MET-IDEA:  Data Extraction Tool for Mass Spectrometry-Based Metabolomics

2006 ◽  
Vol 78 (13) ◽  
pp. 4334-4341 ◽  
Author(s):  
Corey D. Broeckling ◽  
Indira R. Reddy ◽  
Anthony L. Duran ◽  
Xuechun Zhao ◽  
Lloyd W. Sumner
Keyword(s):  
Mass Spectrometry ◽  
Data Extraction ◽  
Data Extraction Tool

scholarly journals MetaboKit: a comprehensive data extraction tool for untargeted metabolomics

2020 ◽  
Vol 16 (5) ◽  
pp. 436-447 ◽  
Author(s):  
Pradeep Narayanaswamy ◽  
Guoshou Teo ◽  
Jin Rong Ow ◽  
Adam Lau ◽  
Philipp Kaldis ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Software Package ◽  
Data Extraction ◽  
Untargeted Metabolomics ◽  
Relative Quantification ◽  
Compound Identification ◽  
Comprehensive Data ◽  
Data Extraction Tool ◽  
Metabolomics Analysis

We have developed MetaboKit, a comprehensive software package for compound identification and relative quantification in mass spectrometry-based untargeted metabolomics analysis.

scholarly journals The utility of the prehospital electrocardiogram

CJEM ◽  
2011 ◽  
Vol 13 (06) ◽  
pp. 372-377 ◽  
Author(s):  
Matthew T. Davis ◽  
Adam Dukelow ◽  
Shelley McLeod ◽  
Severo Rodriguez ◽  
Michael Lewell
Keyword(s):  
Data Extraction ◽  
Tertiary Care ◽  
Medical Personnel ◽  
Data Extraction Tool ◽  
Patient Arrival ◽  
Handover Process ◽  
St Elevation ◽  
Record Review ◽  
Electrocardiogram Ecg ◽  
Retrospective Medical Record Review

ABSTRACTObjectives:The 12-lead electrocardiogram (ECG) can capture valuable information in the prehospital setting. By the time patients are assessed by an emergency department (ED) physician, their symptoms and any ECG changes may have resolved. We sought to determine whether the prehospital electrocardiogram (pECG) could influence ED management and how often the pECG was available to and reviewed by the ED physician.Methods:A retrospective medical record review was conducted on a random sample of patients ≥ 18 years who had a prehospital 12-lead ECG and were transported to one of two tertiary care centres. Data were recorded onto a standardized data extraction tool. Three investigators independently compared the pECG to the first ECG obtained in the ED after patient arrival at the hospital. Any abnormalities not present on the ED ECG were adjudicated to ascertain whether they had the potential to change ED management.Results:Of 115 ambulance runs selected, 47 had no pECG attached to the ambulance call record (ACR) and another 5 were excluded (one ST elevation myocardial infarction, one cardiac arrest, three ACR missing). Of the 63 pECGs reviewed, 16 (25%) showed changes not apparent on the initial ED ECG (κ = 0.83; 95% CI 0.74–0.93), of which 12 had differences that might influence ED management (κ = 0.76; 95% CI 0.72–0.82). Only one hospital record contained a copy of the pECG, despite the current protocol that paramedics print two copies of the pECG on arrival in the ED (one copy for the ACR and one to be handed to the medical personnel). None of 110 ED charts documented that the pECG was reviewed by the ED physician.Conclusion:The pECG has the potential to influence ED management. Improvement in paramedic and physician documentation and a formal pECG handover process appear necessary.

scholarly journals The development and evaluation of an online application to assist in the extraction of data from graphs for use in systematic reviews

2019 ◽  
Vol 3 ◽  
pp. 157
Author(s):  
Fala Cramond ◽  
Alison O'Mara-Eves ◽  
Lee Doran-Constant ◽  
Andrew SC Rice ◽  
Malcolm Macleod ◽  
...  
Keyword(s):  
Systematic Review ◽  
Systematic Reviews ◽  
Statistical Data ◽  
Data Extraction ◽  
Evidence Synthesis ◽  
Online Application ◽  
Web Based ◽  
Graphical Data ◽  
Data Extraction Tool ◽  
Increase In Accuracy

Background: The extraction of data from the reports of primary studies, on which the results of systematic reviews depend, needs to be carried out accurately. To aid reliability, it is recommended that two researchers carry out data extraction independently. The extraction of statistical data from graphs in PDF files is particularly challenging, as the process is usually completely manual, and reviewers need sometimes to revert to holding a ruler against the page to read off values: an inherently time-consuming and error-prone process. Methods: To mitigate some of the above problems we integrated and customised two existing JavaScript libraries to create a new web-based graphical data extraction tool to assist reviewers in extracting data from graphs. This tool aims to facilitate more accurate and timely data extraction through a user interface which can be used to extract data through mouse clicks. We carried out a non-inferiority evaluation to examine its performance in comparison to standard practice. Results: We found that the customised graphical data extraction tool is not inferior to users’ prior preferred current approaches. Our study was not designed to show superiority, but suggests that there may be a saving in time of around 6 minutes per graph, accompanied by a substantial increase in accuracy. Conclusions: Our study suggests that the incorporation of this type of tool in online systematic review software would be beneficial in facilitating the production of accurate and timely evidence synthesis to improve decision-making.

