| 1. |
- van Haarlem, M. P., et al.
(författare)
-
LOFAR : The LOw-Frequency ARray
- 2013
-
Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 556, s. 1-53
-
Tidskriftsartikel (refereegranskat)abstract
- LOFAR, the LOw-Frequency ARray, is a new-generation radio interferometer constructed in the north of the Netherlands and across europe. Utilizing a novel phased-array design, LOFAR covers the largely unexplored low-frequency range from 10–240 MHz and provides a number of unique observing capabilities. Spreading out from a core located near the village of Exloo in the northeast of the Netherlands, a total of 40 LOFAR stations are nearing completion. A further five stations have been deployed throughout Germany, and one station has been built in each of France, Sweden, and the UK. Digital beam-forming techniques make the LOFAR system agile and allow for rapid repointing of the telescope as well as the potential for multiple simultaneous observations. With its dense core array and long interferometric baselines, LOFAR achieves unparalleled sensitivity and angular resolution in the low-frequency radio regime. The LOFAR facilities are jointly operated by the International LOFAR Telescope (ILT) foundation, as an observatory open to the global astronomical community. LOFAR is one of the first radio observatories to feature automated processing pipelines to deliver fully calibrated science products to its user community. LOFAR’s new capabilities, techniques and modus operandi make it an important pathfinder for the Square Kilometre Array (SKA). We give an overview of the LOFAR instrument, its major hardware and software components, and the core science objectives that have driven its design. In addition, we present a selection of new results from the commissioning phase of this new radio observatory.
|
|
| 2. |
- Heald, G. H., et al.
(författare)
-
The LOFAR Multifrequency Snapshot Sky Survey (MSSS) : I. Survey description and first results
- 2015
-
Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 582, s. 1-22
-
Tidskriftsartikel (refereegranskat)abstract
- We present the Multifrequency Snapshot Sky Survey (MSSS), the first northern-sky Low Frequency Array (LOFAR) imaging survey. In this introductory paper, we first describe in detail the motivation and design of the survey. Compared to previous radio surveys, MSSS is exceptional due to its intrinsic multifrequency nature providing information about the spectral properties of the detected sources over more than two octaves (from 30 to 160 MHz). The broadband frequency coverage, together with the fast survey speed generated by LOFAR’s multibeaming capabilities, make MSSS the first survey of the sort anticipated to be carried out with the forthcoming Square Kilometre Array (SKA). Two of the sixteen frequency bands included in the survey were chosen to exactly overlap the frequency coverage of large-area Very Large Array (VLA) and Giant Metrewave Radio Telescope (GMRT) surveys at 74 MHz and 151 MHz respectively. The survey performance is illustrated within the MSSS Verification Field (MVF), a region of 100 square degrees centered at (α,δ)J2000 = (15h,69°). The MSSS results from the MVF are compared with previous radio survey catalogs. We assess the flux and astrometric uncertainties in the catalog, as well as the completeness and reliability considering our source finding strategy. We determine the 90% completeness levels within the MVF to be 100 mJy at 135 MHz with 108″ resolution, and 550 mJy at 50 MHz with 166″ resolution. Images and catalogs for the full survey, expected to contain 150 000–200 000 sources, will be released to a public web server. We outline the plans for the ongoing production of the final survey products, and the ultimate public release of images and source catalogs.
|
|
| 3. |
- van Cappellen, W., et al.
(författare)
-
Apertif: Phased array feeds for the Westerbork Synthesis Radio Telescope: System overview and performance characteristics
- 2022
-
Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 658
-
Tidskriftsartikel (refereegranskat)abstract
- We describe the APERture Tile In Focus (Apertif) system, a phased array feed (PAF) upgrade of the Westerbork Synthesis Radio Telescope that transforms this telescope into a high-sensitivity, wide-field-of-view L-band imaging and transient survey instrument. Using novel PAF technology, up to 40 partially overlapping beams are formed on the sky simultaneously, significantly increasing the survey speed of the telescope. With this upgraded instrument, an imaging survey covering an area of 2300 deg2 is being performed that will deliver both continuum and spectral line datasets, of which the first data have been publicly released. In addition, a time domain transient and pulsar survey covering 15 000 deg2 is in progress. An overview of the Apertif science drivers, hardware, and software of the upgraded telescope is presented, along with its key performance characteristics.
|
|
| 4. |
- Artigas, J., et al.
