered into a prospective database. Patients with symptomatic steroid-refractory mass effect within 6 months of IMRT managed with either RedoSx or BEV were identified for analysis. For the primary endpoint of median overall survival (OS) postintervention, outcome was analyzed in regards to potential prognostic factors, and differences between groups were assessed by log-rank analyses. Results: Of the 399 patients managed with the EORTC-NCIC Protocol, 78 required an intervention within 6 months of IMRT completion for either true or pseudoprogression (49 with RedoSx and 29 with BEV). Subsequently, 20 of the 43 patients managed with RedoSx when BEV was clinically available, required salvage with BEV within 6 months after RedoSx. Median OS postintervention was 8.7 months (95% CI: 7.84-11.61) for the total group; and 8.7 months (95% CI: 6.8-13.1) for RedoSx and 9.4 months (95% CI: 7.8-13.6) for BEV ( Conclusions: At time of symptomatic steroid-refractory true or pseudoprogression following IMRT for GBM, BEV was equivalent to RedoSx in terms of OS. Pseudoprogression with residual cells at RedoSx was not associated with worse outcome compared to pure necrosis.
Language	English
Publishing date	2021-06-09
Publishing country	England
Document type	Journal Article
ZDB-ID	2768945-1
ISSN	2054-2585 ; 2054-2577
ISSN (online)	2054-2585
ISSN	2054-2577
DOI	10.1093/nop/npab034
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Article: Assessing the role of habitat and species interactions in the population decline and detection bias of Neotropical leaf litter frogs in and around La Selva Biological Station, Costa Rica

Alvarez, Maria D. Vera / Fernandez, Christopher / Cove, Michael V

Neotropical Biology and Conservation. 2019 July 15, v. 14, no. 2

2019

Title translation	Avaliação do papel das interações entre espécies e habitats no declínio populacional e no viés de detecção de rãs neotropicais da serapilheira na Estação Biológica La Selva e arredores, Costa Rica
Abstract	Worldwide, amphibian populations have been declining rapidly. This decline can be attributed to many factors including climate change, pesticide exposure, and emerging infectious diseases, among other important factors, but few studies have examined the influence of species interactions. In this study, we examined how habitat factors and co-occurring avian and mammalian species, as well as humans, exert direct and indirect effects on Neotropical amphibian population dynamics. We further examined how these habitat and species interactions could affect our ability to reliably detect amphibian presence to robustly estimate population trends. We conducted amphibian visual encounter surveys at 26 randomly selected sites in the La Selva Biological Station, in northeastern Costa Rica, as well as 26 sites across five additional forest fragments in the region. Furthermore, we used camera traps to collect data on avian and mammalian communities and human visitation at those amphibian survey plots. From these data, we were able to estimate species occupancy probabilities for leaf litter frogs across sites and their relationships to habitat and interspecific species interaction covariates. We also conducted an experiment with plastic model frogs to estimate detection probabilities when a population is known to occur at a site with certainty. Our results suggested that strawberry poison dart frog (Oophagapumilio) occupancy was positively related to secondary forest and their detection was negatively related to increasing air temperatures at the times of the surveys. Leaf litter frog occupancy was negatively related to core La Selva sites and human detections at sites, yet their detection was positively related to human trail presence, which might be related to reduced leaf litter cover due to heavy trampling. Our experimental surveys suggested that Neotropical leaf litter frog communities are difficult to detect when present and future studies should explicitly account for this detection bias to effectively monitor population trends.
Keywords	Neotropics ; Oophaga pumilio ; air temperature ; birds ; cameras ; climate change ; emerging diseases ; frogs ; habitat fragmentation ; habitats ; humans ; models ; pesticides ; plant litter ; population dynamics ; probability ; secondary forests ; surveys ; trampling damage ; Costa Rica
Language	English
Dates of publication	2019-0715
Size	p. 143-156.
Publishing place	Pensoft Publishers
Document type	Article
ZDB-ID	2613449-4
ISSN	2236-3777 ; 1809-9939
ISSN (online)	2236-3777
ISSN	1809-9939
DOI	10.3897/neotropical.14.e37526
Database	NAL-Catalogue (AGRICOLA)

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