| 1. |
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| 2. |
- Faatz, B., et al.
(författare)
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Simultaneous operation of two soft x-ray free-electron lasers driven by one linear accelerator
- 2016
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Ingår i: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 18
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Tidskriftsartikel (refereegranskat)abstract
- Extreme-ultraviolet to x-ray free-electron lasers (FELs) in operation for scientific applications are up to now single-user facilities. While most FELs generate around 100 photon pulses per second, FLASH at DESY can deliver almost two orders of magnitude more pulses in this time span due to its superconducting accelerator technology. This makes the facility a prime candidate to realize the next step in FELs-dividing the electron pulse trains into several FEL lines and delivering photon pulses to several users at the same time. Hence, FLASH has been extended with a second undulator line and self-amplified spontaneous emission (SASE) is demonstrated in both FELs simultaneously. FLASH can now deliver MHz pulse trains to two user experiments in parallel with individually selected photon beam characteristics. First results of the capabilities of this extension are shown with emphasis on independent variation of wavelength, repetition rate, and photon pulse length.
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| 3. |
- Vogel, G. F., et al.
(författare)
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Genotypic and phenotypic spectrum of infantile liver failure due to pathogenic TRMU variants
- 2023
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Ingår i: Genetics in Medicine. - : Elsevier BV. - 1098-3600. ; 25:6
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: This study aimed to define the genotypic and phenotypic spectrum of reversible acute liver failure (ALF) of infancy resulting from biallelic pathogenic TRMU variants and determine the role of cysteine supplementation in its treatment. Methods: Individuals with biallelic (likely) pathogenic variants in TRMU were studied within an international retrospective collection of de-identified patient data. Results: In 62 individuals, including 30 previously unreported cases, we described 47 (likely) pathogenic TRMU variants, of which 17 were novel, and 1 intragenic deletion. Of these 62 individuals, 42 were alive at a median age of 6.8 (0.6-22) years after a median follow-up of 3.6 (0.1-22) years. The most frequent finding, occurring in all but 2 individuals, was liver involvement. ALF occurred only in the first year of life and was reported in 43 of 62 individuals; 11 of whom received liver transplantation. Loss-of-function TRMU variants were associated with poor survival. Supplementation with at least 1 cysteine source, typically N-acetylcysteine, improved survival significantly. Neurodevelopmental delay was observed in 11 individuals and persisted in 4 of the survivors, but we were unable to determine whether this was a primary or a secondary consequence of TRMU deficiency. Conclusion: In most patients, TRMU-associated ALF was a transient, reversible disease and cysteine supplementation improved survival.
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| 4. |
- Maas, R. R., et al.
(författare)
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Progressive deafness–dystonia due to SERAC1 mutations: A study of 67 cases
- 2017
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Ingår i: Annals of Neurology. - : Wiley. - 0364-5134 .- 1531-8249. ; 82:6, s. 1004-1015
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Tidskriftsartikel (refereegranskat)abstract
- Objective: 3-Methylglutaconic aciduria, dystonia–deafness, hepatopathy, encephalopathy, Leigh-like syndrome (MEGDHEL) syndrome is caused by biallelic variants in SERAC1. Methods: This multicenter study addressed the course of disease for each organ system. Metabolic, neuroradiological, and genetic findings are reported. Results: Sixty-seven individuals (39 previously unreported) from 59 families were included (age range = 5 days–33.4 years, median age = 9 years). A total of 41 different SERAC1 variants were identified, including 20 that have not been reported before. With the exception of 2 families with a milder phenotype, all affected individuals showed a strikingly homogeneous phenotype and time course. Severe, reversible neonatal liver dysfunction and hypoglycemia were seen in >40% of all cases. Starting at a median age of 6 months, muscular hypotonia (91%) was seen, followed by progressive spasticity (82%, median onset = 15 months) and dystonia (82%, 18 months). The majority of affected individuals never learned to walk (68%). Seventy-nine percent suffered hearing loss, 58% never learned to speak, and nearly all had significant intellectual disability (88%). Magnetic resonance imaging features were accordingly homogenous, with bilateral basal ganglia involvement (98%); the characteristic “putaminal eye” was seen in 53%. The urinary marker 3-methylglutaconic aciduria was present in virtually all patients (98%). Supportive treatment focused on spasticity and drooling, and was effective in the individuals treated; hearing aids or cochlear implants did not improve communication skills. Interpretation: MEGDHEL syndrome is a progressive deafness–dystonia syndrome with frequent and reversible neonatal liver involvement and a strikingly homogenous course of disease. Ann Neurol 2017;82:1004–1015. © 2017 American Neurological Association
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| 5. |
- Hikmat, O., et al.
