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Article ; Online: What if Bacteria Could Tell Us What They Have Seen?

Maire, Amandine / Bikard, David

2022 Volume 5, Issue 4, Page(s) 488–489

MeSH term(s)	Bacteria/genetics ; CRISPR-Cas Systems ; Gene Editing
Language	English
Publishing date	2022-08-16
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	3017891-5
ISSN	2573-1602 ; 2573-1599
ISSN (online)	2573-1602
ISSN	2573-1599
DOI	10.1089/crispr.2022.29151.bik
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Zs.A 7195: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Clostridioides difficile Infection in Pediatric Inflammatory Bowel Disease: A Clinician's Dilemma.

Conrad, Máire A / Kelsen, Judith R

Journal of the Pediatric Infectious Diseases Society

2021 Volume 10, Issue Supplement_3, Page(s) S41–S45

Abstract: Clostridioides difficile infection (CDI) in children with inflammatory bowel disease (IBD) can present and manifest differently from the general population with CDI, and it can worsen the underlying disease course. Furthermore, current clinical assays ... ...

Abstract	Clostridioides difficile infection (CDI) in children with inflammatory bowel disease (IBD) can present and manifest differently from the general population with CDI, and it can worsen the underlying disease course. Furthermore, current clinical assays used to test for CDI do not accurately distinguish between true CDI or colonization. This uncertainty leads to difficulty in identifying the etiology and therapy for symptomatic patients with IBD. Improved diagnostic tests, biomarkers, and safe and effective treatment options are greatly needed for this vulnerable population.
MeSH term(s)	Child ; Clostridioides ; Clostridioides difficile ; Clostridium Infections/complications ; Clostridium Infections/diagnosis ; Humans ; Inflammatory Bowel Diseases/complications ; Inflammatory Bowel Diseases/diagnosis ; Treatment Outcome
Language	English
Publishing date	2021-08-03
Publishing country	England
Document type	Journal Article
ZDB-ID	2668791-4
ISSN	2048-7207 ; 2048-7193
ISSN (online)	2048-7207
ISSN	2048-7193
DOI	10.1093/jpids/piab069
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Article ; Online: Development of a workforce self-assessment tool for public health emergency preparedness.

Hayes, Jessica S / Barreto, Marta / Kalin-Mänttäri, Laura / Mexia, Ricardo / Connolly, Máire A / Voutilainen, Liina

European journal of public health

2024

Abstract: Background: In collaboration with six European public health agencies as part of the PANDEM-2 consortium, we have developed and validated a self-assessment tool that captures the workforce capacities and capabilities needed at the institutional level ... ...

Abstract	Background: In collaboration with six European public health agencies as part of the PANDEM-2 consortium, we have developed and validated a self-assessment tool that captures the workforce capacities and capabilities needed at the institutional level within National Public Health Institutes (NPHIs) to deal with public health emergencies. Methods: The work carried out in this study included (i) a review of existing tools for workforce assessment, (ii) focus group discussions and interviews to map the experiences and needs of NPHI's, (iii) the development of a tool for NPHI's to assess their workforce capacity and capabilities in public health emergency preparedness (PHEP) and (iv) refinement of the assessment tool via a Delphi study. Results: Capacity markers were identified to assess the workforce required for PHEP functions and the availability of surge capacity during a public health emergency. The tool also enables NPHIs to analyze gaps in PHEP staff competencies. The assessment scores can assist NPHI pandemic preparedness by identifying and prioritizing training and recruitment needs. Conclusions: In line with EU Regulation 2022/2371 on serious cross-border threats to health, article 11 Training of healthcare staff and public health staff, Member States (MS) are tasked with assessing current workforce capacity and capability gaps. The PANDEM-2 workforce self-assessment tool aligns with this requirement and will support effective planning and development to strengthen the public health workforce capacity in EU MS.
Language	English
Publishing date	2024-04-01
Publishing country	England
Document type	Journal Article
ZDB-ID	1129243-x
ISSN	1464-360X ; 1101-1262
ISSN (online)	1464-360X
ISSN	1101-1262
DOI	10.1093/eurpub/ckae030
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Zs.A 3499: Show issues

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Article ; Online: Reply to: A Pattern-based Approach and Multidisciplinary Discussion Are Fundamental for Diagnosis in Very Early Onset Inflammatory Bowel Disease (VEO-IBD).