(författare)
-
Towards a renewed research agenda in ecotoxicology
- 2012
-
Ingår i: Environmental Pollution. - : Elsevier BV. - 0269-7491. ; 160, s. 201-206
-
Tidskriftsartikel (refereegranskat)abstract
- New concerns about biodiversity, ecosystem services and human health triggered several new regulations increasing the need for sound ecotoxicological risk assessment. The PEER network aims to share its view on the research issues that this challenges. PEER scientists call for an improved biologically relevant exposure assessment. They promote comprehensive effect assessment at several biological levels. Biological traits should be used for Environmental risk assessment (ERA) as promising tools to better understand relationships between structure and functioning of ecosystems. The use of modern high throughput methods could also enhance the amount of data for a better risk assessment. Improved models coping with multiple stressors or biological levels are necessary to answer for a more scientifically based risk assessment. Those methods must be embedded within life cycle analysis or economical models for efficient regulations. Joint research programmes involving humanities with ecological sciences should be developed for a sound risk management. (C) 2011 Elsevier Ltd. All rights reserved.
|
|
| 5. |
|
|
| 6. |
- Batkovskyte, D., et al.
(författare)
-
Al-Gazali Skeletal Dysplasia Constitutes the Lethal End of ADAMTSL2-Related Disorders
- 2023
-
Ingår i: Journal of Bone and Mineral Research. - : Wiley. - 0884-0431 .- 1523-4681. ; 38:5, s. 692-706
-
Tidskriftsartikel (refereegranskat)abstract
- Lethal short-limb skeletal dysplasia Al-Gazali type (OMIM %601356), also called dysplastic cortical hyperostosis, Al-Gazali type, is an ultra-rare disorder previously reported in only three unrelated individuals. The genetic etiology for Al-Gazali skeletal dysplasia has up until now been unknown. Through international collaborative efforts involving seven clinical centers worldwide, a cohort of nine patients with clinical and radiographic features consistent with short-limb skeletal dysplasia Al-Gazali type was collected. The affected individuals presented with moderate intrauterine growth restriction, relative macrocephaly, hypertrichosis, large anterior fontanelle, short neck, short and stiff limbs with small hands and feet, severe brachydactyly, and generalized bone sclerosis with mild platyspondyly. Biallelic disease-causing variants in ADAMTSL2 were detected using massively parallel sequencing (MPS) and Sanger sequencing techniques. Six individuals were compound heterozygous and one individual was homozygous for pathogenic variants in ADAMTSL2. In one of the families, pathogenic variants were detected in parental samples only. Overall, this study sheds light on the genetic cause of Al-Gazali skeletal dysplasia and identifies it as a semi-lethal part of the spectrum of ADAMTSL2-related disorders. Furthermore, we highlight the importance of meticulous analysis of the pseudogene region of ADAMTSL2 where disease-causing variants might be located.
|
|
| 7. |
- Rodriguez-Palmero, Agusti, et al.
