Plasma atomic layer deposition

Plasma atomic layer deposition (ALD) is optimized through modulation of the gas residence time during an excited species phase, wherein activated reactant is supplied such as from a plasma. Reduced residence time increases the quality of the deposited layer, such as reducing wet etch rates, increasing index of refraction and/or reducing impurities in the layer. For example, dielectric layers, particularly silicon nitride films, formed from such optimized plasma ALD processes have low levels of impurities remaining from the silicon precursor

Nidovirus replication structures : hijacking membranes to support viral RNA synthesis

Positive-stranded RNA viruses replicate in the cytoplasm of host cells and their replication complexes are associated with modified cell membranes. We investigated the structure of the nidovirus-induced membrane modifications and found that nidoviruses transform the endoplasmic reticulum into a reticulovesicular network (RVN) that integrates numerous inter-connected double-membrane vesicles (DMVs), and, in the case of coronaviruses, __vesicle packets__ and convoluted membranes (CM). The membranes of DMVs and CM labeled abundantly for replicase proteins, whereas the DMV interior contained the double-stranded RNA and therefore is the presumed site of viral RNA synthesis. Electron tomography, semi-permeabilization and nuclease digestion experiments suggested that the DMV interior is inaccessible from the cytosol, implying that double-stranded RNA is compartmentalized by membranes. Furthermore, brefeldin A treatment showed that early secretory pathway proteins do not play a direct role in RVN morphogenesis or functionality of the SARS-CoV replication complex. Continued translation was not an absolute requirement for viral RNA synthesis, however, was necessary for RVN development thus suggesting a link between accumulation of replicase proteins and RVN formation. Together with biochemical studies of the viral enzyme complex, our ultrastructural description of the RVN aids to further dissect the early stages of the nidovirus infection and virus-host interactions.Stichting tot Bevordering van de Electronenmicroscopie in Nederland (SEN)UBL - phd migration 201

Optical modeling of plasma-deposited ZnO films : electron scattering at different length scales

In this work, an optical modeling study on electron scattering mechanisms in plasma-deposited ZnO layers is presented. Because various applications of ZnO films pose a limit on the electron carrier density due to its effect on the film transmittance, higher electron mobility values are generally preferred instead. Hence, insights into the electron scattering contributions affecting the carrier mobility are required. In optical models, the Drude oscillator is adopted to represent the free-electron contribution and the obtained optical mobility can be then correlated with the macroscopic material properties. However, the influence of scattering phenomena on the optical mobility depends on the considered range of photon energy. For example, the grain-boundary scattering is generally not probed by means of optical measurements and the ionized-impurity scattering contribution decreases toward higher photon energies. To understand this frequency dependence and quantify contributions from different scattering phenomena to the mobility, several case studies were analyzed in this work by means of spectroscopic ellipsometry and Fourier transform infrared (IR) spectroscopy. The obtained electrical parameters were compared to the results inferred by Hall measurements. For intrinsic ZnO (i-ZnO), the in-grain mobility was obtained by fitting reflection data with a normal Drude model in the IR range. For Al-doped ZnO (Al:ZnO), besides a normal Drude fit in the IR range, an Extended Drude fit in the UV-vis range could be used to obtain the in-grain mobility. Scattering mechanisms for a thickness series of Al:ZnO films were discerned using the more intuitive parameter "scattering frequency" instead of the parameter "mobility". The interaction distance concept was introduced to give a physical interpretation to the frequency dependence of the scattering frequency. This physical interpretation furthermore allows the prediction of which Drude models can be used in a specific frequency range

In cellulo serial crystallography of alcohol oxidase crystals inside yeast cells

The possibility of using femtosecond pulses from an X-ray free-electron laser to collect diffraction data from protein crystals formed in their native cellular organelle has been explored. X-ray diffraction of submicrometre-sized alcohol oxidase crystals formed in peroxisomes within cells of genetically modified variants of the methylotrophic yeast Hansenula polymorpha is reported and characterized. The observations are supported by synchrotron radiation-based powder diffraction data and electron microscopy. Based on these findings, the concept of in cellulo serial crystallography on protein targets imported into yeast peroxisomes without the need for protein purification as a requirement for subsequent crystallization is outlined