(författare)
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Expanding the phenotypic spectrum of BCS1L-related mitochondrial disease
- 2021
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Ingår i: Annals of Clinical and Translational Neurology. - : Wiley. - 2328-9503. ; 8:11, s. 2155-2165
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Tidskriftsartikel (refereegranskat)abstract
- Objective: To delineate the full phenotypic spectrum of BCS1L-related disease, provide better understanding of the genotype-phenotype correlations and identify reliable prognostic disease markers. Methods: We performed a retrospective multinational cohort study of previously unpublished patients followed in 15 centres from 10 countries. Patients with confirmed biallelic pathogenic BCS1L variants were considered eligible. Clinical, laboratory, neuroimaging and genetic data were analysed. Patients were stratified into different groups based on the age of disease onset, whether homozygous or compound heterozygous for the c.232A>G (p.Ser78Gly) variant, and those with other pathogenic BCS1L variants. Results: Thirty-three patients were included. We found that growth failure, lactic acidosis, tubulopathy, hepatopathy and early death were more frequent in those with disease onset within the first month of life. In those with onset after 1 month, neurological features including movement disorders and seizures were more frequent. Novel phenotypes, particularly involving movement disorder, were identified in this group. The presence of the c.232A>G (p.Ser78Gly) variant was associated with significantly worse survival and exclusively found in those with disease onset within the first month of life, whilst other pathogenic BCS1L variants were more frequent in those with later symptom onset. Interpretation: The phenotypic spectrum of BCS1L-related disease comprises a continuum of clinical features rather than a set of separate syndromic clinical identities. Age of onset defines BCS1L-related disease clinically and early presentation is associated with poor prognosis. Genotype correlates with phenotype in the presence of the c.232A>G (p.Ser78Gly) variant.
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| 6. |
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| 7. |
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| 8. |
- Wortmann, Saskia B, et al.
(författare)
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Eyes on MEGDEL: Distinctive Basal Ganglia Involvement in Dystonia Deafness Syndrome.
- 2015
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Ingår i: Neuropediatrics. - : Georg Thieme Verlag KG. - 1439-1899 .- 0174-304X. ; 46:2, s. 098-103
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Tidskriftsartikel (refereegranskat)abstract
- Pediatric movement disorders are still a diagnostic challenge, as many patients remain without a (genetic) diagnosis. Magnetic resonance imaging (MRI) pattern recognition can lead to the diagnosis. MEGDEL syndrome (3-MethylGlutaconic aciduria, Deafness, Encephalopathy, Leigh-like syndrome MIM #614739) is a clinically and biochemically highly distinctive dystonia deafness syndrome accompanied by 3-methylglutaconic aciduria, severe developmental delay, and progressive spasticity. Mutations are found in SERAC1, encoding a phosphatidylglycerol remodeling enzyme essential for both mitochondrial function and intracellular cholesterol trafficking. Based on the homogenous phenotype, we hypothesized an accordingly characteristic MRI pattern. A total of 43 complete MRI studies of 30 patients were systematically reevaluated. All patients presented a distinctive brain MRI pattern with five characteristic disease stages affecting the basal ganglia, especially the putamen. In stage 1, T2 signal changes of the pallidum are present. In stage 2, swelling of the putamen and caudate nucleus is seen. The dorsal putamen contains an "eye" that shows no signal alteration and (thus) seems to be spared during this stage of the disease. It later increases, reflecting progressive putaminal involvement. This "eye" was found in all patients with MEGDEL syndrome during a specific age range, and has not been reported in other disorders, making it pathognomonic for MEDGEL and allowing diagnosis based on MRI findings.