(författare)
-
DLG4-related synaptopathy : a new rare brain disorder
- 2021
-
Ingår i: Genetics in Medicine. - : Elsevier BV. - 1098-3600 .- 1530-0366. ; 23:5, s. 888-899
-
Tidskriftsartikel (refereegranskat)abstract
- PurposePostsynaptic density protein-95 (PSD-95), encoded by DLG4, regulates excitatory synaptic function in the brain. Here we present the clinical and genetic features of 53 patients (42 previously unpublished) with DLG4 variants.MethodsThe clinical and genetic information were collected through GeneMatcher collaboration. All the individuals were investigated by local clinicians and the gene variants were identified by clinical exome/genome sequencing.ResultsThe clinical picture was predominated by early onset global developmental delay, intellectual disability, autism spectrum disorder, and attention deficit–hyperactivity disorder, all of which point to a brain disorder. Marfanoid habitus, which was previously suggested to be a characteristic feature of DLG4-related phenotypes, was found in only nine individuals and despite some overlapping features, a distinct facial dysmorphism could not be established. Of the 45 different DLG4 variants, 39 were predicted to lead to loss of protein function and the majority occurred de novo (four with unknown origin). The six missense variants identified were suggested to lead to structural or functional changes by protein modeling studies.ConclusionThe present study shows that clinical manifestations associated with DLG4 overlap with those found in other neurodevelopmental disorders of synaptic dysfunction; thus, we designate this group of disorders as DLG4-related synaptopathy.
|
|
| 8. |
|
|
| 9. |
|
|
| 10. |
- Peiser, M., et al.
(författare)
-
Allergic contact dermatitis: Epidemiology, molecular mechanisms, in vitro methods and regulatory aspects
- 2012
-
Ingår i: Cellular and Molecular Life Sciences. - : Springer Science and Business Media LLC. - 1420-682X .- 1420-9071. ; 69:5, s. 763-781
-
Forskningsöversikt (refereegranskat)abstract
- Contact allergies are complex diseases, and one of the important challenges for public health and immunology. The German 'Federal Institute for Risk Assessment' hosted an 'International Workshop on Contact Dermatitis'. The scope of the workshop was to discuss new discoveries and developments in the field of contact dermatitis. This included the epidemiology and molecular biology of contact allergy, as well as the development of new in vitro methods. Furthermore, it considered regulatory aspects aiming to reduce exposure to contact sensitisers. An estimated 15-20% of the general population suffers from contact allergy. Workplace exposure, age, sex, use of consumer products and genetic predispositions were identified as the most important risk factors. Research highlights included: advances in understanding of immune responses to contact sensitisers, the importance of autoxidation or enzyme-mediated oxidation for the activation of chemicals, the mechanisms through which hapten-protein conjugates are formed and the development of novel in vitro strategies for the identification of skin-sensitising chemicals. Dendritic cell cultures and structure-activity relationships are being developed to identify potential contact allergens. However, the local lymph node assay (LLNA) presently remains the validated method of choice for hazard identification and characterisation. At the workshop the use of the LLNA for regulatory purposes and for quantitative risk assessment was also discussed. © The Author(s) 2011.
|
|
| 11. |
- Scarpellini, E., et al.
(författare)
-
International consensus on the diagnosis and management of dumping syndrome
- 2020
-
Ingår i: Nature Reviews Endocrinology. - : Springer Science and Business Media LLC. - 1759-5029 .- 1759-5037. ; 16:8, s. 448-466
-
Tidskriftsartikel (refereegranskat)abstract
- Dumping syndrome is a common but underdiagnosed complication of gastric and oesophageal surgery. We initiated a Delphi consensus process with international multidisciplinary experts. We defined the scope, proposed statements and searched electronic databases to survey the literature. Eighteen experts participated in the literature summary and voting process evaluating 62 statements. We evaluated the quality of evidence using grading of recommendations assessment, development and evaluation (GRADE) criteria. Consensus (defined as >80% agreement) was reached for 33 of 62 statements, including the definition and symptom profile of dumping syndrome and its effect on quality of life. The panel agreed on the pathophysiological relevance of rapid passage of nutrients to the small bowel, on the role of decreased gastric volume capacity and release of glucagon-like peptide 1. Symptom recognition is crucial, and the modified oral glucose tolerance test, but not gastric emptying testing, is useful for diagnosis. An increase in haematocrit >3% or in pulse rate >10 bpm 30 min after the start of the glucose intake are diagnostic of early dumping syndrome, and a nadir hypoglycaemia level <50 mg/dl is diagnostic of late dumping syndrome. Dietary adjustment is the agreed first treatment step; acarbose is effective for late dumping syndrome symptoms and somatostatin analogues are preferred for patients who do not respond to diet adjustments and acarbose. Dumping syndrome is a frequent complication of oesophageal and gastric surgery, as well as bariatric surgery; however, guidance on how to manage patients with this condition is lacking. In this Evidence-based guideline, the authors use a Delphi consensus process to develop uniform guidance for the definition, diagnosis and management of dumping syndrome.
|
|
| 12. |
- Spaan, Suzanne, et al.
