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- 2019
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Tidskriftsartikel (refereegranskat)
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- Nijkamp, J. F., et al.
(författare)
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De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology
- 2012
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Ingår i: Microbial Cell Factories. - : Springer Science and Business Media LLC. - 1475-2859. ; 11, s. Article Number: 36-
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Tidskriftsartikel (refereegranskat)abstract
- Saccharomyces cerevisiae CEN.PK 113-7D is widely used for metabolic engineering and systems biology research in industry and academia. We sequenced, assembled, annotated and analyzed its genome. Single-nucleotide variations (SNV), insertions/deletions (indels) and differences in genome organization compared to the reference strain S. cerevisiae S288C were analyzed. In addition to a few large deletions and duplications, nearly 3000 indels were identified in the CEN.PK113-7D genome relative to S288C. These differences were overrepresented in genes whose functions are related to transcriptional regulation and chromatin remodelling. Some of these variations were caused by unstable tandem repeats, suggesting an innate evolvability of the corresponding genes. Besides a previously characterized mutation in adenylate cyclase, the CEN. PK113-7D genome sequence revealed a significant enrichment of non-synonymous mutations in genes encoding for components of the cAMP signalling pathway. Some phenotypic characteristics of the CEN. PK113-7D strains were explained by the presence of additional specific metabolic genes relative to S288C. In particular, the presence of the BIO1 and BIO6 genes correlated with a biotin prototrophy of CEN. PK113-7D. Furthermore, the copy number, chromosomal location and sequences of the MAL loci were resolved. The assembled sequence reveals that CEN. PK113-7D has a mosaic genome that combines characteristics of laboratory strains and wild-industrial strains.
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- van Bergen, Jan E. A. M., et al.
(författare)
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Where to go to in chlamydia control? : From infection control towards infectious disease control
- 2021
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Ingår i: Sexually Transmitted Infections. - : BMJ Publishing Group Ltd. - 1368-4973 .- 1472-3263. ; 97:7, s. 501-506
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Forskningsöversikt (refereegranskat)abstract
- Objectives: The clinical and public health relevance of widespread case finding by testing for asymptomatic chlamydia infections is under debate. We wanted to explore future directions for chlamydia control and generate insights that might guide for evidence-based strategies. In particular, we wanted to know the extent to which we should pursue testing for asymptomatic infections at both genital and extragenital sites.Methods: We synthesised findings from published literature and from discussions among national and international chlamydia experts during an invitational workshop. We described changing perceptions in chlamydia control to inform the development of recommendations for future avenues for chlamydia control in the Netherlands.Results: Despite implementing a range of interventions to control chlamydia, there is no practice-based evidence that population prevalence can be reduced by screening programmes or widespread opportunistic testing. There is limited evidence about the beneficial effect of testing on pelvic inflammatory disease prevention. The risk of tubal factor infertility resulting from chlamydia infection is low and evidence on the preventable fraction remains uncertain. Overdiagnosis and overtreatment with antibiotics for self-limiting and non-viable infections have contributed to antimicrobial resistance in other pathogens and may affect oral, anal and genital microbiota. These changing insights could affect the outcome of previous cost-effectiveness analysis.Conclusion: The balance between benefits and harms of widespread testing to detect asymptomatic chlamydia infections is changing. The opinion of our expert group deviates from the existing paradigm of 'test and treat' and suggests that future strategies should reduce, rather than expand, the role of widespread testing for asymptomatic chlamydia infections.
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- Campbell, M, et al.
(författare)
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Detection of single electrons by means of a Micromegas-covered Medipix2 pixel CMOS readout circuit
- 2005
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 540:2-3, s. 295-304
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Tidskriftsartikel (refereegranskat)abstract
- A small drift chamber was read out by means of a MediPix2 readout chip as a direct anode. A Micromegas foil was placed above the chip, and electron multiplication occurred in the gap. With a He/isobutane 80/20 mixture, gas multiplication factors up to tens of thousands were achieved, resulting in an efficiency for detecting single electrons of better than 90%. We recorded many frames containing 2D images with tracks from cosmic muons. Along these tracks, electron clusters were observed, as well as δ-rays.
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- Ballabriga, Rafael, et al.
(författare)
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The Medipix3RX: a high resolution, zero dead-time pixel detector readout chip allowing spectroscopic imaging
- 2013
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Ingår i: Journal of Instrumentation. - 1748-0221. ; 8:2, s. C02016-
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Tidskriftsartikel (refereegranskat)abstract
- The Medipix3 chips have been designed to permit spectroscopic imaging in highly segmented hybrid pixel detectors. Spectral degradation due to charge sharing in the sensor has been addressed by means of an architecture in which adjacent pixels communicate in the analog and digital domains on an event-by-event basis to reconstruct the deposited charge in a neighbourhood prior to the assignation of the hit to a single pixel. The Medipix3RX chip architecture is presented. The first results for the characterization of the chip with 300 μm thick Si sensors are given. ~ 72e− r.m.s. noise and ~ 40e− r.m.s. of threshold dispersion after chip equalization have been measured in Single Pixel Mode of operation. The homogeneity of the image in Charge Summing mode is comparable to the Single Pixel Mode image. This demonstrates both modes are suitable for X-ray imaging applications.
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- Colas, P, et al.
(författare)
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The readout of a GEM or Micromegas-equipped TPC by means of the Medipix2 CMOS sensor as direct anode
- 2004
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - 0168-9002 .- 1872-9576. ; 535:1-2, s. 506-510
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Tidskriftsartikel (refereegranskat)abstract
- We have applied the Medipix2 pixel CMOS chip as direct anode readout for a TPC. For the gas amplification two options have been investigated: (i) a three-stage GEM system and (ii) a Micromegas mesh. The structure of the cloud of primary electrons, left after interactions of 55Fe quanta with the gas is visible with unprecedented precision. This proof-of-principle is an essential step in our project to realize a monolithic pixel sensor with integrated Micromegas, to be developed specially for the readout of TPCs, and applicable for drift chambers in general.
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- Tlustos, L, et al.
(författare)
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Imaging properties of the Medipix2 system exploiting single and dual enery thresholds
- 2006
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Ingår i: IEEE Transactions on Nuclear Science. - 0018-9499 .- 1558-1578. ; 53, s. 1323-1328
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Tidskriftsartikel (refereegranskat)abstract
- Low noise, high resolution and high dose efficiency are the common requirements for most X-ray imaging applications. Especially in medical applications the dose efficiency is a necessity for detector systems. We present the imaging performance of the Medipix2 readout chip bump bonded to a 300 mu m thick Si detector as a function of the detection threshold, a free parameter not available in conventional integrating imaging systems. Spatial resolution has been measured using the modulation transfer function (MTF) and it varies between 8.2 Ip/mm and 11.0 Ip/mm at 70%. An associated measurement of noise power spectrum (NPS) permits us to derive the detective quantum efficiency (DQE) which can be as a high as 25.5 % for a broadband incoming spectrum. The influence of charge diffusion in the sensor together with threshold variation in the readout chip is discussed. Although the Medipix2 system is used in photon counting mode with a single threshold in energy, the system is also capable of counting within a given energy window of down to ~1.4 keV. First measurements and images using this feature reveal capabilities that allow to identify fluorescence and other sources of disturbance.
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