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| 9. |
- Bucchiarone, A., et al.
(författare)
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What Is the Future of Modeling?
- 2021
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Ingår i: IEEE Software. - : IEEE Computer Society. - 0740-7459 .- 1937-4194. ; 38:2, s. 119-127
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Tidskriftsartikel (refereegranskat)abstract
- Modeling languages and frameworks have been the key technology for advancing model-driven engineering (MDE) methods and tools. Many industrial and research tools have been realized and are used across many domains. Hence, we think it is the right time to define what should be the future of modeling technologies, especially the requirements for the next generation of modeling frameworks and languages.
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| 10. |
- Del Dotto, V., et al.
(författare)
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SSBP1 mutations cause mtDNA depletion underlying a complex optic atrophy disorder
- 2020
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Ingår i: Journal of Clinical Investigation. - : American Society for Clinical Investigation. - 0021-9738 .- 1558-8238. ; 130:1, s. 108-125
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Tidskriftsartikel (refereegranskat)abstract
- Inherited optic neuropathies include complex phenotypes, mostly driven by mitochondrial dysfunction. We report an optic atrophy spectrum disorder, including retinal macular dystrophy and kidney insufficiency leading to transplantation, associated with mitochondrial DNA (mtDNA) depletion without accumulation of multiple deletions. By whole-exome sequencing, we identified mutations affecting the mitochondrial single-strand binding protein (SSBP1) in 4 families with dominant and 1 with recessive inheritance. We show that SSBP1 mutations in patient-derived fibroblasts variably affect the amount of SSBP1 protein and alter multimer formation, but not the binding to ssDNA. SSBP1 mutations impaired mtDNA, nucleoids, and 7S-DNA amounts as well as mtDNA replication, affecting replisome machinery. The variable mtDNA depletion in cells was reflected in severity of mitochondrial dysfunction, including respiratory efficiency, OXPHOS subunits, and complex amount and assembly. mtDNA depletion and cytochrome c oxidase-negative cells were found ex vivo in biopsies of affected tissues, such as kidney and skeletal muscle. Reduced efficiency of mtDNA replication was also reproduced in vitro, confirming the pathogenic mechanism. Furthermore, ssbp1 suppression in zebrafish induced signs of nephropathy and reduced optic nerve size, the latter phenotype complemented by WT mRNA but not by SSBP1 mutant transcripts. This previously unrecognized disease of mtDNA maintenance implicates SSBP1 mutations as a cause of human pathology.
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| 11. |
- Seidel, M., et al.
(författare)
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Multi-pass Cell Based Nonlinear Pulse Compression of Yb : YAG Pump-Probe Lasers at FLASH
- 2023
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Ingår i: X-Ray Free-Electron Lasers : Advances in Source Development and Instrumentation VI - Advances in Source Development and Instrumentation VI. - 1996-756X .- 0277-786X. - 9781510662827 ; 12581
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Konferensbidrag (refereegranskat)abstract
- The majority of user experiments at the high repetition-rate free electron laser (FEL) facility FLASH are of pump-probe type, combining the extreme ultraviolet (XUV) or soft x-ray radiation from the FEL with ultrashort pulses generated by optical lasers. In this contribution, we demonstrate the advantages of using high-power Yb:YAG lasers with subsequent nonlinear pulse compression stages based on multi-pass cells (MPC). The approach enables the combination of hundreds of kHz to MHz repetition-rates, hundreds of watts of average powers and excellent intensity stabilities. We present the characteristics of the MPC-based pump-probe laser at the FLASH plane-grating beamlines. Furthermore, we report pulse compression to 8.2 fs pulse duration and the seeding of an optical parametric amplifier generating mid-IR radiation tunable from 1.4 µm to 16 µm.
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| 12. |
- Bradley, Patrick, et al.
(författare)
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Taking stock: A multistakeholder perspective on improving the delivery of care and the development of treatments for Alzheimer's disease.