(författare)
-
Endotoxin Exposure In Sewage Treatment Workers: Investigation Of Exposure Variability And Comparison Of Analytical Techniques
- 2008
-
Ingår i: Annals of Agricultural and Environmental Medicine. - 1898-2263. ; 15:2, s. 251-261
-
Tidskriftsartikel (refereegranskat)abstract
- Introduction: Objectives were to give an overview of endotoxin exposure and its determinants in sewage treatment workers, and to study exposure to culturable and non-culturable microorganisms and the applicability of the LAL assay in this work environment. Material and methods: In 43 Dutch sewage treatment plants 470 full-shift, 123 task-based personal and 54 stationary inhalable dust samples were collected. Endotoxin concentration was determined with the LAL-assay. Mixed effects models were used to investigate possible determinants of exposure. Simultaneous parallel filter Samples, impinger samples and viable total bacteria and Gram-negative bacterial samples were taken to compare analytical techniques. Filter and impinger samples were analyzed with the LAL-assay, gas chromatography-mass spectrometry (GC-MS) and fluorescence microscopy. Results: Endotoxin exposure levels were moderate to low (geometric mean personal exposure 27 EU/m(3), stationary 33 EU/m(3), task-based 64 EU/m(3)), yet differences between jobs and sources and some determinants of exposure were identified. Exposure varied more from day to day than between workers. Concentrations in filter samples were higher and more consistent than in impinger samples. Fungi and Gram-positive bacteria were found in higher levels than Gram-negative bacteria. The LAL assay and GC-MS showed comparable endotoxin levels. Discussion and conclusion: Endotoxin exposure in Dutch sewage treatment workers was relatively low,. Comparison of sampling and analytical techniques suggests that the LAL-assay did not result in much exposure misclassification. It thus seems justified to perform filter measurements in combination with the LAL-assay to measure endotoxin exposure in sewage treatment plants.
|
|
| 13. |
- Benthem, P., et al.
(författare)
-
Aperture array development for future large radio telescopes
- 2011
-
Ingår i: European Conference on Antennas and Propagation 2011, 11-15 April 2011, Rome.
-
Konferensbidrag (refereegranskat)abstract
- We present the design of a phased array system for future radio telescopes. This includes a system overview and recent results of the designed and implemented system, the Electronic Multi-Beam Radio Astronomy Concept (EMBRACE). Furthermore, simulations with a full-EM antenna simulator, combined with measurements on actual hardware, will provide information for the next design step, the Aperture Array Verification System (AAVS). With AAVS, we will prove design readiness of this novel array technology.
|
|
| 14. |
- de Leeuw, Nicole, et al.
(författare)
-
Diagnostic Interpretation of Array Data Using Public Databases and Internet Sources
- 2012
-
Ingår i: Human Mutation. - : Hindawi Limited. - 1059-7794 .- 1098-1004. ; 33:6, s. 930-940
-
Tidskriftsartikel (refereegranskat)abstract
- The range of commercially available array platforms and analysis software packages is expanding and their utility is improving, making reliable detection of copy-number variants (CNVs) relatively straightforward. Reliable interpretation of CNV data, however, is often difficult and requires expertise. With our knowledge of the human genome growing rapidly, applications for array testing continuously broadening, and the resolution of CNV detection increasing, this leads to great complexity in interpreting what can be daunting data. Correct CNV interpretation and optimal use of the genotype information provided by single-nucleotide polymorphism probes on an array depends largely on knowledge present in various resources. In addition to the availability of host laboratories' own datasets and national registries, there are several public databases and Internet resources with genotype and phenotype information that can be used for array data interpretation. With so many resources now available, it is important to know which are fit-for-purpose in a diagnostic setting. We summarize the characteristics of the most commonly used Internet databases and resources, and propose a general data interpretation strategy that can be used for comparative hybridization, comparative intensity, and genotype-based array data.
|
|
| 15. |
- Delfin, Carl, et al.
