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Article ; Online: Chronic Granulomatous Disease.

Roos, Dirk

Methods in molecular biology (Clifton, N.J.)

2019 Volume 1982, Page(s) 531–542

Abstract: Chronic granulomatous disease is a clinical condition that stems from inactivating mutations in NOX2 and its auxiliary proteins. Together, these proteins form the phagocyte NADPH oxidase enzyme that generates superoxide. Superoxide ( ... ...

Abstract	Chronic granulomatous disease is a clinical condition that stems from inactivating mutations in NOX2 and its auxiliary proteins. Together, these proteins form the phagocyte NADPH oxidase enzyme that generates superoxide. Superoxide (O
MeSH term(s)	Biomarkers ; Combined Modality Therapy ; Disease Management ; Enzyme Activation ; Granulomatous Disease, Chronic/diagnosis ; Granulomatous Disease, Chronic/etiology ; Granulomatous Disease, Chronic/metabolism ; Granulomatous Disease, Chronic/therapy ; Humans ; Hydrogen Peroxide/metabolism ; Mutation ; NADPH Oxidases/chemistry ; NADPH Oxidases/genetics ; NADPH Oxidases/metabolism ; Phagocytes/immunology ; Phagocytes/metabolism ; Phenotype ; Protein Binding ; Reactive Oxygen Species/metabolism ; Symptom Assessment ; Treatment Outcome
Chemical Substances	Biomarkers ; Reactive Oxygen Species ; Hydrogen Peroxide (BBX060AN9V) ; NADPH Oxidases (EC 1.6.3.-)
Language	English
Publishing date	2019-06-06
Publishing country	United States
Document type	Journal Article ; Review
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-9424-3_32
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Article ; Online: Comments on J Clin Immunol (2014) 34:633-641 DOI 10.1007/s10875-014-0061-0 : Clinical and Molecular Findings of 38 Children with Chronic Granulomatous Disease in Mainland China, by Huan Xu et al.

Roos, Dirk

Journal of clinical immunology

2016 Volume 37, Issue 1, Page(s) 3–4

MeSH term(s)	Child ; China ; DNA Mutational Analysis ; Granulomatous Disease, Chronic/genetics ; Humans ; Mutation/genetics
Language	English
Publishing date	2016-08-31
Publishing country	Netherlands
Document type	Letter
ZDB-ID	779361-3
ISSN	1573-2592 ; 0271-9142
ISSN (online)	1573-2592
ISSN	0271-9142
DOI	10.1007/s10875-016-0329-7
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Zs.A 1640: Show issues

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Article ; Online: Mutations in cis that affect mRNA synthesis, processing and translation.

Roos, Dirk / de Boer, Martin

Biochimica et biophysica acta. Molecular basis of disease

2021 Volume 1867, Issue 9, Page(s) 166166

Abstract: Genetic mutations that cause hereditary diseases usually affect the composition of the transcribed mRNA and its encoded protein, leading to instability of the mRNA and/or the protein. Sometimes, however, such mutations affect the synthesis, the ... ...

Abstract	Genetic mutations that cause hereditary diseases usually affect the composition of the transcribed mRNA and its encoded protein, leading to instability of the mRNA and/or the protein. Sometimes, however, such mutations affect the synthesis, the processing or the translation of the mRNA, with similar disastrous effects. We here present an overview of mRNA synthesis, its posttranscriptional modification and its translation into protein. We then indicate which elements in these processes are known to be affected by pathogenic mutations, but we restrict our review to mutations in cis, in the DNA of the gene that encodes the affected protein. These mutations can be in enhancer or promoter regions of the gene, which act as binding sites for transcription factors involved in pre-mRNA synthesis. We also describe mutations in polyadenylation sequences and in splice site regions, exonic and intronic, involved in intron removal. Finally, we include mutations in the Kozak sequence in mRNA, which is involved in protein synthesis. We provide examples of genetic diseases caused by mutations in these DNA regions and refer to databases to help identify these regions. The over-all knowledge of mRNA synthesis, processing and translation is essential for improvement of the diagnosis of patients with genetic diseases.
MeSH term(s)	Animals ; Humans ; Mutation/genetics ; Protein Biosynthesis/genetics ; Protein Processing, Post-Translational/genetics ; RNA, Messenger/genetics
Chemical Substances	RNA, Messenger
Language	English
Publishing date	2021-05-08
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	60-7
ISSN	1879-260X ; 1879-2596 ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1879-260X ; 1879-2596 ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
ISSN	0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbadis.2021.166166
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Article ; Online: RANKL blockade for erosive hand osteoarthritis: a randomized placebo-controlled phase 2a trial.

