scholarly journals CARPEM-LYNCH: a program linking hospital and NutriNet-Santé e-cohort data to test dynamic consent

2020 ◽  
Vol 30 (Supplement_5) ◽  
Author(s):  
G Wendeu-Foyet ◽  
P Fassier ◽  
G Perrod ◽  
G Perkins ◽  
E Coffin ◽  
...  
Keyword(s):  
Informed Consent ◽  
Translational Research ◽  
Clinical Data ◽  
Large Scale ◽  
Health Impact ◽  
Nutritional Risk ◽  
Sustainable Solutions ◽  
Cohort Data ◽  
Dynamic Consent ◽  
Patient Consent

Abstract Background Technological innovations have contributed to rapid changes in translational research, allowing greater amounts of shared data on an unprecedented scale. However, methods for involving patients in research have not kept pace with changes in research capacity. Modern tools offering more flexibility in the management of patient consent are needed. The CARPEM-LYNCH program aims to explore the acceptance and feasibility of the concept of dynamic informed consent. It is a pilot program to test a research platform at the interface between hospital follow-up clinical data and data provided by patients through the NutriNet-Santé e-cohort platform. Methods Patients diagnosed with Lynch Syndrome followed at the European hospital Georges Pompidou (HEGP) are recruited and followed-up within the NutriNet-Santé online platform. In addition to generic NutriNet questionnaires (very detailed data on diet, physical activity, lifestyle, etc.), participants receive specific questionnaires related to their syndrome, perception of nutritional risk factors, and quality of life. Clinical data collected during standard hospital care will be linked to NutriNet data for participants who provide a dynamic consent. This dispositive will allow to investigate multiple dimensions of dietary behaviors and their health impact in these at-risk patients. Results The pilot phase has started. The first 20 patients have been included, showing good acceptance of the dynamic consent. Qualitative analysis of their responses is ongoing to optimize tools before large-scale deployment and extension to other hospital centers. Conclusions This experience of merging hospital and e-cohort data through dynamic consent to advance knowledge on health impact of diet and lifestyle in Lynch patients opens up a multitude of perspectives. Key messages Dynamic informed consent offers opportunities for data sharing between clinicians, researchers and patients with a promising impact on translational research. Dynamic informed consent can provide practical and sustainable solutions to the challenges of recruiting and retaining participants, managing consent and it can also be a source of economic efficiency.

scholarly journals iConsent an Electronic Consent Platform with the MS Register

2017 ◽  
Vol 1 (1) ◽  
Author(s):  
Rod Middleton ◽  
David Ford ◽  
Daniel Naeh
Keyword(s):  
Informed Consent ◽  
Large Scale ◽  
Routine Data ◽  
Ethics Committee ◽  
Ease Of Use ◽  
Consent Form ◽  
Observational Research ◽  
Number Of Patients ◽  
Patient Consent ◽  
Patient Reported

ABSTRACT ObjectivesThe UK MS Register is a large scale observational research platform, capturing data from patients, NHS and carries out linkage with routine data from the SAIL databank. We have 14,000 People with MS (PwMS) submitting Patient Reported Outcome Measures (PRoMS) quarterly and over 3000 patients consenting at NHS Sites around the UK A differentiating factor between Register and previous attempts to capture PRoMS and clinical data was the goal that it be paperless. One area, where paper had to be used, was obtaining informed consent. Clinical participants are consented using a triplicate consent form, one copy for the patient, one for medical notes and one for the Register It’s desirable for patients to be able to electronically consent, providing the following benefits: Tablet computers already in use to collect PRoMS Printing costs Participant expectations Improved content and user experience: improved feedback, of multimedia elements about informed consent Increased familiarity with tablets ApproachChanging consent methodology is complex, all documentation, processes and changes are reviewed by the ethics committee. A privacy protecting, secure software package (iConsent) was developed by modifying an existing package from Welsh Cancer Bank. The software is server based, running on a Secured MS SQLServer 2014 and developed in .net to iOS/Android tablets The practitioner taking consent explains the process, participants then see the approved documentation and materials. Finally they fill in their email address and name, and are presented with the consent form, the participant uses a stylus to sign. The practitioner then countersigns. Once completed a digitally signed, secure pdf is generated on the server. Links are sent by email to the participant, the Register and unit administrator. The pdf is functionally identical to the paper. ResultsThe South West Central Bristol ethics committee approved the software following guidance on security and documentation design. Staff were trained in system usage. A number of patients were successfully e-consented, Of note was a potential issue with some patients and how MS impacts their ability to sign without resting a hand on the screen. ConclusionPatients who have been e-consented have expressed satisfaction in the ease of use and security of the software. Patients being unable to rest their hands on the screen is being examined. Newer tablets can ignore inputs other than the stylus. The MS Register intends to use the software in additional centres to capture patient consent.