- 2015
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Ingår i: Alzheimer's & dementia : the journal of the Alzheimer's Association. - : Wiley. - 1552-5279. ; 11:4, s. 455-461
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Tidskriftsartikel (refereegranskat)abstract
- Health-care stakeholders increasingly recognize that the scientific and economic challenges associated with Alzheimer's disease (AD) are simply too great for individual stakeholder groups to address solely from within their own silos. In the necessary spirit of collaboration, we present in this perspective a set of multicountry multistakeholder recommendations to improve the organization of existing AD and dementia care and the development of new treatments. In brief, the five recommendations are (1) health-care systems must make choices regarding the patient populations to be diagnosed and treated, (2) health-care systems should use an evidence-based standard of care, (3) increased collaboration between public and private institutions is needed to enhance research, (4) reimbursement end points need to be agreed on and validated, and (5) innovative business models should be used to spur the introduction of new medicines.
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| 13. |
- Wylensek, David, et al.
(författare)
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A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity
- 2020
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Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Our knowledge about the gut microbiota of pigs is still scarce, despite the importance of these animals for biomedical research and agriculture. Here, we present a collection of cultured bacteria from the pig gut, including 110 species across 40 families and nine phyla. We provide taxonomic descriptions for 22 novel species and 16 genera. Meta-analysis of 16S rRNA amplicon sequence data and metagenome-assembled genomes reveal prevalent and pig-specific species within Lactobacillus, Streptococcus, Clostridium, Desulfovibrio, Enterococcus, Fusobacterium, and several new genera described in this study. Potentially interesting functions discovered in these organisms include a fucosyltransferase encoded in the genome of the novel species Clostridium porci, and prevalent gene clusters for biosynthesis of sactipeptide-like peptides. Many strains deconjugate primary bile acids in in vitro assays, and a Clostridium scindens strain produces secondary bile acids via dehydroxylation. In addition, cells of the novel species Bullifex porci are coccoidal or spherical under the culture conditions tested, in contrast with the usual helical shape of other members of the family Spirochaetaceae. The strain collection, called 'Pig intestinal bacterial collection' (PiBAC), is publicly available at www.dsmz.de/pibac and opens new avenues for functional studies of the pig gut microbiota. The authors present a public collection of 117 bacterial isolates from the pig gut, including the description of 38 novel taxa. Interesting functions discovered in these organisms include a new fucosyltransferease and sactipeptide-like molecules encoded by biosynthetic gene clusters.
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| 14. |
- Bergström, Fredrik, et al.
(författare)
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Dimers of dipyrrometheneboron difluoride (BODIPY) with light spectroscopic applications in chemistry and biology.
- 2002
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Ingår i: Journal of the American Chemical Society. - 0002-7863 .- 1520-5126. ; 124:2, s. 196-204
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Tidskriftsartikel (refereegranskat)abstract
- A ground-state dimer (denoted D(I)) exhibiting a strong absorption maximum at 477 nm (epsilon = 97 000 M(-1)cm(-1)) can form between adjacent BODIPY groups attached to mutant forms of the protein, plasminogen activator inhibitor type 1 (PAI-1). No fluorescence from excited D(I) was detected. A locally high concentration of BODIPY groups was also achieved by doping lipid phases (micelles, vesicles) with BODIPY-labeled lipids. In addition to an absorption band located at about 480 nm, a new weak absorption band is also observed at ca. 570 nm. Both bands are ascribed to the formation of BODIPY dimers of different conformation (D(I) and D(II)). Contrary to D(I) in PAI-1, the D(II) aggregates absorbing at 570 nm are emitting light observed as a broad band centered at about 630 nm. The integrated absorption band of D(I) is about twice that of the monomer, which is compatible with exciton coupling within a dimer. The Förster radius of electronic energy transfer between a BODIPY excited monomer and the ground-state dimer (D(I)()) is 57 +/- 2 A. A simple model of exciton coupling suggests that in D(I) two BODIPY groups are stacked on top of each other in a sandwich-like configuration with parallel electronic transition dipoles. For D(II) the model suggests that the S(0) --> S(1) transition dipoles are colinear. An explanation for the previously reported (J. Am. Chem. Soc. 1994, 116, 7801) exceptional light spectroscopic properties of BODIPY is also presented. These are ascribed to the extraordinary electric properties of the BODIPY chromophore. First, changes of the permanent electric dipole moment (Delta(mu) approximately -0.05 D) and polarizability (-26 x 10(-40) C m(2) V(-1)) between the ground and the first excited states are small. Second, the S(0) <--> S(1) electronic transition dipole moments are perpendicular to Delta(mu).