scholarly journals ORIGAMI: A Software Suite for Activated Ion Mobility Mass Spectrometry (aIM-MS) Applied To Multimeric Protein Assemblies

2017 ◽  
Author(s):  
Lukasz G. Migas ◽  
Aidan P. France ◽  
Bruno Bellina ◽  
Perdita E. Barran
Keyword(s):  
Mass Spectrometry ◽  
Alcohol Dehydrogenase ◽  
Data Acquisition ◽  
Concanavalin A ◽  
Ion Mobility ◽  
Data Extraction ◽  
Ion Mobility Mass Spectrometry ◽  
List Type ◽  
Software Suite ◽  
Rapid Acquisition

AbstractWe present here a software suite (ORIGAMI) that facilitates the rapid acquisition and analysis of ion mobility data following collisional activation. ORIGAMI was developed for use on Waters Synapt instruments where data acquisition is achieved by interfacing WREnS (Waters Research Enabled Software) and MassLynx. Two components are presented, the first is ORIGAMIMS which enables activation of ions by sequential increase of collision voltages prior to ion mobility analysis. We demonstrate the use of ORIGAMI on the tetrameric assemblies formed by the proteins concanavalin A (103 kDa) and alcohol dehydrogenase (143 kDa). Activation is performed in the trap collision cell of the Synapt TriWave assembly, where the collision voltage can be ramped from 0-200 V. All of the acquired data is recorded in a single file which simplifies data acquisition. This substantially decreases the time needed to perform a typical activated IM-MS experiment on a single protein charge state from approx. 2 hours to ~25 minutes. Following data acquisition the data is analysed in the second component, ORIGAMIANALYSE, which allows the user to visualise the effect of activation on the mobility of the parent ion, as well as on any produced fragment ion. The user can export the data in the form of heat maps, waterfall or wire plots. In addition, tools implemented in ORIGAMI enable easy data extraction from single or multiple MassLynx .raw files, in-depth interrogation of large datasets, statistical analysis and figure creation capabilities. We demonstrate the use of ORIGAMI on concanavalin A and alcohol dehydrogenase acquired using the traditional protocols and the ORIGAMIMS method.Highlights-New methodology for faster acquisition and data analysis following activation of ions separated by ion mobility mass spectrometry-Software package capable of simultaneous analysis of multiple MassLynx .raw files-Visualization of the change in mobility of parent and fragment ions following activation-Easy extraction, data processing and extensive plotting tools

scholarly journals Protocol for data extraction: how real-world data have been used in the National Institute for Health and Care Excellence appraisals of cancer therapy

BMJ Open ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. e055985
Author(s):  
Jiyeon Kang ◽  
John Cairns
Keyword(s):  
Real World ◽  
Data Extraction ◽  
Systematic Research ◽  
London School ◽  
Real World Data ◽  
World Data ◽  
Data Extraction Tool ◽  
Potential Benefits ◽  
Critical Components ◽  
Randomised Controlled

IntroductionDue to the limitations of relying on randomised controlled trials, the potential benefits of real-world data (RWD) in enriching evidence for health technology assessment (HTA) are highlighted. Despite increased interest in RWD, there is limited systematic research investigating how RWD have been used in HTA. The main purpose of this protocol is to extract relevant data from National Institute for Health and Care Excellence (NICE) appraisals in a transparent and reproducible manner in order to determine how NICE has incorporated a broader range of evidence in the appraisal of oncology medicines.Methods and analysisThe appraisals issued between January 2011 and May 2021 are included following inclusion criteria. The data extraction tool newly developed for this research includes the critical components of economic evaluation. The information is extracted from identified appraisals in accordance with extraction rules. The data extraction tool will be validated by a second researcher independently. The extracted data will be analysed quantitatively to investigate to what extent RWD have been used in appraisals. This is the first protocol to enable data to be extracted comprehensively and systematically in order to review the use of RWD.Ethics and disseminationThis study is approved by the Ethics Committee of the London School of Hygiene and Tropical Medicine on 14 November 2019 (17315). Results will be published in peer-reviewed journals.

scholarly journals Effects of natural environment on mental health: an umbrella review of systematic reviews and meta-analyses