Wittoek, Ruth / Verbruggen, Gust / Vanhaverbeke, Tine / Colman, Roos / Elewaut, Dirk

Nature medicine

2024 Volume 30, Issue 3, Page(s) 829–836

Abstract: Erosive hand osteoarthritis (OA) is a prevalent and disabling disease with limited treatment options. Here we present the results of a monocentric, placebo-controlled, double-blind, randomized phase 2a clinical trial with denosumab, a receptor activator ... ...

Abstract	Erosive hand osteoarthritis (OA) is a prevalent and disabling disease with limited treatment options. Here we present the results of a monocentric, placebo-controlled, double-blind, randomized phase 2a clinical trial with denosumab, a receptor activator of nuclear factor-κB ligand inhibitor, evaluating the effects on structure modification in erosive hand OA. Patients were randomized to 48 weeks treatment with denosumab 60 mg every 3 months (n = 51, 41 females) or placebo (n = 49, 37 females). The primary (radiographic) endpoint was the change in the total Ghent University Scoring System (GUSS) at week 24, where positive changes correspond to remodeling and negative changes to erosive progression. Secondary endpoints were the change in the GUSS at week 48 and the number of new erosive joints at week 48 by the anatomical phase scoring system. Baseline mean GUSS (standard deviation) of target joints was 155.9 (69.3) in the denosumab group and 158.7 (46.8) in the placebo group. The primary endpoint was met with an estimated difference between groups of 8.9 (95% confidence interval (CI) 1.0 to 16.9; P = 0.024) at week 24. This effect was confirmed at week 48 (baseline adjusted GUSS (standard error of the mean) denosumab and placebo were 163.5 (2.9) and 149.2 (3.9), respectively; with an estimated difference between groups of 14.3 (95% CI 4.6 to 24.0; P = 0.003)). At patient level, more new erosive joints were developed in the placebo group compared with denosumab at week 48 (odds ratio 0.24 (95% CI 0.08 to 0.72); P = 0.009). More adverse events occurred in the placebo group (125 events in 44 patients (90%)) compared with the denosumab group (97 events in 41 patients (80%)). These results demonstrate that denosumab has structure modifying effects in erosive hand OA by inducing remodeling and preventing new erosive joints. EU Clinical Trials Register identifier 2015-003223-53 .
MeSH term(s)	Female ; Humans ; Denosumab/adverse effects ; Double-Blind Method ; Osteoarthritis/diagnostic imaging ; Osteoarthritis/drug therapy ; RANK Ligand ; Treatment Outcome ; Male
Chemical Substances	Denosumab (4EQZ6YO2HI) ; RANK Ligand
Language	English
Publishing date	2024-02-15
Publishing country	United States
Document type	Randomized Controlled Trial ; Clinical Trial, Phase II ; Journal Article
ZDB-ID	1220066-9
ISSN	1546-170X ; 1078-8956
ISSN (online)	1546-170X
ISSN	1078-8956
DOI	10.1038/s41591-024-02822-0
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Zs.A 4212: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Chronic granulomatous disease.

Roos, Dirk

British medical bulletin

2016 Volume 118, Issue 1, Page(s) 50–63

Abstract: Introduction: Chronic granulomatous disease (CGD) is a primary immunodeficiency characterized by recurrent, life-threatening bacterial and fungal infections of the skin, the airways, the lymph nodes, the liver, the brain and the bones. Frequently found ... ...

Abstract	Introduction: Chronic granulomatous disease (CGD) is a primary immunodeficiency characterized by recurrent, life-threatening bacterial and fungal infections of the skin, the airways, the lymph nodes, the liver, the brain and the bones. Frequently found pathogens are Staphylococcus aureus, Aspergillus species, Klebsiella species, Burkholderia cepacia, Serratia marcescens and Salmonella species. Sources of data: CGD is a rare (∼1:250 000 individuals) disease caused by mutations in any one of the five components of the NADPH oxidase in phagocytic leucocytes. This enzyme generates superoxide and is essential for intracellular killing of pathogens by phagocytes. Areas of agreement: CGD patients suffer not only from life-threatening infections, but also from excessive inflammatory reactions. Areas of controversy: Neither the cause of these inflammatory reactions nor the way to treat them is clear. Areas timely for developing research: Patient selection for and timing of bone marrow transplantation along with gene therapy.
MeSH term(s)	Bacterial Infections/genetics ; Bacterial Infections/microbiology ; Bacterial Infections/therapy ; Bone Marrow Transplantation ; Genetic Predisposition to Disease/genetics ; Genetic Therapy ; Granulomatous Disease, Chronic/diagnosis ; Granulomatous Disease, Chronic/genetics ; Granulomatous Disease, Chronic/microbiology ; Granulomatous Disease, Chronic/therapy ; Humans ; Molecular Diagnostic Techniques ; Mutation/genetics ; Mycoses/genetics ; Mycoses/microbiology ; Mycoses/therapy ; NADPH Oxidases/genetics ; Phagocytes
Chemical Substances	NADPH Oxidases (EC 1.6.3.-)
Language	English
Publishing date	2016-03-16
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	213294-1
ISSN	1471-8391 ; 0007-1420
ISSN (online)	1471-8391
ISSN	0007-1420
DOI	10.1093/bmb/ldw009
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Article ; Online: Complement and phagocytes - A complicated interaction.