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| 15. |
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| 16. |
- Casalaro, G. L., et al.
(författare)
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Model-driven engineering for mobile robotic systems: a systematic mapping study
- 2022
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Ingår i: Software and Systems Modeling. - : Springer Science and Business Media LLC. - 1619-1366 .- 1619-1374. ; 21, s. 19-49
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Tidskriftsartikel (refereegranskat)abstract
- Mobile robots operate in various environments (e.g. aquatic, aerial, or terrestrial), they come in many diverse shapes and they are increasingly becoming parts of our lives. The successful engineering of mobile robotics systems demands the interdisciplinary collaboration of experts from different domains, such as mechanical and electrical engineering, artificial intelligence, and systems engineering. Research and industry have tried to tackle this heterogeneity by proposing a multitude of model-driven solutions to engineer the software of mobile robotics systems. However, there is no systematic study of the state of the art in model-driven engineering (MDE) for mobile robotics systems that could guide research or practitioners in finding model-driven solutions and tools to efficiently engineer mobile robotics systems. The paper is contributing to this direction by providing a map of software engineering research in MDE that investigates (1) which types of robots are supported by existing MDE approaches, (2) the types and characteristics of MRSs that are engineered using MDE approaches, (3) a description of how MDE approaches support the engineering of MRSs, (4) how existing MDE approaches are validated, and (5) how tools support existing MDE approaches. We also provide a replication package to assess, extend, and/or replicate the study. The results of this work and the highlighted challenges can guide researchers and practitioners from robotics and software engineering through the research landscape.
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| 17. |
- Chan, P., et al.
(författare)
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Multicentennial record of Labrador Sea primary productivity and sea-ice variability archived in coralline algal barium
- 2017
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Accelerated warming and melting of Arctic sea-ice has been associated with significant increases in phytoplankton productivity in recent years. Here, utilizing a multiproxy approach, we reconstruct an annually resolved record of Labrador Sea productivity related to sea-ice variability in Labrador, Canada that extends well into the Little Ice Age (LIA; 1646 AD). Barium-to-calcium ratios (Ba/Ca) and carbon isotopes (delta C-13) measured in long-lived coralline algae demonstrate significant correlations to both observational and proxy records of sea-ice variability, and show persistent patterns of co-variability broadly consistent with the timing and phasing of the Atlantic Multidecadal Oscillation (AMO). Results indicate reduced productivity in the Subarctic Northwest Atlantic associated with AMO cool phases during the LIA, followed by a step-wise increase from 1910 to present levels-unprecedented in the last 363 years. Increasing phytoplankton productivity is expected to fundamentally alter marine ecosystems as warming and freshening is projected to intensify over the coming century.
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| 18. |
- Ciccozzi, Federico, 1983-, et al.
(författare)
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Message from the RoSE 2018 Co-Organizers
- 2018
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Ingår i: Proceedings - International Conference on Software Engineering, Volume Part F137815. - 9781450357609
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 19. |
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| 20. |
- Jolak, Rodi, et al.
(författare)
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Design thinking and creativity of colocated versus globally distributed software developers
- 2021
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Ingår i: Journal of Software-Evolution and Process. - : Wiley. - 2047-7473 .- 2047-7481.