scholarly journals ‘CTRL’: an online, Dynamic Consent and participant engagement platform working towards solving the complexities of consent in genomic research

2021 ◽  
Author(s):  
Matilda A. Haas ◽  
Harriet Teare ◽  
Megan Prictor ◽  
Gabi Ceregra ◽  
Miranda E. Vidgen ◽  
...  
Keyword(s):  
Large Scale ◽  
Genomic Medicine ◽  
International Standards ◽  
Security And Privacy ◽  
Genomic Research ◽  
Return Of Results ◽  
Future Research ◽  
Design And Development ◽  
Participant Engagement ◽  
Dynamic Consent

AbstractThe complexities of the informed consent process for participating in research in genomic medicine are well-documented. Inspired by the potential for Dynamic Consent to increase participant choice and autonomy in decision-making, as well as the opportunities for ongoing participant engagement it affords, we wanted to trial Dynamic Consent and to do so developed our own web-based application (web app) called CTRL (control). This paper documents the design and development of CTRL, for use in the Australian Genomics study: a health services research project building evidence to inform the integration of genomic medicine into mainstream healthcare. Australian Genomics brought together a multi-disciplinary team to develop CTRL. The design and development process considered user experience; security and privacy; the application of international standards in data sharing; IT, operational and ethical issues. The CTRL tool is now being offered to participants in the study, who can use CTRL to keep personal and contact details up to date; make consent choices (including indicate preferences for return of results and future research use of biological samples, genomic and health data); follow their progress through the study; complete surveys, contact the researchers and access study news and information. While there are remaining challenges to implementing Dynamic Consent in genomic research, this study demonstrates the feasibility of building such a tool, and its ongoing use will provide evidence about the value of Dynamic Consent in large-scale genomic research programs.

scholarly journals Flavonoid-Modifying Capabilities of the Human Gut Microbiome—An In Silico Study

Nutrients ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 2688
Author(s):  
Tobias Goris ◽  
Rafael R. C. Cuadrat ◽  
Annett Braune
Keyword(s):  
Gut Microbiome ◽  
Large Scale ◽  
Health Impact ◽  
Gut Bacteria ◽  
Human Gut ◽  
Positive Health ◽  
Human Gut Microbiome ◽  
Nutritional Recommendations ◽  
Genes Encoding ◽  
A Minor