Roos, Dirk

Molecular immunology

2015 Volume 68, Issue 1, Page(s) 31–34

Abstract: Mohamed Daha and I share a common interest in innate immunity. Working in institutes only 25 miles away from each other, that meant ample opportunity and relevance for collaboration. And so we did. Moreover, we have both been members of boards and ... ...

Abstract	Mohamed Daha and I share a common interest in innate immunity. Working in institutes only 25 miles away from each other, that meant ample opportunity and relevance for collaboration. And so we did. Moreover, we have both been members of boards and councils of Dutch national organizations, and we have also become good friends. In this short recollection, I look back on 40 years of common activities in complement research and friendship.
MeSH term(s)	Allergy and Immunology/history ; Antibodies/genetics ; Antibodies/immunology ; Biomedical Research/history ; Complement Activation ; Complement System Proteins/genetics ; Complement System Proteins/immunology ; Cooperative Behavior ; History, 20th Century ; History, 21st Century ; Humans ; Immunity, Innate ; Inflammation/genetics ; Inflammation/immunology ; Inflammation/pathology ; Macrophages/immunology ; Macrophages/pathology ; Neutrophils/immunology ; Neutrophils/pathology ; Opsonin Proteins/genetics ; Opsonin Proteins/immunology ; Phagocytosis
Chemical Substances	Antibodies ; Opsonin Proteins ; Complement System Proteins (9007-36-7)
Language	English
Publishing date	2015-11
Publishing country	England
Document type	Historical Article ; Journal Article ; Review
ZDB-ID	424427-8
ISSN	1872-9142 ; 0161-5890
ISSN (online)	1872-9142
ISSN	0161-5890
DOI	10.1016/j.molimm.2015.05.001
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Article ; Online: A Critical Evaluation of International Agreements Towards a Revised Categorization for Transfrontier Conservation Areas (TFCAs).

Retief, Francois Pieter / Alberts, Reece Cronje / Lubbe, Willem Daniel / Roos, Claudine / Cilliers, Dirk Petrus

Environmental management

2023 Volume 72, Issue 6, Page(s) 1099–1110

Abstract: Transfrontier Conservation Areas (TFCAs) are widely promoted as an international instrument to achieve certain conservation, cooperation and developmental goals, especially within the Southern African Development Community (SADC). In the SADC context, ... ...

Abstract	Transfrontier Conservation Areas (TFCAs) are widely promoted as an international instrument to achieve certain conservation, cooperation and developmental goals, especially within the Southern African Development Community (SADC). In the SADC context, the status of TFCAs is categorized based on the extent to which international agreements have been signed. These agreements take different forms such as treaties, memorandums of understanding (MoUs), protocols and bilateral agreements. However, the efficacy of agreement-based approaches towards the categorization of TFCAs has been questioned because it does not acknowledge the implementation complexities of TFCAs and lacks a sound conceptual basis. This research evaluates the international TFCA agreements in SADC with a view to recommending a revised categorization. This is achieved by applying Theory of Change (ToC) to a sample of ten signed TFCAs agreements. The results show a lack of enforcement mechanisms, weak provision for implementation and poorly defined objectives. These weaknesses of agreement-based approaches can best be addressed by expanding the categorization of TFCAs to also include the extent of legislative and operational alignment. The revised categorization supports a more complete understanding of TFCA implementation.
Language	English
Publishing date	2023-09-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	1478932-2
ISSN	1432-1009 ; 0364-152X
ISSN (online)	1432-1009
ISSN	0364-152X
DOI	10.1007/s00267-023-01872-3
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Book ; Online: Gradient and Uncertainty Enhanced Sequential Sampling for Global Fit

Lämmle, Sven / Bogoclu, Can / Cremanns, Kevin / Roos, Dirk

2023

Abstract: Surrogate models based on machine learning methods have become an important part of modern engineering to replace costly computer simulations. The data used for creating a surrogate model are essential for the model accuracy and often restricted due to ... ...