Wilkins, Benjamin J / Kelsen, Judith R / Conrad, Maire A

Advances in anatomic pathology

2022 Volume 29, Issue 4, Page(s) 260–261

MeSH term(s)	Humans ; Inflammatory Bowel Diseases/diagnosis ; Phenotype
Language	English
Publishing date	2022-04-08
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	1212493-x
ISSN	1533-4031 ; 1072-4109
ISSN (online)	1533-4031
ISSN	1072-4109
DOI	10.1097/PAP.0000000000000344
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Article ; Online: The Treatment of Pediatric Inflammatory Bowel Disease with Biologic Therapies.

Conrad, Máire A / Kelsen, Judith R

Current gastroenterology reports

2020 Volume 22, Issue 8, Page(s) 36

Abstract: Purpose of review: Biologics for the treatment of inflammatory bowel disease (IBD) have been transformative to the therapeutic goals in the pediatric population. We review the biologics used to treat IBD, highlighting the importance of patient selection, ...

Abstract	Purpose of review: Biologics for the treatment of inflammatory bowel disease (IBD) have been transformative to the therapeutic goals in the pediatric population. We review the biologics used to treat IBD, highlighting the importance of patient selection, dosing considerations, and therapeutic drug monitoring in children. Recent findings: Infliximab is well-established as a safe and efficacious therapy for Crohn's disease and ulcerative colitis. Both dose escalation strategies and therapeutic drug monitoring increase the likelihood of response to anti-TNFα therapies. Early real-world experience of vedolizumab and ustekinumab in pediatric IBD shows promising results, including clinical response rates comparable to what is seen in adults, but there are limited data using them as first-line therapies. Biologic therapies have improved outcomes in pediatric IBD, including achieving mucosal healing as well as improved growth and pubertal development. Therapeutic drug monitoring improves likelihood of response to anti-TNFα therapies, but further studies for vedolizumab and ustekinumab are necessary.
MeSH term(s)	Antibodies, Monoclonal, Humanized/therapeutic use ; Biological Products/therapeutic use ; Biological Therapy ; Child ; Dose-Response Relationship, Drug ; Drug Monitoring ; Gastrointestinal Agents/therapeutic use ; Humans ; Inflammatory Bowel Diseases/therapy ; Infliximab/therapeutic use ; Patient Selection ; Ustekinumab/therapeutic use
Chemical Substances	Antibodies, Monoclonal, Humanized ; Biological Products ; Gastrointestinal Agents ; vedolizumab (9RV78Q2002) ; Infliximab (B72HH48FLU) ; Ustekinumab (FU77B4U5Z0)
Language	English
Publishing date	2020-06-15
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2041376-2
ISSN	1534-312X ; 1522-8037
ISSN (online)	1534-312X
ISSN	1522-8037
DOI	10.1007/s11894-020-00773-3
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Article ; Online: Editorial to Temporal Gut Microbial Changes Predict Recurrent Clostridium difficile Infection in Patients With and Without Ulcerative Colitis.

Conrad, Maire A / Kelsen, Judith R

Inflammatory bowel diseases

2020 Volume 26, Issue 11, Page(s) 1759–1760

MeSH term(s)	Clostridioides difficile ; Clostridium Infections/diagnosis ; Colitis, Ulcerative/complications ; Gastrointestinal Microbiome ; Humans ; Reinfection
Language	English
Publishing date	2020-02-11
Publishing country	England
Document type	Editorial ; Comment
ZDB-ID	1340971-2
ISSN	1536-4844 ; 1078-0998
ISSN (online)	1536-4844
ISSN	1078-0998
DOI	10.1093/ibd/izz336
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Zs.A 4530: Show issues

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Article ; Online: Biosafety Issues in Patient Transport during COVID-19: A Case Study on the Portuguese Emergency Services.

Vandenberghe, Pierre / Ladeira, Luis Manuel / Gil, Margarida / Cardoso, Ivo / Rato, Fatima / Hayes, Jessica S / Connolly, Maire A / Gala, Jean-Luc

International journal of environmental research and public health

2024 Volume 21, Issue 1

Abstract: During the COVID-19 pandemic, first responders faced significant biosafety challenges, especially while handling patient transport, potentially exposing them to infection. The PANDEM-2 (European project on pandemic preparedness and response) project, ... ...