(författare)
-
A Federated Database for Obesity Research : An IMI-SOPHIA Study
- 2024
-
Ingår i: Life. - 0024-3019. ; 14:2
-
Tidskriftsartikel (refereegranskat)abstract
- Obesity is considered by many as a lifestyle choice rather than a chronic progressive disease. The Innovative Medicines Initiative (IMI) SOPHIA (Stratification of Obesity Phenotypes to Optimize Future Obesity Therapy) project is part of a momentum shift aiming to provide better tools for the stratification of people with obesity according to disease risk and treatment response. One of the challenges to achieving these goals is that many clinical cohorts are siloed, limiting the potential of combined data for biomarker discovery. In SOPHIA, we have addressed this challenge by setting up a federated database building on open-source DataSHIELD technology. The database currently federates 16 cohorts that are accessible via a central gateway. The database is multi-modal, including research studies, clinical trials, and routine health data, and is accessed using the R statistical programming environment where statistical and machine learning analyses can be performed at a distance without any disclosure of patient-level data. We demonstrate the use of the database by providing a proof-of-concept analysis, performing a federated linear model of BMI and systolic blood pressure, pooling all data from 16 studies virtually without any analyst seeing individual patient-level data. This analysis provided similar point estimates compared to a meta-analysis of the 16 individual studies. Our approach provides a benchmark for reproducible, safe federated analyses across multiple study types provided by multiple stakeholders.
|
|
| 16. |
|
|
| 17. |
|
|
| 18. |
|
|
| 19. |
- Arts, M. J., et al.
(författare)
-
Analysis of the EMBRACE aperture array antenna by the characteristic Basis Function Method
- 2011
-
Ingår i: Proceedings - 13th International Conference on Electromagnetics in Advanced Applications, ICEAA'11, Torino, 12-16 September 2011. - 9781612849782 ; , s. 959-962
-
Konferensbidrag (refereegranskat)abstract
- This paper describes the use of the Characteristic Basis Function Method for the simulation of large phased array antennas for radio astronomy. It will be shown how the antenna effective area and the receiver noise temperature depend on array size. Also the receiving sensitivity Aeff /T sys normalised with respect to the physical area of the array will be shown for different array sizes and scan angles.
|
|
| 20. |
- Arts, Thomas, 1969, et al.
(författare)
-
Model-based testing of data types with side effects
- 2011
-
Ingår i: Proceedings of the 2011 ACM SIGPLAN Erlang Workshop, Tokyo, 23 September 2011. - New York, NY, USA : ACM. - 9781450308595 ; , s. 30-38
-
Konferensbidrag (refereegranskat)abstract
- Data types are the core of many applications, and libraries offering implementations of data types should better be solid and well tested. Testing purely functional data types with QuickCheck provides a complete test method for data types, but establishing a complete test method for data types with side-effects is still an open issue. In this paper we show how we can use a stateful QuickCheck model to establish a complete test method for any data type. Considering side effects allows us to move from the purely functional world to the imperative world, as needed to face the testing of data types implementations in languages such as C. We therefore applied our method to some of the data types provided by the well-known GNOME Glib library.
|
|
| 21. |
- Arts, Thomas, 1969, et al.
(författare)
-
Testing Data Consistency of Data-Intensive Applications using QuickCheck
- 2010
-
Ingår i: Programming and Computer Languages.