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Tidskriftsartikel (refereegranskat)abstract
- Designing software is an activity in which software developers think and make design decisions that shape the structure and behavior of software products. Designing software is one of the least understood software engineering activities. In a collaborative design setting, various types of distances can lead to challenges and effects that potentially affect how software is designed. To contribute to a better understanding of collaborative software design, we investigate how communication gaps caused by social and geographic distances affect its design thinking and the creativity of its discussions. To this end, we conducted a multiple-case study exploring the design thinking and creativity of colocated and distributed software developers in a collaborative design setting. Compared with colocated developers, distributed developers spend less time on exploring the problem space, which could be related to different sociotechnical challenges, such as lack of awareness and common understanding. Distributed development does not seem to affect the creativity of their activities. Developers engaging in collaborative design need to be aware that problem space exploration is reduced in a distributed setting. Unless distributed teams take compensatory measures, this could adversely affect the development. Regarding the effect distance has on creativity, our results are inconclusive and further studies are needed.
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| 21. |
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| 22. |
- Jolak, Rodi, et al.
(författare)
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Software engineering whispers: The effect of textual vs. graphical software design descriptions on software design communication
- 2020
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Ingår i: Empirical Software Engineering. - : Springer Science and Business Media LLC. - 1382-3256 .- 1573-7616. ; 25, s. 4427-4471
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Tidskriftsartikel (refereegranskat)abstract
- Context Software engineering is a social and collaborative activity. Communicating and sharing knowledge between software developers requires much effort. Hence, the quality of communication plays an important role in influencing project success. To better understand the effect of communication on project success, more in-depth empirical studies investigating this phenomenon are needed. Objective We investigate the effect of using a graphical versus textual design description on co-located software design communication. Method Therefore, we conducted a family of experiments involving a mix of 240 software engineering students from four universities. We examined how different design representations (i.e., graphical vs. textual) affect the ability toExplain,Understand,Recall, andActively Communicateknowledge. Results We found that the graphical design description is better than the textual in promotingActive Discussionbetween developers and improving theRecallof design details. Furthermore, compared to its unaltered version, a well-organized and motivated textual design description-that is used for the same amount of time-enhances the recall of design details and increases the amount of active discussions at the cost of reducing the perceived quality of explaining.
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| 23. |
- Kennedy, Vanessa E., et al.
(författare)
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Mast cell leukemia : clinical and molecular features and survival outcomes of patients in the ECNM Registry
- 2023
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Ingår i: Blood Advances. - : American Society of Hematology. - 2473-9529 .- 2473-9537. ; 7:9, s. 1713-1724
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Tidskriftsartikel (refereegranskat)abstract
- Mast cell leukemia (MCL) is a rare subtype of systemic mastocytosis defined by >= 20% mast cells (MC) on a bone marrow aspirate. We evaluated 92 patients with MCL from the European Competence Network on Mastocytosis registry. Thirty-one (34%) patients had a diagnosis of MCL with an associated hematologic neoplasm (MCL-AHN). Chronic MCL (lack of C-findings) comprised 14% of patients, and only 4.5% had "leukemic MCL" (>= 10% circulating MCs). KIT D816V was found in 62/85 (73%) evaluable patients; 9 (11%) individuals exhibited alternative KIT mutations, and no KIT variants were detected in 14 (17%) subjects. Ten evaluable patients (17%) had an abnormal karyotype and the poor-risk SRSF2, ASXL1, and RUNX1 (S/A/R) mutations were identified in 16/36 (44%) patients who underwent next-generation sequencing. Midostaurin was the most common therapy administered to 65% of patients and 45% as first-line therapy. The median overall survival (OS) was 1.6 years. In multivariate analysis (S/A/R mutations excluded owing to low event rates), a diagnosis of MCL-AHN (hazard ratio [HR], 4.7; 95% confidence interval [CI], 1.7-13.0; P = .001) and abnormal karyotype (HR, 5.6; 95% CI, 1.4-13.3; P = .02) were associated with inferior OS; KIT D816V positivity (HR, 0.33; 95% CI, 0.11-0.98; P = .04) and midostaurin treatment (HR, 0.32; 95% CI, 0.08-0.72; P = .008) were associated with superior OS. These data provide the most comprehensive snapshot of the clinicopathologic, molecular, and treatment landscape of MCL to date, and should help further inform subtyping and prognostication of MCL.
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