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"Bow-tie" optimal pathway discovery analysis of sepsis hospital admissions using the Hospital Episode Statistics database in England

Hugo De Oliveira, Martin Prodel, Ludovic Lamarsalle, Matt Inada-Kim, Kenny Ajayi, Julia Wilkins, Sara Sekelj, Sue Beecroft, Sally Snow, Ruth Slater, Andi Orlowski
2020 JAMIA Open  
Objective The "Bow-tie" optimal pathway discovery analysis uses large clinical event datasets to map clinical pathways and to visualize risks (improvement opportunities) before, and outcomes after, a specific  ...  This proof-of-concept study assesses the use of NHS Hospital Episode Statistics (HES) in England as a potential clinical event dataset for this pathway discovery analysis approach.  ...  INTRODUCTION Process mining using pathway discovery analysis in healthcare Process mining (PM) in a healthcare setting is gaining increasing focus due to the vast amounts of clinical data collected and  ... 
doi:10.1093/jamiaopen/ooaa039 fatcat:kj44xu37ovgfndsgqrh3rw66km

Towards Process Mining of EMR Data - Case Study for Sepsis Management

Gert-Jan de Vries, Ricardo Alfredo Quintano Neira, Gijs Geleijnse, Prabhakar Dixit, Bruno Franco Mazza
2017 Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies  
In this paper, we provide insight into the steps required to perform process mining to EMR data in the challenging domain of sepsis treatment and provide learnings from our preliminary analysis of these  ...  data using process mining techniques.  ...  ACKNOWLEDGEMENTS We would like to thank the clinical and technical staff at Hospital Samaritano for their help in collecting the event data, as well as our colleagues from Philips Research for making this  ... 
doi:10.5220/0006274405850593 dblp:conf/biostec/VriesNGDM17 fatcat:6apzdf64erb5fkfokzpdje72ua

Clinical pathways analysis of patients in medical institutions based on hard and fuzzy clustering methods

Elizaveta Prokofyeva, Roman Zaytsev
2020 Business Informatics  
The problem of automatic analysis and determination of clinical pathways groups of patients based on clustering methods is considered in this research.  ...  One approach to achieving this goal is the development and implementation of clinical pathways, or patient trajectories.  ...  Methods of cluster analysis of clinical pathways of patients Terms and definitions The specific structure of clinical pathways allows us to use cluster analysis of time series.  ... 
doi:10.17323/2587-814x.2020.1.19.31 fatcat:tviqqj4e3rcznn7i4iypdkhjra

Known knowns, known unknowns, and unknown unknowns: can systems medicine provide a new approach to sepsis?

J.P. Thompson, T.J. Coats, M.R. Sims
2015 British Journal of Anaesthesia  
A novel actuator for simulation of epidural anesthesia and other needle insertion procedures. Simul Healthc 2010; 5: 179-84 22. Oon Tan C, Botha C, Weinberg L, Story DA, McNicol L.  ...  Computerized tomographic anatomic relationships of the thoracic paravertebral space. As we know, there are known knowns; there are things we know we know.  ...  We know that sepsis is a syndrome comprising a non-specific group of symptoms and signs of biological responses to infection with inflammatory processes generated by many downstream and interlinked pathways  ... 
doi:10.1093/bja/aev097 pmid:25904640 fatcat:pigsdcnjpncbfabq76udgeg4eq

Candidate genes and pathogenesis investigation for sepsis-related acute respiratory distress syndrome based on gene expression profile

Min Wang, Jingjun Yan, Xingxing He, Qiang Zhong, Chengye Zhan, Shusheng Li
2016 Biological Research  
This study aimed to predict some genes or pathways associated with sepsis-related ARDS based on a public microarray dataset and to further explore the molecular mechanism of ARDS.  ...  Genes including CCNB1, CCNB2 and TOP2A, as well as transcription factors like FOXM1 might be used as the novel gene therapy targets for sepsis related ARDS.  ...  IRegulon plugin [31] in cytoscape is used to detect transcription factors, motifs and their optimal sets of direct targets from a set of genes.  ... 
doi:10.1186/s40659-016-0085-4 pmid:27090785 pmcid:PMC4835843 fatcat:rgue2qbjy5h33is623ovgp3hee