Flavonoids are a major group of dietary plant polyphenols and have a positive health impact, but their modification and degradation in the human gut is still widely unknown. Due to the rise of metagenome data of the human gut microbiome and the assembly of hundreds of thousands of bacterial metagenome-assembled genomes (MAGs), large-scale screening for potential flavonoid-modifying enzymes of human gut bacteria is now feasible. With sequences of characterized flavonoid-transforming enzymes as queries, the Unified Human Gastrointestinal Protein catalog was analyzed and genes encoding putative flavonoid-modifying enzymes were quantified. The results revealed that flavonoid-modifying enzymes are often encoded in gut bacteria hitherto not considered to modify flavonoids. The enzymes for the physiologically important daidzein-to-equol conversion, well studied in Slackiaisoflavoniconvertens, were encoded only to a minor extent in Slackia MAGs, but were more abundant in Adlercreutzia equolifaciens and an uncharacterized Eggerthellaceae species. In addition, enzymes with a sequence identity of about 35% were encoded in highly abundant MAGs of uncultivated Collinsella species, which suggests a hitherto uncharacterized daidzein-to-equol potential in these bacteria. Of all potential flavonoid modification steps, O-deglycosylation (including derhamnosylation) was by far the most abundant in this analysis. In contrast, enzymes putatively involved in C-deglycosylation were detected less often in human gut bacteria and mainly found in Agathobacter faecis (formerly Roseburia faecis). Homologs to phloretin hydrolase, flavanonol/flavanone-cleaving reductase and flavone reductase were of intermediate abundance (several hundred MAGs) and mainly prevalent in Flavonifractor plautii. This first comprehensive insight into the black box of flavonoid modification in the human gut highlights many hitherto overlooked and uncultured bacterial genera and species as potential key organisms in flavonoid modification. This could lead to a significant contribution to future biochemical-microbiological investigations on gut bacterial flavonoid transformation. In addition, our results are important for individual nutritional recommendations and for biotechnological applications that rely on novel enzymes catalyzing potentially useful flavonoid modification reactions.

A High-Fidelity Model to Predict Length of Stay in the Neonatal Intensive Care Unit

2021 ◽  
Author(s):  
Kanix Wang ◽  
Walid Hussain ◽  
John R. Birge ◽  
Michael D. Schreiber ◽  
Daniel Adelman
Keyword(s):  
Length Of Stay ◽  
Clinical Data ◽  
Neonatal Intensive Care ◽  
Large Scale ◽  
Expert Knowledge ◽  
Clinical Analysis ◽  
Healthcare Operations ◽  
Lengths Of Stay ◽  
Health Trajectories ◽  
Widespread Implementation

Having an interpretable, dynamic length-of-stay model can help hospital administrators and clinicians make better decisions and improve the quality of care. The widespread implementation of electronic medical record (EMR) systems has enabled hospitals to collect massive amounts of health data. However, how to integrate this deluge of data into healthcare operations remains unclear. We propose a framework grounded in established clinical knowledge to model patients’ lengths of stay. In particular, we impose expert knowledge when grouping raw clinical data into medically meaningful variables that summarize patients’ health trajectories. We use dynamic, predictive models to output patients’ remaining lengths of stay, future discharges, and census probability distributions based on their health trajectories up to the current stay. Evaluated with large-scale EMR data, the dynamic model significantly improves predictive power over the performance of any model in previous literature and remains medically interpretable. Summary of Contribution: The widespread implementation of electronic health systems has created opportunities and challenges to best utilize mounting clinical data for healthcare operations. In this study, we propose a new approach that integrates clinical analysis in generating variables and implementations of computational methods. This approach allows our model to remain interpretable to the medical professionals while being accurate. We believe our study has broader relevance to researchers and practitioners of healthcare operations.

scholarly journals Cancer metabolic subtypes and their association with molecular and clinical features

2021 ◽  
Author(s):  
Enrico Moiso ◽  
Paolo Provero
Keyword(s):  
Clinical Data ◽  
Large Scale ◽  
Tumor Grade ◽  
Point Of View ◽  
General Point ◽  
Protein Abundance ◽  
Phenotypic Data ◽  
Cancer Subtypes ◽  
Molecular Features

Alteration of metabolic pathways in cancer has been investigated for many years, beginning way before the discovery of the role of oncogenes and tumor suppressors, and the last few years have witnessed a renewed interest in this topic. Large-scale molecular and clinical data on tens of thousands of samples allow us today to tackle the problem from a general point of view. Here we show that trancriptomic profiles of tumors can be exploited to define metabolic cancer subtypes, that can be systematically investigated for association with other molecular and clinical data. We find thousands of significant associations between metabolic subtypes and molecular features such as somatic mutations, structural variants, epigenetic modifications, protein abundance and activation; and with clinical/phenotypic data including survival probability, tumor grade, and histological types. Our work provides a methodological framework and a rich database of statistical associations, accessible from https://metaminer.unito.it, that will contribute to the understanding of the role of metabolic alterations in cancer and to the development of precision therapeutic strategies.