Quantifying the effect of corrective surgery for trigonocephaly: A non-invasive, non-ionizing method using three-dimensional handheld scanning and statistical shape modelling

Trigonocephaly in patients with metopic synostosis is corrected by fronto-orbital remodelling (FOR). The aim of this study was to quantitatively assess aesthetic outcomes of FOR by capturing 3D forehead scans of metopic patients pre- and post-operatively and comparing them with controls. Ten single-suture metopic patients undergoing FOR and 15 age-matched non-craniosynostotic controls were recruited at Great Ormond Street Hospital for Children (UK). Scans were acquired with a three-dimensional (3D) handheld camera and post-processed combining 3D imaging software. 3D scans were first used for cephalometric measurements. Statistical shape modelling was then used to compute the 3D mean head shapes of the three groups (FOR pre-op, post-op and controls). Head shape variations were described via principal component analysis (PCA). Cephalometric measurements showed that FOR significantly increased the forehead volume and improved trigonocephaly. This improvement was supported visually by pre- and post-operative computed mean 3D shapes and numerically by PCA (p < 0.001). Compared with controls, post-operative scans showed flatter foreheads (p < 0.001). In conclusion, 3D scanning followed by 3D statistical shape modelling enabled the 3D comparison of forehead shapes of metopic patients and non-craniosynostotic controls, and demonstrated that the adopted FOR technique was successful in correcting bitemporal narrowing but overcorrected the rounding of the forehead

Extensive coronavirus-induced membrane rearrangements are not a determinant of pathogenicity

Positive-strand RNA (+RNA) viruses rearrange cellular membranes during replication, possibly in order to concentrate and arrange viral replication machinery for efficient viral RNA synthesis. Our previous work showed that in addition to the conserved coronavirus double membrane vesicles (DMVs), Beau-R, an apathogenic strain of avian Gammacoronavirus infectious bronchitis virus (IBV), induces regions of ER that are zippered together and tethered open-necked double membrane spherules that resemble replication organelles induced by other +RNA viruses. Here we compared structures induced by Beau-R with the pathogenic lab strain M41 to determine whether membrane rearrangements are strain dependent. Interestingly, M41 was found to have a low spherule phenotype. We then compared a panel of pathogenic, mild and attenuated IBV strains in ex vivo tracheal organ culture (TOC). Although the low spherule phenotype of M41 was conserved in TOCs, each of the other tested IBV strains produced DMVs, zippered ER and spherules. Furthermore, there was a significant correlation for the presence of DMVs with spherules, suggesting that these structures are spatially and temporally linked. Our data indicate that virus induced membrane rearrangements are fundamentally linked to the viral replicative machinery. However, coronavirus replicative apparatus clearly has the plasticity to function in different structural contexts

Measurement of the cross-section and charge asymmetry of WW bosons produced in proton-proton collisions at s=8\sqrt{s}=8 TeV with the ATLAS detector

This paper presents measurements of the $W^+ \rightarrow \mu^+\nu$ and $W^- \rightarrow \mu^-\nu$ cross-sections and the associated charge asymmetry as a function of the absolute pseudorapidity of the decay muon. The data were collected in proton--proton collisions at a centre-of-mass energy of 8 TeV with the ATLAS experiment at the LHC and correspond to a total integrated luminosity of 20.2~\mbox{fb^{-1}}. The precision of the cross-section measurements varies between 0.8% to 1.5% as a function of the pseudorapidity, excluding the 1.9% uncertainty on the integrated luminosity. The charge asymmetry is measured with an uncertainty between 0.002 and 0.003. The results are compared with predictions based on next-to-next-to-leading-order calculations with various parton distribution functions and have the sensitivity to discriminate between them.Comment: 38 pages in total, author list starting page 22, 5 figures, 4 tables, submitted to EPJC. All figures including auxiliary figures are available at https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/STDM-2017-13

