| 1. |
- Barrios, C. A., et al.
(author)
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Reconfiguration of microring resonators by liquid adhesion
- 2008
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In: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 93:20
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Journal article (peer-reviewed)abstract
- We present a procedure to reconfigure microring resonators based on liquid surface adhesion. Droplets of organic solvents were deposited over Si3N4/SiO2 strip- and slot-waveguide ring resonators, and the transmission spectra were measured several hours after the evaporation of the droplets at room temperature. Our measurements show that the optical properties of the microrings are significantly modified by liquid adhered to the waveguides, persisting even 96 h after bulk evaporation. Liquid-solid interfacial forces slow down liquid evaporation at the nanoscale, enabling permanent photonic configurations. Rewriteability is achieved by removing the adhered liquid with heat.
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| 2. |
- Fernlund, Eva, et al.
(author)
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Hereditary hypertrophic cardiomyopathy in children and young adults—The value of reevaluating and expanding gene panel analyses
- 2020
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In: Genes. - : MDPI AG. - 2073-4425. ; 11:12
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Journal article (peer-reviewed)abstract
- Introduction: Sudden cardiac death (SCD) and early onset cardiomyopathy (CM) in the young will always lead to suspicion of an underlying genetic disorder. Incited by the rapid advances in genetic testing for disease we have revisited families, which previously tested “gene-negative” for familial predominantly pediatric CM, in hopes of finding a causative gene variant. Methods: 10 different families with non-syndromic pediatric CM or hypertrophic cardiomyopathy (HCM) with severe disease progression and/or heredity for HCM/CM related SCD with “gene-negative” results were included. The index patient underwent genetic testing with a recently updated gene panel for CM and SCD. In case of failure to detect a pathogenic variant in a relevant gene, the index patient and both parents underwent clinical (i.e., partial) exome sequencing (trio-exome) in order to catch pathogenic variants linked to the disease in genes that were not included in the CM panel. Results: The mean age at clinical presentation of the 10 index cases was 12.5 years (boys 13.4 years, n = 8; girls 9 years, n = 2) and the family history burden was 33 HCM/CM cases including 9 HCM-related SCD and one heart transplantation. In 5 (50%) families we identified a genetic variant classified as pathogenic or likely pathogenic, in accordance with the American College of Medical Genetics and Genomics (ACMG) criteria, in MYH7 (n = 2), RBM20, ALPK3, and PGM1, respectively, and genetic variants of unknown significance (VUS) segregating with the disease in an additional 3 (30%) families, in MYBPC3, ABCC9, and FLNC, respectively. Conclusion: Our results show the importance of renewed thorough clinical assessment and the necessity to challenge previous genetic test results with more comprehensive updated gene panels or exome sequencing if the initial test failed to identify a causative gene for early onset CM or SCD in children. In pediatric cardiomyopathy cases when the gene panel still fails to detect a causative variant, a trio exome sequencing strategy might resolve some unexplained cases, especially if a multisystemic condition is clinically missed.
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| 3. |
- Fernlund, Eva, et al.