Abstract	Surrogate models based on machine learning methods have become an important part of modern engineering to replace costly computer simulations. The data used for creating a surrogate model are essential for the model accuracy and often restricted due to cost and time constraints. Adaptive sampling strategies have been shown to reduce the number of samples needed to create an accurate model. This paper proposes a new sampling strategy for global fit called Gradient and Uncertainty Enhanced Sequential Sampling (GUESS). The acquisition function uses two terms: the predictive posterior uncertainty of the surrogate model for exploration of unseen regions and a weighted approximation of the second and higher-order Taylor expansion values for exploitation. Although various sampling strategies have been proposed so far, the selection of a suitable method is not trivial. Therefore, we compared our proposed strategy to 9 adaptive sampling strategies for global surrogate modeling, based on 26 different 1 to 8-dimensional deterministic benchmarks functions. Results show that GUESS achieved on average the highest sample efficiency compared to other surrogate-based strategies on the tested examples. An ablation study considering the behavior of GUESS in higher dimensions and the importance of surrogate choice is also presented.
Keywords	Statistics - Machine Learning ; Computer Science - Machine Learning
Subject code	310
Publishing date	2023-09-29
Publishing country	us
Document type	Book ; Online
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Article ; Online: Identifying key risks to the achievement of protected area system objectives

Reece Alberts / Francois Retief / Claudine Roos / Dirk Cilliers / Willem Lubbe

Nature Conservation, Vol 49, Iss , Pp 53-

2022 Volume 75

Abstract: Protected area systems are designed in law and policy towards achieving certain policy objectives. These systems rely on legal frameworks that determine how countries designate, declare and manage their protected areas. To date, little research has been ... ...

Abstract	Protected area systems are designed in law and policy towards achieving certain policy objectives. These systems rely on legal frameworks that determine how countries designate, declare and manage their protected areas. To date, little research has been conducted on the risks faced by protected area systems. To this end, this paper aims to identify the key risks for protected area systems achieving their objectives. This is achieved through the application of Theory of Change (ToC), which is internationally recognised as the preferred method to identify underlying assumptions and risks within policy and legal frameworks. We achieve this aim through a case study analysis of the South African protected area system as embedded in law and policy. The application of the ToC method identified 25 underlying assumptions and risks which are central to the protected area system achieving its objectives. Understanding these risks allows for a better understanding of the potential failure of the system and how to avoid it. The paper then explores and discusses the identified risks in terms of existing literature and concludes by making recommendations related to further research for the identified risks.
Keywords	Ecology ; QH540-549.5 ; General. Including nature conservation ; geographical distribution ; QH1-199.5
Subject code	360
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	Pensoft Publishers
Document type	Article ; Online
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Article ; Online: Identifying key risks to the performance of privately protected areas (PPAs) through theory of change (ToC).

Retief, Francois P / Alberts, Reece C / Roos, Claudine / Cilliers, Dirk C / Siebert, Frances

Journal of environmental management

2022 Volume 308, Page(s) 114575

Abstract: Privately protected areas (PPAs) are internationally considered to be important policy implementation instruments to augment and strengthen protected area networks. However, there has been limited reflection on the performance of PPAs over time. This ... ...

Abstract	Privately protected areas (PPAs) are internationally considered to be important policy implementation instruments to augment and strengthen protected area networks. However, there has been limited reflection on the performance of PPAs over time. This paper aims to identify key risks to the performance of PPAs as policy implementation instruments through the application of Theory of Change (ToC). Identifying and understanding these risks are important to allow for the evaluation and monitoring of PPA performance. The ToC method was applied to a specific PPA policy instrument namely, private nature reserves (PNRs) in the South African context. The research results produced 29 key assumptions translated into 29 key risks. These risk are critically discussed against existing South African and international literature. To test and refine the risks further it is recommended that they be applied to PPA case studies in different contexts.
Language	English
Publishing date	2022-02-03
Publishing country	England
Document type	Journal Article
ZDB-ID	184882-3
ISSN	1095-8630 ; 0301-4797
ISSN (online)	1095-8630
ISSN	0301-4797
DOI	10.1016/j.jenvman.2022.114575
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