Machine Learning Algorithms Identify Pathogen-Specific Biomarkers of Clinical and Metabolomic Characteristics in Septic Patients with Bacterial Infections

Lingling Zheng, Fangqin Lin, Changxi Zhu, Guangjian Liu, Xiaohui Wu, Zhiyuan Wu, Jianbin Zheng, Huimin Xia, Yi Cai, Huiying Liang
2020 BioMed Research International  
Pathway and blood disease enrichment analyses of clinical and metabolomic biomarkers among infected patients showed that sepsis disease was accompanied by abnormal nitrogen metabolism, cell respiratory  ...  We adopted machine learning methods for training different classifiers with a clinical-metabolomic database from sepsis cases to identify the pathogen of sepsis.  ...  Acknowledgments We are grateful to Langley et al. for sending us data generously and detailed explanation patiently. We thank all participants for their contribution in this research effort.  ... 
doi:10.1155/2020/6950576 pmid:32802867 pmcid:PMC7403934 fatcat:meynmia4pfdajhdv75rn534gni

Translational Systems Biology of Inflammation

Yoram Vodovotz, Marie Csete, John Bartels, Steven Chang, Gary An, Johanna McEntyre
2008 PLoS Computational Biology  
Inflammation is a complex, multi-scale biologic  ...  Acknowledgments The authors would like to acknowledge the contributions to this work of the following investigators, students, and postdoctoral fellows: Sven  ...  Models thus refined have already been used to assist in the analysis of ongoing clinical trials.  ... 
doi:10.1371/journal.pcbi.1000014 pmid:18437239 pmcid:PMC2329781 fatcat:orhah6kvgbep3h5gs2ay6auxda

Discovery and Validation of Urinary Molecular Signature of Early Sepsis

Sabyasachi Bandyopadhyay, Nicholas Lysak, Lasith Adhikari, Laura M. Velez, Larysa Sautina, Rajesh Mohandas, Maria-Cecilia Lopez, Ricardo Ungaro, Ying-Chih Peng, Ferdous Kadri, Philip Efron, Scott Brakenridge (+7 others)
2020 Critical Care Explorations  
Future studies need to confirm whether this approach can complement blood transcriptomic approaches for sepsis diagnosis and prognostication.  ...  We identified unique urinary gene expression profile in early sepsis.  ...  Ingenuity pathway analysis on these 239 genes show that many of them are involved in sepsis-specific canonical pathways (Supplementary Figure S9) .  ... 
doi:10.1097/cce.0000000000000195 pmid:33063018 pmcid:PMC7523873 fatcat:vml6h4dbrfgk3knnha6pyt6iqq

Network pharmacology to explore the anti-inflammatory mechanism of Xuebijing in the treatment of sepsis

Wuai Zhou, Xinxing Lai, Xin Wang, Xiaoqing Yao, Weihua Wang, Shao Li
2021 Phytomedicine  
Clinically, combined with the clinical results recorded in literature, computational and experimental results were used to interpret the anti-inflammatory effect of XBJ for treating sepsis.  ...  The network pharmacology framework integrating computational prediction, experimental validation and literature reported clinical results analysis provides a novel approach for analyzing MoA of XBJ for  ...  The computational and experimental results were used to interpret the clinical anti-inflammatory effect of XBJ for treating sepsis.  ... 
doi:10.1016/j.phymed.2021.153543 pmid:33799226 fatcat:fm3hjwuxjrbqfcxah3ncf4c2pa

Bioinformatics Analysis Identifies Hub Genes and Molecular Pathways Involved in Sepsis-Induced Myopathy

Yi-Le Ning, Zhong-Qi Yang, Shao-Xiang Xian, Jian-Zhong Lin, Xin-Feng Lin, Wei-Tao Chen
2020 Medical Science Monitor  
BACKGROUND Sepsis-induced myopathy (SIM) is a complication of sepsis that results in prolonged mechanical ventilation, long-term functional disability, and increased patient mortality.  ...  The differentially expressed genes (DEGs) in cases of SIM and healthy controls, and the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed  ...  Acknowledgments The authors thank all the members of the study research group for their active participation and contribution to this study. Conflict of interest None.  ... 
doi:10.12659/msm.919665 pmid:32008037 pmcid:PMC7009723 fatcat:nsphqn4tszgqbf2hudcginz6a4