-
Konferensbidrag (refereegranskat)abstract
- Many information systems are data-intensive, and most of them rely on trustworthy data management systems for data storage, such as Relational Database Management Systems (RDBMS). RDBMSs are used to store information in a structured manner and to define several types of constraints on the data, to keep basic consistencies.There are several scenarios in which passing the responsibility of consistency checking completely onto the RDBMS is inconvenient, or simply not possible. In such cases, the alternative is to perform those consistency checks at the business logic level of the system. From a point of view of testing data-intensive applications, one of the most relevant aspects is to ensure correctness of the business logic.In this article, we show how QuickCheck, a tool for random testing against specifications, can be used to test this business logic to increase confidence on data integrity. We build an abstract model of the data containing the minimum amount necessary to create meaningful test cases. This is important in order to make sure the state of the model is substantially smaller than the data in the complete database. From the abstract model we automatically generate and execute test cases which check that data invariants are preserved.
|
|
| 22. |
|
|
| 23. |
|
|
| 24. |
|
|
| 25. |
|
|
| 26. |
- Castro, Laura M., et al.
(författare)
-
Testing Data Consistency of Data-Intensive Applications Using QuickCheck
- 2011
-
Ingår i: Electronic Notes in Theoretical Computer Science. - : Elsevier BV. - 1571-0661. ; 271, s. 41-62
-
Tidskriftsartikel (refereegranskat)abstract
- Many software systems are data-intensive and use a data management systems for data storage, such as Relational Database Management Systems (RDBMS). RDBMSs are used to store information in a structured manner, and to define several types of constraints on the data, to maintain basic consistency. The RDBMSs are mature, well tested, software products that one can trust to reliably store data and keep it consistent within the defined constraints.There are, however, scenarios in which passing the responsibility of consistency enforcement to the RDBMS is not convenient, or simply not possible. In such cases, the alternative is to have that responsibility at the business logic level of the system. Hence, from the point of view of testing data-intensive applications, one of the most relevant aspects is to ensure correctness of the business logic in terms of data consistency.In this article, we show how QuickCheck, a tool for random testing against specifications, can be used to test the business logic of an application to increase confidence on data integrity. We build an abstract model of the data containing the minimum information necessary to create meaningful test cases, while keeping its state substantially smaller than the data in the complete database. From the abstract model we automatically generate and execute test cases which check that data constraints are preserved.
|
|
| 27. |
- Cherp, Aleh, et al.
(författare)
-
SEA follow-up
- 2011
-
Ingår i: Handbook of Strategic Environmental Assessment. - 9781844073658
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)
|
|
| 28. |
|
|
| 29. |
- Crowson, Cynthia S., et al.
(författare)
-
Impact of risk factors associated with cardiovascular outcomes in patients with rheumatoid arthritis
- 2018
-
Ingår i: Annals of the Rheumatic Diseases. - : BMJ Publishing Group Ltd. - 0003-4967 .- 1468-2060. ; 77:1, s. 48-54
-
Tidskriftsartikel (refereegranskat)abstract
- Objectives: Patients with rheumatoid arthritis (RA) have an excess risk of cardiovascular disease (CVD). We aimed to assess the impact of CVD risk factors, including potential sex differences, and RA-specific variables on CVD outcome in a large, international cohort of patients with RA. Methods: In 13 rheumatology centres, data on CVD risk factors and RA characteristics were collected at baseline. CVD outcomes (myocardial infarction, angina, revascularisation, stroke, peripheral vascular disease and CVD death) were collected using standardised definitions. Results: 5638 patients with RA and no prior CVD were included (mean age: 55.3 (SD: 14.0) years, 76% women). During mean follow-up of 5.8 (SD: 4.4) years, 148 men and 241 women developed a CVD event (10-year cumulative incidence 20.9% and 11.1%, respectively). Men had a higher burden of CVD risk factors, including increased blood pressure, higher total cholesterol and smoking prevalence than women (all p<0.001). Among the traditional CVD risk factors, smoking and hypertension had the highest population attributable risk (PAR) overall and among both sexes, followed by total cholesterol. The PAR for Disease Activity Score and for seropositivity were comparable in magnitude to the PAR for lipids. A total of 70% of CVD events were attributable to all CVD risk factors and RA characteristics combined (separately 49% CVD risk factors and 30% RA characteristics). Conclusions: In a large, international cohort of patients with RA, 30% of CVD events were attributable to RA characteristics. This finding indicates that RA characteristics play an important role in efforts to reduce CVD risk among patients with RA.