scholarly journals Clinical disease characteristics of patients with Niemann-Pick Disease Type C – findings from the International Niemann-Pick Disease Registry (INPDR)

2021 ◽  
Author(s):  
Shaun Christopher Bolton ◽  
Vina Soran ◽  
Mercedes Pineda Marfa ◽  
Jackie Imrie ◽  
Paul Gissen ◽  
...  
Keyword(s):  
Clinical Data ◽  
Large Scale ◽  
Disease Type ◽  
Adult Onset ◽  
Neurological Manifestations ◽  
Disease Registry ◽  
Niemann Pick Disease ◽  
Type C ◽  
Niemann Pick ◽  
Pick Disease

Abstract Background Niemann-Pick Disease Type C (NPC) is an autosomal recessive rare disease characterised by progressive neurovisceral manifestations. The collection of on-going large-scale NPC clinical data may generate better understandings of the natural history of the disease. Here we report NPC patient data from the International Niemann-Pick Disease Registry (INPDR). Method The INPDR is a web-based, patient-led independent registry for the collection of prospective and retrospective clinical data from Niemann-Pick Disease patients. Baseline data from NPC patients enrolled into the INPDR from September 2014 to December 2019 was extracted to analyse the demographic, genetic and clinical features. Results A total of 203 NPC patients from six European countries were included in this study. The mean age (SD) at diagnosis was 11.2 years (14.2). Among enrolled patients, 168 had known neurological manifestations; 43 (24.2%) had early-infantile onset, 47 (26.4%) had late-infantile onset, 41 (23.0%) had juvenile onset, and 37 (20.8%) had adult onset. 10 (5.6%) patients had the neonatal rapidly fatal systemic form. Among the 97 patients with identified NPC1 variants, the most common variant was the c. 3182T > C variant responsible for the p.lle1061Thr protein change, reported in 35.1% (N = 34) of patients. The frequencies of hepatomegaly and neonatal jaundice were greatest in patients with early-infantile and late-infantile onset. Splenomegaly was the most commonly reported observation, including 80% of adult-onset patients. The most commonly reported neurological manifestations were cognitive impairment (78.5%), dysarthria (75.9%), ataxia (75.9%), vertical supranuclear gaze palsy (VSGP) (70.9%), dysphagia (69.6%). A 6-domain composite disability scale was used to calculate the overall disability score according to neurological-onset. Across all with neurological onset, the majority of patients showed moderate to severe impairments in all domains, excluding ‘swallowing’ and ‘seizure’. The age at diagnosis and death increased with increased age of neurological symptom onset. Miglustat use was recorded in 62.43% of patients and the most common symptomatic therapies used by patients were antiepileptics (32.94%), antidepressants (11.76%) and antacids (9.41%). Conclusion The proportion of participants at each age of neurological onset was relatively consistent across the cohort. Neurological manifestations, such as ataxia, dysphagia, and dysarthria, were frequently observed across all age categories.

scholarly journals The Yale Department of Medicine COVID-19 Data Explorer and Repository (DOM-CovX): An Innovative Approach to Promoting Collaborative Scholarship During a Pandemic

2021 ◽  
Author(s):  
Tanima Arora ◽  
Michael Simonov ◽  
Jameel Alausa ◽  
Labeebah Subair ◽  
Brett Gerber ◽  
...  
Keyword(s):  
Clinical Data ◽  
Large Scale ◽  
Innovative Approach ◽  
Academic Productivity ◽  
List Type ◽  
Digital Revolution ◽  
Institutional Climate ◽  
Novel Approach ◽  
Dissemination Of Research ◽  
Academic Faculty