2020 ◽  
Author(s):  
Mahbub Hossain ◽  
Abida Sultana ◽  
Ping Ma ◽  
Qiping Fan ◽  
Rachit Sharma ◽  
...  
Keyword(s):  
Mental Health ◽  
Systematic Reviews ◽  
Natural Environment ◽  
Data Extraction ◽  
Experimental Studies ◽  
Mental Wellbeing ◽  
Umbrella Review ◽  
Data Extraction Tool ◽  
Study Characteristics ◽  
Meta Analyses

Objectives: To synthesize the evidence on the effects of exposure to natural environment on mental health to inform future policymaking, practice, and research. Methods: A systematic search of nine major databases and additional sources were conducted using relevant keywords for the natural environment and mental health till November 2019. We included systematic reviews or meta-analyses reporting any measures of associations between the natural environment and mental health. The data on study characteristics and research findings were extracted using the JBI data extraction tool and synthesized narratively.Results: Twenty reviews were included in this umbrella review reporting both correlational and experimental studies. Among diverse population groups, the exposure to the natural environment was associated with improvements in depressive symptoms, anxiety, mood disorders, stress, cognitive and emotional functions, affect, happiness, and overall mental wellbeing. Conclusions: The findings of this review inform beneficial mental health outcomes associated with exposure to the natural environment. This umbrella review suggests collaborative policymaking, advanced research, and evidence-based practice protecting the natural environment and improving mental health across populations.

scholarly journals The development and evaluation of an online application to assist in the extraction of data from graphs for use in systematic reviews

2018 ◽  
Vol 3 ◽  
pp. 157
Author(s):  
Fala Cramond ◽  
Alison O'Mara-Eves ◽  
Lee Doran-Constant ◽  
Andrew SC Rice ◽  
Malcolm Macleod ◽  
...  
Keyword(s):  
Systematic Review ◽  
Systematic Reviews ◽  
Statistical Data ◽  
Data Extraction ◽  
Evidence Synthesis ◽  
Online Application ◽  
Web Based ◽  
Graphical Data ◽  
Data Extraction Tool ◽  
Increase In Accuracy

Background: The extraction of data from the reports of primary studies, on which the results of systematic reviews depend, needs to be carried out accurately. To aid reliability, it is recommended that two researchers carry out data extraction independently. The extraction of statistical data from graphs in PDF files is particularly challenging, as the process is usually completely manual, and reviewers need sometimes to revert to holding a ruler against the page to read off values: an inherently time-consuming and error-prone process. Methods: To mitigate some of the above problems we developed a new web-based graphical data extraction tool to assist reviewers in extracting data from graphs. This tool aims to facilitate more accurate and timely data extraction through a user interface which can be used to extract data through mouse clicks. We carried out a non-inferiority evaluation to examine its performance in comparison to standard practice. Results: We found that our new graphical data extraction tool is not inferior to users’ prior preferred current approaches. Our study was not designed to show superiority, but suggests that there may be a saving in time of around 6 minutes per graph, accompanied by a substantial increase in accuracy. Conclusions: Our study suggests that the incorporation of this type of tool in online systematic review software would be beneficial in facilitating the production of accurate and timely evidence synthesis to improve decision-making.

scholarly journals The clinical effect of hippotherapy on gross motor function of children with Cerebral Palsy

2013 ◽  
Vol 69 (2) ◽  
Author(s):  
K Litlle ◽  
N Nel ◽  
V Ortell ◽  
H Van Wyk ◽  
M Badenhorst ◽  
...  
Keyword(s):  
Cerebral Palsy ◽  
Motor Function ◽  
Clinical Effect ◽  
Data Extraction ◽  
Bibliographic Databases ◽  
Gross Motor ◽  
Gross Motor Function ◽  
Data Extraction Tool ◽  
Added Benefit ◽  
Mean Differences

Background: Cerebral palsy (CP) is the most common cause of physical disability affecting gross motor function (GMF ) in early childhood. Hippotherapy is a treatment approach aimed at improving GMF in children with CP. Several systematic reviews have been published showing an improvement in Dimension E of the Gross Motor Function Measure (GMFM ) after hippotherapy. However, these reviews failed to evaluate the clinical effect of hippotherapy in improving GMF in children with CP.Objective: To critically appraise the evidence of hippotherapy to ascertain whether it is a clinically meaningful approach for children with CP.Methodology: Five computerised bibliographic databases were searched. Predetermined inclusion and exclusion criteria were set. The PEDro scale was used to assess the quality of the studies. A revised JBI Data extraction tool was used to extract data from the selected articles. Revman© Review Manager Software was used to create forest plots for comparisons of results.Results: All studies used the GMFM as an outcome measure for gross motor function. The added benefit of hippotherapy is a minimum 1% and a maximum 7% increase on the GMFM scores. However, all 95% confidence intervals (CI ) around all the mean differences were insignificant.Conclusion: The clinical effect of hippotherapy on the GMF of children with CP is small. Larger studies are required to provide evidence of the effect of hippotherapy within this population.

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