|
|
| 30. |
- Ivashina, Marianna, 1975, et al.
(författare)
-
An axi-symmetric segmented composite SKA dish design: Performance and production analysis
- 2011
-
Ingår i: Asia-Pacific Microwave Conference, APMC 2011; Melbourne, VIC; 5 - 8 December 2011. - 9780858259744 ; , s. 1182-1185
-
Konferensbidrag (refereegranskat)abstract
- A concept of an axi-symmetric dish as antenna reflector for the next generation radio telescope - the Square Kilometre Array (SKA) - is presented. The reflector is based on the use of novel thermoplastic composite material (reinforced with carbon fibre) in the context of the telescope design with wide band single pixel feeds. The baseline of this design represents an array of 100's to 1000's reflector antennas of 15-m diameter and covers frequencies from
|
|
| 31. |
|
|
| 32. |
|
|
| 33. |
- Martins Dos Santos, Vitor, et al.
(författare)
-
Systems Biology in ELIXIR: modelling in the spotlight
- 2022
-
Ingår i: F1000Research. - : F1000 Research Ltd. - 1759-796X .- 2046-1402. ; 11
-
Tidskriftsartikel (refereegranskat)abstract
- In this white paper, we describe the founding of a new ELIXIR Community - the Systems Biology Community - and its proposed future contributions to both ELIXIR and the broader community of systems biologists in Europe and worldwide. The Community believes that the infrastructure aspects of systems biology - databases, (modelling) tools and standards development, as well as training and access to cloud infrastructure - are not only appropriate components of the ELIXIR infrastructure, but will prove key components of ELIXIR's future support of advanced biological applications and personalised medicine. By way of a series of meetings, the Community identified seven key areas for its future activities, reflecting both future needs and previous and current activities within ELIXIR Platforms and Communities. These are: overcoming barriers to the wider uptake of systems biology; linking new and existing data to systems biology models; interoperability of systems biology resources; further development and embedding of systems medicine; provisioning of modelling as a service; building and coordinating capacity building and training resources; and supporting industrial embedding of systems biology. A set of objectives for the Community has been identified under four main headline areas: Standardisation and Interoperability, Technology, Capacity Building and Training, and Industrial Embedding. These are grouped into short-term (3-year), mid-term (6-year) and long-term (10-year) objectives.
|
|
| 34. |
- Nilsson, Agneta, 1968, et al.
(författare)
-
Assessing the effects of introducing a new software development process: a methodological description
- 2015
-
Ingår i: International Journal on Software Tools for Technology Transfer. - : Springer Science and Business Media LLC. - 1433-2779 .- 1433-2787. ; 17, s. 1-16
-
Tidskriftsartikel (refereegranskat)abstract
- © 2013, Springer-Verlag Berlin Heidelberg. In this article, we report from a 22-months long action research study in which we evaluate the usefulness of a set of software development tools in an industrial setting, a small software company. We focus on how developers in the industry use and adopt these tools, what expectations they have on them, how the tools can be improved, and how the adoption process itself can be improved. We describe these change processes from a methodological perspective, how we monitored the processes, how we reviewed the outcomes, and the strategies that we applied. We show how the processes evolved, intermediate results, and the steps that were taken along the way based on the outcomes. We believe that the described study may inspire other tool-developers and/or researchers to organize similar studies to further our understanding of the complex processes involved in the adoption of software development tools in industry.
|
|
| 35. |
|
|
| 36. |
- Schoen, Michael, et al.