ABSTRACTBackgroundThe COVID-19 pandemic has led to an explosion of research publications spanning epidemiology, basic and clinical science. While a digital revolution has allowed for open access to large datasets enabling real-time tracking of the epidemic, detailed, locally-specific clinical data has been less readily accessible to a broad range of academic faculty and their trainees. This perpetuates the separation of the primary missions of clinically-focused and primary research faculty resulting in lost opportunities for improved understanding of the local epidemic; expansion of the scope of scholarship; limitation of the diversity of the research pool; lack of creation of initiatives for growth and dissemination of research skills needed for the training of the next generation of clinicians and faculty.ObjectivesCreate a common, easily accessible and up-to-date database that would promote access to local COVID-19 clinical data, thereby increasing efficiency, streamlining and democratizing the research enterprise. By providing a robust dataset, a broad range of researchers (faculty, trainees) and clinicians are encouraged to explore and collaborate on novel clinically relevant research questions.MethodsWe constructed a research platform called the Yale Department of Medicine COVID-19 Explorer and Repository (DOM-CovX), to house cleaned, highly granular, de-identified, continually-updated data from over 7,000 patients hospitalized with COVID-19 (1/2020-present) across the Yale New Haven Health System. This included a front-end user interface for simple data visualization of aggregate data and more detailed clinical datasets for researchers after a review board process. The goal is to promote access to local COVID-19 clinical data, thereby increasing efficiency, streamlining and democratizing the research enterprise.Expected OutcomesAccelerate generation of new knowledge and increase scholarly productivity with particular local relevanceImprove the institutional academic climate by:Broadening research scopeExpanding research capability to more diverse group of stakeholders including clinical and research-based faculty and traineesEnhancing interdepartmental collaborationsConclusionsThe DOM-CovX Data Explorer and Repository have great potential to increase academic productivity. By providing an accessible tool for simple data analysis and access to a consistently updated, standardized and large-scale dataset, it overcomes barriers for a wide variety of researchers. Beyond academic productivity, this innovative approach represents an opportunity to improve the institutional climate by fostering collaboration, diversity of scholarly pursuits and expanding medical education. It provides a novel approach that can be expanded to other diseases beyond COVID 19.

Health Impacts of Large-Scale Floods: Governmental Decision-Making and Resilience of the Citizens

2008 ◽  
Vol 23 (S2) ◽  
pp. s70-s73 ◽  
Author(s):  
Dick Q.P. Fundter ◽  
Bas Jonkman ◽  
Steve Beerman ◽  
Corsmas L.P.M. Goemans ◽  
Rosanna Briggs ◽  
...  
Keyword(s):  
Decision Making ◽  
Large Scale ◽  
Health Impact ◽  
Population Based ◽  
Chronic Illnesses ◽  
Decision Makers ◽  
Natural Resistance ◽  
First Year ◽  
The Public ◽  
Life Saving

AbstractDuring the 15th World Congress on Disaster and Emergency Medicine in Amsterdam, May 2007 (15WCDEM), a targeted agenda program (TAP) about the public health aspects of large-scale floods was organized. The main goal of the TAP was the establishment of an overview of issues that would help governmental decision-makers to develop policies to increase the resilience of the citizens during floods. During the meetings, it became clear that citizens have a natural resistance to evacuations. This results in death due to drowning and injuries. Recently, communication and education programs have been developed that may increase awareness that timely evacuation is important and can be life-saving. After a flood, health problems persist over prolonged periods, including increased death rates during the first year after a flood and a higher incidence of chronic illnesses that last for decades after the flood recedes. Population-based resilience (bottom-up) and governmental responsibility (top-down) must be combined to prepare regions for the health impact of evacuations and floods. More research data are needed to become better informed about the health impact and consequences of translocation of health infrastructures after evacuations. A better understanding of the consequences of floods will support governmental decision-making to mitigate the health impact. A top-10 priority action list was formulated.

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