Practical management of Chronic Myeloid Leukemia in Belgium

peer reviewedImatinib has drastically changed the outcome of patients with chronic myeloid leukemia (CML), with the majority of them showing a normal life span. Recently, the development of second and third generation tyrosine kinase inhibitors (TKIs) and the possibility of treatment discontinuation made the management of these patients more challenging. In this review, practical management guidelines of CML are presented, adapted to the Belgian situation in 2014. In first line chronic phase patients, imatinib, nilotinib and dasatinib can be prescribed. While second generation TKIs give faster and deeper responses, their impact on long-term survival remain to be determined. The choice of the TKI depends on CML risk score, priority for a deep response to allow a treatment-free remission protocol, age, presence of comorbid conditions, side effect profile, drug interactions, compliance concerns and price. Monitoring the response has to be made according the 2013 ELN criteria, and is based on the bone-marrow cytogenetic response during the first months and on the blood molecular response. Molecular follow-up is sufficient in patients with a complete cytogenetic response. For patients who fail frontline therapy, nilotinib, dasatinib, bosutinib and ponatinib are an option depending of the type of intolerance or resistance. T315I patients are only sensitive to ponatinib, which has to be carefully handled due to cardiovascular toxicity. Advanced phase diseases are more difficult to handle, with treatments including allogeneic stem cell transplantation, which is also an option for patients failing at least two TKIs. The possibility of treatment-free remission and pregnancy are also discussed

Measurement of χ c1 and χ c2 production with s√ = 7 TeV pp collisions at ATLAS

The prompt and non-prompt production cross-sections for the χ c1 and χ c2 charmonium states are measured in pp collisions at s√ = 7 TeV with the ATLAS detector at the LHC using 4.5 fb−1 of integrated luminosity. The χ c states are reconstructed through the radiative decay χ c → J/ψγ (with J/ψ → μ + μ −) where photons are reconstructed from γ → e + e − conversions. The production rate of the χ c2 state relative to the χ c1 state is measured for prompt and non-prompt χ c as a function of J/ψ transverse momentum. The prompt χ c cross-sections are combined with existing measurements of prompt J/ψ production to derive the fraction of prompt J/ψ produced in feed-down from χ c decays. The fractions of χ c1 and χ c2 produced in b-hadron decays are also measured

Measurements of fiducial and differential cross sections for Higgs boson production in the diphoton decay channel at s√=8 TeV with ATLAS

Measurements of fiducial and differential cross sections are presented for Higgs boson production in proton-proton collisions at a centre-of-mass energy of s√=8 TeV. The analysis is performed in the H → γγ decay channel using 20.3 fb−1 of data recorded by the ATLAS experiment at the CERN Large Hadron Collider. The signal is extracted using a fit to the diphoton invariant mass spectrum assuming that the width of the resonance is much smaller than the experimental resolution. The signal yields are corrected for the effects of detector inefficiency and resolution. The pp → H → γγ fiducial cross section is measured to be 43.2 ±9.4(stat.) − 2.9 + 3.2 (syst.) ±1.2(lumi)fb for a Higgs boson of mass 125.4GeV decaying to two isolated photons that have transverse momentum greater than 35% and 25% of the diphoton invariant mass and each with absolute pseudorapidity less than 2.37. Four additional fiducial cross sections and two cross-section limits are presented in phase space regions that test the theoretical modelling of different Higgs boson production mechanisms, or are sensitive to physics beyond the Standard Model. Differential cross sections are also presented, as a function of variables related to the diphoton kinematics and the jet activity produced in the Higgs boson events. The observed spectra are statistically limited but broadly in line with the theoretical expectations