(författare)
-
Definition and clinical variability of SHANK3-related Phelan-McDermid syndrome
- 2023
-
Ingår i: European Journal of Medical Genetics. - : ELSEVIER. - 1769-7212 .- 1878-0849. ; 66:7
-
Tidskriftsartikel (refereegranskat)abstract
- Phelan-McDermid syndrome (PMS) is an infrequently described syndrome that presents with a disturbed development, neurological and psychiatric characteristics, and sometimes other comorbidities. As part of the development of European medical guidelines we studied the definition, phenotype, genotype-phenotype characteristics, and natural history of the syndrome. The number of confirmed diagnoses of PMS in different European countries was also assessed and it could be concluded that PMS is underdiagnosed. The incidence of PMS in European countries is estimated to be at least 1 in 30,000. Next generation sequencing, including analysis of copy number variations, as first tier in diagnostics of individuals with intellectual disability will likely yield a larger number of individuals with PMS than presently known. A definition of PMS by its phenotype is at the present not possible, and therefore PMS-SHANK3 related is defined by the presence of SHANK3 haploinsufficiency, either by a deletion involving region 22q13.2-33 or a pathogenic/likely pathogenic variant in SHANK3. In summarizing the phenotype, we subdivided it into that of individuals with a 22q13 deletion and that of those with a pathogenic/likely pathogenic SHANK3 variant. The phenotype of individuals with PMS is variable, depending in part on the deletion size or whether only a variant of SHANK3 is present. The core phenotype in the domains development, neurology, and senses are similar in those with deletions and SHANK3 variants, but individuals with a SHANK3 variant more often are reported to have behavioural disorders and less often urogenital malformations and lymphedema. The behavioural disorders may, however, be a less outstanding feature in individuals with deletions accompanied by more severe intellectual disability. Data available on the natural history are limited. Results of clinical trials using IGF-1, intranasal insulin, and oxytocin are available, other trials are in progress. The present guidelines for PMS aim at offering tools to caregivers and families to provide optimal care to individuals with PMS.
|
|
| 37. |
- Sigurlásdóttir, Sara, et al.
(författare)
-
Deletion of D-Lactate Dehydrogenase A in Neisseria meningitidis Promotes Biofilm Formation Through Increased Autolysis and Extracellular DNA Release
- 2019
-
Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 10
-
Tidskriftsartikel (refereegranskat)abstract
- Neisseria meningitidis is a Gram-negative bacterium that asymptomatically colonizes the human nasopharyngeal mucosa. Pilus-mediated initial adherence of N. meningitidis to the epithelial mucosa is followed by the formation of three-dimensional aggregates, called microcolonies. Dispersal from microcolonies contributes to the transmission of N. meningitidis across the epithelial mucosa. We have recently discovered that environmental concentrations of host cell-derived lactate influences N. meningitidis microcolony dispersal. Here, we examined the ability of N. meningitidis mutants deficient in lactate metabolism to form biofilms. A lactate dehydrogenease A (idhA) mutant had an increased level of biofilm formation. Deletion of IdhA increased the N. meningitidis cell surface hydrophobicity and aggregation. In this study, we used FAM20, which belongs to clonal complex ST-11 that forms biofilms independently of extracellular DNA (eDNA). However, treatment with DNase I abolished the increased biofilm formation and aggregation of the ldhA-delicient mutant, suggesting a critical role for eDNA. Compared to wild-type, the IdhA-deficient mutant exhibited an increased autolytic rate, with significant increases in the eDNA concentrations in the culture supernatants and in biofilms. Within the IdhA mutant biofilm, the transcription levels of the capsule, pilus, and bacterial lysis genes were downregulated, while norB, which is associated with anaerobic respiration, was upregulated. These findings suggest that the absence of IdhA in N. meningitidis promotes biofilm formation and aggregation through autolysis-mediated DNA release.
|
|
| 38. |
|
|
| 39. |
|
|