(author)
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The congenital disorder of glycosylation in PGM1 (PGM1-CDG) can cause severe cardiomyopathy and unexpected sudden cardiac death in childhood
- 2019
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In: Forensic Science International. - : ELSEVIER IRELAND LTD. - 1872-4973 .- 1878-0326. ; 43
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Journal article (peer-reviewed)abstract
- Introduction: Sudden cardiac death (SCD) in the young is rare and should always lead to suspicion of a genetic cardiac disorder. We describe a family, in which the proband was a girl deceased by sudden cardiac death in the playground at thirteen years of age. The index-patient had short stature, cleft palate but no previous cardiac symptoms. We found an uncommon cause of cardiomyopathy, due to a congenital disorder of glycosylation (CDG), previously described to cause a variable range of usually mild symptoms, and not previously found to cause SCD as the first symptom of the condition. Methods: The index patient underwent postmortem genetic testing/molecular autopsy for genes known to cause SCD, without a detection of causative agent, why two siblings of similar phenotype as the deceased sister underwent clinical-exome genetic sequencing (next generation sequencing). All first-degree relatives underwent clinical examination including cardiac ultrasound, Holzer-ECG, exercise stress test and biochemistry panel. Results: A genetic variant in the gene for phosphoglucomutase 1 (PGM1) was identified in the index patient and her two brothers, all were found to be homozygous for the genetic variant (G230E) NM_002633.2:c.689 G amp;gt; A in PGM1. This variant has been linked to a congenital disorder of glycosylation (PGM1-CDG), explaining the clinical picture of short stature, cleft palate, liver engagement and cardiomyopathy. During follow-up one of the brothers died unexpectedly after physical exertion during daily life at the age of twelve years. The other brother fainted during similar circumstances at the age of thirteen years. Both parents and three other siblings were found to be heterozygous gene carriers without risk for the disease. Conclusion: Our findings suggest that there is a need of multidisciplinary discussion and genetic testing after unexpected cardiac death in the young. We have to be more flexible in our evaluation of diseases and to consider even uncommon diseases including rare recessive inherited disorders. Our findings also suggest that the autosomal recessive PGM1-CDG might be highly associated with life-threatening cardiomyopathy with arrhythmia or sudden cardiac death as the first symptom presenting from childhood and adolescence.
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| 4. |
- Herrera, Fernando, 1975-, et al.
(author)
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Combining Analytical and Simulation-based Design Space Exploration for Time-Critical Systems
- 2013
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In: Forum on Specification & Design Languages (FDL), 2013. - : IEEE conference proceedings. - 9782953050486 ; , s. 6646657-
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Conference paper (peer-reviewed)abstract
- In the context of the design on time-critical systems, analytical models with worst case workloads are used to identify safe solutions that guarantee hard timing constraints. However, the focus on the worst case often leads to unnecessarily pessimistic and inefficient solutions, in particular for mixed-critical systems. To overcome the situation, the paper proposes a novel design flow integrating analytical and simulation-based design space exploration (DSE). This combined approach is capable to find more efficient design solutions, without sacrificing timing guarantees. For it, a first analytical DSE phase obtains a set of solutions compliant with the critical time constraints. Search of the optimum solution is done among this set, but it is delegated to a second simulation-based search, for fine tuning and average-case optimisation. The potential of our approach is illustrated by a proof-of-concept implementation of the proposed DSE flow and an accompanying DSE example.
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| 5. |
- Sadigh, B., et al.
(author)
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Calculation of excess free energies of precipitates via direct thermodynamic integration across phase boundaries
- 2012
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In: Physical Review B - Condensed Matter and Materials Physics. - 2469-9950 .- 2469-9969. ; 86:13
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Journal article (peer-reviewed)abstract
- We describe a technique for constraining macroscopic fluctuations in thermodynamic variables well-suited for Monte Carlo (MC) simulations of multiphase equilibria. In particular for multicomponent systems this amounts to a statistical ensemble that implements constraints on both the average composition as well as its fluctuations. The variance-constrained semi-grand-canonical (VC-SGC) ensemble allows for MC simulations, in which single-phase systems can be reversibly switched into multiphase equilibria allowing the calculation of excess free energies of precipitates of complex shapes by thermodynamic integration. The basic features as well as the scaling and convergence properties of this technique are demonstrated by an application to an Ising model. Finally, the VC-SGC MC simulation technique is used to calculate alpha/alpha' interface free energies in Fe-Cr alloys as a function of orientation and temperature taking into account configurational, vibrational, and structural degrees of freedom.