Abstract	During the COVID-19 pandemic, first responders faced significant biosafety challenges, especially while handling patient transport, potentially exposing them to infection. The PANDEM-2 (European project on pandemic preparedness and response) project, funded by the Horizon 2020 program, sought to investigate the challenges confronting Emergency Medical Systems throughout the EU. First responders from Portugal's National Institute of Medical Emergency (INEM) were considered as a representative operational model of the national first responder agencies of European member states because they played a critical role during the COVID-19 pandemic. As a result, they were asked to complete an online survey about their COVID-19 pandemic-related professional activities. The survey focused on their perspectives on current biosafety guidelines and their operational practices. It covered opinions on existing protocols, technical concerns during patient transport, and issues after the patients arrived at the hospital. The key findings revealed concerns about risk assessment, the inadequacy of guidelines, and disparities in equipment access. This survey emphasizes the importance of developing streamlined, adaptable biosafety protocols, better coordination between prehospital and in-hospital services, and the development of scalable, cost-effective biosafety solutions. Based on our findings, we propose improvements to national and European biosafety directives and advocate for streamlined adaptation during pandemics.
MeSH term(s)	Humans ; Portugal/epidemiology ; Containment of Biohazards ; Pandemics ; COVID-19/epidemiology ; Emergency Medical Services
Language	English
Publishing date	2024-01-16
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2175195-X
ISSN	1660-4601 ; 1661-7827
ISSN (online)	1660-4601
ISSN	1661-7827
DOI	10.3390/ijerph21010099
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Article ; Online: PANDEM-Source, a tool to collect or generate surveillance indicators for pandemic management: a use case with COVID-19 data.

Orchard, Francisco / Clain, Charline / Madie, William / Hayes, Jessica S / Connolly, Máire A / Sevin, Etienne / Sentís, Alexis

Frontiers in public health

2024 Volume 12, Page(s) 1295117

Abstract: Introduction: PANDEM-Source (PS) is a tool to collect and integrate openly available public health-related data from heterogeneous data sources to support the surveillance of infectious diseases for pandemic management. The tool may also be used for ... ...

Abstract	Introduction: PANDEM-Source (PS) is a tool to collect and integrate openly available public health-related data from heterogeneous data sources to support the surveillance of infectious diseases for pandemic management. The tool may also be used for pandemic preparedness by generating surveillance data for training purposes. It was developed as part of the EU-funded Horizon 2020 PANDEM-2 project during the COVID-19 pandemic as a result of close collaboration in a consortium of 19 partners, including six European public health agencies, one hospital, and three first responder organizations. This manuscript describes PS's features and design to disseminate its characteristics and capabilities to strengthen pandemic preparedness and response. Methods: A requirement-gathering process with EU pandemic managers in the consortium was performed to identify and prioritize a list of variables and indicators useful for surveillance and pandemic management. Using the COVID-19 pandemic as a use case, we developed PS with the purpose of feeding all necessary data to be displayed in the PANDEM-2 dashboard. Results: PS routinely monitors, collects, and standardizes data from open or restricted heterogeneous data sources (users can upload their own data). It supports indicators and health resources related data from traditional data sources reported by national and international agencies, and indicators from non-traditional data sources such as those captured in social and mass media, participatory surveillance, and seroprevalence studies. The tool can also calculate indicators and be used to produce data for training purposes by generating synthetic data from a minimal set of indicators to simulate pandemic scenarios. PS is currently set up for COVID-19 surveillance at the European level but can be adapted to other diseases or threats and regions. Conclusion: With the lessons learnt during the COVID-19 pandemic, it is important to keep building capacity to monitor potential threats and develop tools that can facilitate training in all the necessary aspects to manage future pandemics. PS is open source and its design provides flexibility to collect heterogeneous data from open data sources or to upload end users's own data and customize surveillance indicators. PS is easily adaptable to future threats or different training scenarios. All these features make PS a unique and valuable tool for pandemic management.
MeSH term(s)	Humans ; COVID-19/epidemiology ; Pandemics ; Seroepidemiologic Studies ; Public Health
Language	English
Publishing date	2024-03-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2711781-9
ISSN	2296-2565 ; 2296-2565
ISSN (online)	2296-2565
ISSN	2296-2565
DOI	10.3389/fpubh.2024.1295117
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Article ; Online: Genomic and Immunologic Drivers of Very Early-Onset Inflammatory Bowel Disease.

Conrad, Maire A / Kelsen, Judith R

Pediatric and developmental pathology : the official journal of the Society for Pediatric Pathology and the Paediatric Pathology Society

2019 Volume 22, Issue 3, Page(s) 183–193

Abstract: Purpose of review: Inflammatory bowel disease (IBD) is a multifactorial disease caused by dysregulated immune responses to commensal or pathogenic intestinal microbes, resulting in chronic intestinal inflammation. However, a subset of patients with IBD ... ...