The Optimization and Biological Significance of a 29-Host-Immune-mRNA Panel for the Diagnosis of Acute Infections and Sepsis

Yudong D. He, Eric M. Wohlford, Florian Uhle, Ljubomir Buturovic, Oliver Liesenfeld, Timothy E. Sweeney
2021 Journal of Personalized Medicine  
The test, being implemented in a rapid point-of-care platform with a turnaround time of 30 min, enables accurate and rapid diagnostic use at the point of impact.  ...  One such test (InSep™, Inflammatix, Inc.) uses a 29-mRNA panel to determine the likelihood of bacterial infection, the separate likelihood of viral infection, and the risk of physiologic decompensation  ...  Marker Downseleciton Rational and Methods, 2. Databases Used for Functional Annotation and Pathway Analysis, 3.  ... 
doi:10.3390/jpm11080735 pmid:34442377 pmcid:PMC8402342 fatcat:ues32ssc4bgntlxyhzzimtcpe4

Computational and systems biology in trauma and sepsis: current state and future perspectives

Gary An, Gary Nieman, Yoram Vodovotz
2012 International Journal of Burns and Trauma  
We propose a rational framework for transitioning through the currently fragmented process from identification of biological networks that are potential therapeutic targets, through clinical trial design  ...  Trauma, often accompanied by hemorrhage, is a leading cause of death worldwide, often leading to inflammation-related late complications that include sepsis and multiple organ failure.  ...  designers of clinical trials seeking to optimize clinical trial design (including patient sub-groups to target as well as optimal timing and dosage of drug administration) [37] [38] [39] , and finally  ... 
pmid:22928162 pmcid:PMC3415970 fatcat:avq6go3nzrbs7hvbkxap2pstsm

Can process mining automatically describe care pathways of patients with long-term conditions in UK primary care? A study protocol

Ian Litchfield, Ciaron Hoye, David Shukla, Ruth Backman, Alice Turner, Mark Lee, Phil Weber
2018 BMJ Open  
The study will be conducted in three phases; first, we will apply process mining algorithms to the data held on the clinical management system of four practices of varying characteristics in the West Midlands  ...  In the UK, primary care is seen as the optimal context for delivering care to an ageing population with a growing number of long-term conditions.  ...  patients with a particular condition, distinctive care pathways can be determined. 28 32 To do this, process mining has used records of the various sequences of events encountered in a care pathway  ... 
doi:10.1136/bmjopen-2017-019947 pmid:30518578 pmcid:PMC6286474 fatcat:eamphfs75fbujkbwfpgz7hmihy

Translational research

Alastair G. Proudfoot, Danny F. McAuley, Matthew Hind, Mark J.D. Griffiths
2011 Current Opinion in Critical Care  
Whereas the primary focus of translational science is the 'bench to bedside' journey, in its simplest form it can constitute the analysis of human samples to gain insight a Royal Brompton & Harefield NHS  ...  Acknowledgements Conflicts of interest  ...  When possible, humans, human tissues or human data, as opposed to animals, are used to optimize the validity and reliability of data generated. into a specific pathway of interest (Fig. 1 ).  ... 
doi:10.1097/mcc.0b013e32834a4b19 pmid:21825976 fatcat:vbh4oxkxmfdkppbhxtfb6bwasy

Knowledge translation following the implementation of a state-wide Paediatric Sepsis Pathway in the emergency department- a multi-centre survey study

Amanda Harley, Luregn J. Schlapbach, Paula Lister, Debbie Massey, Patricia Gilholm, Amy N. B. Johnston
2021 BMC Health Services Research  
sepsis following implementation of a sepsis pathway.  ...  Successful implementation of clinical pathways is challenging and dependent on nurse engagement.  ...  Acknowledgements The authors would like to acknowledge and thank all the participating clinicians in Queensland Health, and the Clinical Excellence Queensland Sepsis Collaborative team.  ... 
doi:10.1186/s12913-021-07128-2 pmid:34702256 fatcat:ldm4flnddbbs5ee6cu353agvvm
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