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| 6. |
- Sadigh, Babak
(author)
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Electronic and dynamical aspects of the stability of metallic structures
- 1997
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Doctoral thesis (other academic/artistic)abstract
- The structural phase stability of several transition metalsystems have been studied, using first-principles electronicstructure calculations. Frozen phonon techniques have been usedto study the details of structural phase transformations e.g.the transition paths, while linear response calculations of theharmonic phonon frequencies have been performed in order tostudy the vibrational properties and dynamical stability ofsystems. Thermodynamical properties of liquid copper have beenstudied using molecular dynamics simulations withsemi-empirical interatomic potentials. Simulation techniqueshave further been used to study the structure and dynamics of amodel quasicrystal.The main results in the thesis are: A variational higher order interpolation scheme forBrillouin zone integration of the band structure energy issuggested. The constant pressure heat capacity, Cp,for liquid copper is essentially independent of thetemperature, while the constant volume heat capacityCv,decreases with temperature and extrapolates toapproximately 2kB/atom well above the meltingtemperature. An approach to generate optimally soft and very accuratepseudopotentials for use with plane-wave basedelectronic-structure methods is developed. The cubic-tetragonal transition in Nb3Sn is due to theinstability of the cubic structure with respect to sublatticedistortions, discovered by Shirane and Axe [Phys. Rev.B4,2957 (1971)]. Electronic excitations play an importantrole for stabilizing the cubic phase at highertemperatures. The bcc W is dynamically very stable, but at higherpressures incipient instabilities occur at certain phononmodes. The fcc W is dynamically unstable under all shear atnormal pressure. The region of instability in the BZ, isquite extended. Increasing pressure stablizes the fcc W. The bcc Fe undergoes a pressure-induced martenisticbcc-hcp transition, at the pressure 50 GPa, well above thecalculated transition pressure 10.3 GPa. We suggest thatmagnetism stabilizes the bcc structure. The long-wavelength prepeak appearing in the structurefactor of a simple monatomic liquid with icosahedralshort-range order arises from the ordering of structuralvoids. A quasicrystal cluster subjected to external stressresponds, due to phason dynamics, in a plastic manner withoutbreaking its long-range dodecagonal symmetry.Key words:Electronic structures, pseudopotentials,density functional theory, linear response, phonons, transitionmetal, quasicrystals, glasses, liquids, martensitictransformation.
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| 7. |
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| 8. |
- Sadigh, B., et al.
(author)
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Scalable parallel Monte Carlo algorithm for atomistic simulations of precipitation in alloys
- 2012
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In: Physical Review B - Condensed Matter and Materials Physics. - 2469-9950 .- 2469-9969. ; 85:18
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Journal article (peer-reviewed)abstract
- We present an extension of the semi-grand-canonical (SGC) ensemble that we refer to as the variance-constrained semi-grand-canonical (VC-SGC) ensemble. It allows for transmutation Monte Carlo simulations of multicomponent systems in multiphase regions of the phase diagram and lends itself to scalable simulations on massively parallel platforms. By combining transmutation moves with molecular dynamics steps, structural relaxations and thermal vibrations in realistic alloys can be taken into account. In this way, we construct a robust and efficient simulation technique that is ideally suited for large-scale simulations of precipitation in multicomponent systems in the presence of structural disorder. To illustrate the algorithm introduced in this work, we study the precipitation of Cu in nanocrystalline Fe.
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| 9. |
- Vosseberg, Julian, et al.
(author)
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Draft Genome Sequence of "Candidatus Moanabacter tarae," Representing a Novel Marine Verrucomicrobial Lineage
- 2018
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In: Microbiology Resource Announcements. - : AMER SOC MICROBIOLOGY. - 2576-098X. ; 7:15
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Journal article (peer-reviewed)abstract
- The Tara Oceans Consortium has published various metagenomes of marine environmental samples. Here, we report a contig of 2.6 Mbp from the assembly of a sample collected near the Marquesas Islands in the Pacific Ocean, covering a nearly complete novel verrucomicrobial genome. We propose the name "Candidates Moanabacter tarae" for the corresponding bacterium.
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