Abstract	Purpose of review: Inflammatory bowel disease (IBD) is a multifactorial disease caused by dysregulated immune responses to commensal or pathogenic intestinal microbes, resulting in chronic intestinal inflammation. However, a subset of patients with IBD diagnosed <6 years of age, known as very early-onset (VEO)-IBD, can be phenotypically and genetically distinct from older onset IBD. We aim to review the clinical presentation of children with VEO-IBD and recent discoveries that point to the underlying genomic and immunologic drivers of disease, and the significant impact on our therapeutic decisions. Recent findings: VEO-IBD is increasing in incidence and is associated with more severe disease, aggressive progression, and poor response to most conventional therapies. This article will review some of the genetic findings in this population and the subsequent impact on therapy, with targeted approaches. Summary: Children with VEO-IBD may present with a different phenotype and more severe disease than older children and adults. An integrated approach combining genetics, immunology, and traditional IBD evaluations can lead to the identification of causal defects that directly impact management. These strategies can also be employed in older onset refractory IBD.
MeSH term(s)	Age of Onset ; Child, Preschool ; Genetic Predisposition to Disease ; Genomics ; Humans ; Infant ; Inflammatory Bowel Diseases/classification ; Inflammatory Bowel Diseases/genetics ; Inflammatory Bowel Diseases/immunology ; Inflammatory Bowel Diseases/therapy ; Mutation ; Phenotype
Language	English
Publishing date	2019-03-06
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1463498-3
ISSN	1615-5742 ; 1093-5266
ISSN (online)	1615-5742
ISSN	1093-5266
DOI	10.1177/1093526619834807
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Article ; Online: Contrast-enhanced to non-contrast-enhanced image translation to exploit a clinical data warehouse of T1-weighted brain MRI.

Bottani, Simona / Thibeau-Sutre, Elina / Maire, Aurélien / Ströer, Sebastian / Dormont, Didier / Colliot, Olivier / Burgos, Ninon

BMC medical imaging

2024 Volume 24, Issue 1, Page(s) 67

Abstract: Background: Clinical data warehouses provide access to massive amounts of medical images, but these images are often heterogeneous. They can for instance include images acquired both with or without the injection of a gadolinium-based contrast agent. ... ...

Abstract	Background: Clinical data warehouses provide access to massive amounts of medical images, but these images are often heterogeneous. They can for instance include images acquired both with or without the injection of a gadolinium-based contrast agent. Harmonizing such data sets is thus fundamental to guarantee unbiased results, for example when performing differential diagnosis. Furthermore, classical neuroimaging software tools for feature extraction are typically applied only to images without gadolinium. The objective of this work is to evaluate how image translation can be useful to exploit a highly heterogeneous data set containing both contrast-enhanced and non-contrast-enhanced images from a clinical data warehouse. Methods: We propose and compare different 3D U-Net and conditional GAN models to convert contrast-enhanced T1-weighted (T1ce) into non-contrast-enhanced (T1nce) brain MRI. These models were trained using 230 image pairs and tested on 77 image pairs from the clinical data warehouse of the Greater Paris area. Results: Validation using standard image similarity measures demonstrated that the similarity between real and synthetic T1nce images was higher than between real T1nce and T1ce images for all the models compared. The best performing models were further validated on a segmentation task. We showed that tissue volumes extracted from synthetic T1nce images were closer to those of real T1nce images than volumes extracted from T1ce images. Conclusion: We showed that deep learning models initially developed with research quality data could synthesize T1nce from T1ce images of clinical quality and that reliable features could be extracted from the synthetic images, thus demonstrating the ability of such methods to help exploit a data set coming from a clinical data warehouse.
MeSH term(s)	Humans ; Data Warehousing ; Gadolinium ; Brain/diagnostic imaging ; Magnetic Resonance Imaging/methods ; Neuroimaging/methods ; Image Processing, Computer-Assisted/methods
Chemical Substances	Gadolinium (AU0V1LM3JT)
Language	English
Publishing date	2024-03-20
Publishing country	England
Document type	Journal Article
ZDB-ID	2061975-3
ISSN	1471-2342 ; 1471-2342
ISSN (online)	1471-2342
ISSN	1471-2342
DOI	10.1186/s12880-024-01242-3
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