Reaction mechanisms of atomic layer deposition of TaNx from Ta(NMe2)5 precursor and H2-based plasmas

The reaction mechanisms of plasma-assisted atomic layer deposition (ALD) of TaNx using Ta(NMe2)5 were studied using quadrupole mass spectrometry (QMS). The fact that molecule dissociation and formation in the plasma have to be considered for such ALD processes was illustrated by the observation of 4% NH3 in a H2-N2 (1:1) plasma. Using QMS measurements the reaction products during growth of conductive TaNx using a H2 plasma were determined. During the Ta(NMe2)5 exposure the reaction product HNMe2 was detected. The amount of adsorbed Ta(NMe2)5 and the amount of HNMe2 released were found to depend on the number of surface groups generated during the plasma step. At the beginning of the plasma exposure step the molecules HNMe2, CH4, HCN, and C2H2 were measured. After an extended period of plasma exposure, the reaction products CH4 and C2H2 were still present in the plasma. This change in the composition of the reaction products can be explained by an interplay of aspects including the plasma-surface interaction, the ALD surface reactions, and the reactions of products within the plasma. The species formed in the plasma (e.g., CHx radicals) can re-deposit on the surface and influence to a large extent the TaNx material composition and propertie

In situ spectroscopic ellipsometry for atomic layer deposition

The application of in situ spectroscopic ellipsometry during thin film synthesis by atomic layer deposition (ALD) is examined for results obtained on Al2O3, TaN2, and TiN films with thicknesses ranging from 0.1 to 100 nm. By analyzing the film thickness and the energy dispersion of the optical constants of the films, the layer-by-layer growth and material properties of the ALD films can be studied in detail. The growth rate per cycle and the nucleation behavior of the films can be addressed by monitoring the thickness as a function of the number of cycles. It is shown that from the energy dispersion relation, insight into the conductive properties of metallic films can be derived. Moreover, the shape of the dispersion relation can be used to discriminate between different material compositions

SARS-Coronavirus Replication/Transcription Complexes Are Membrane-Protected and Need a Host Factor for Activity In Vitro

SARS-coronavirus (SARS-CoV) replication and transcription are mediated by a replication/transcription complex (RTC) of which virus-encoded, non-structural proteins (nsps) are the primary constituents. The 16 SARS-CoV nsps are produced by autoprocessing of two large precursor polyproteins. The RTC is believed to be associated with characteristic virus-induced double-membrane structures in the cytoplasm of SARS-CoV-infected cells. To investigate the link between these structures and viral RNA synthesis, and to dissect RTC organization and function, we isolated active RTCs from infected cells and used them to develop the first robust assay for their in vitro activity. The synthesis of genomic RNA and all eight subgenomic mRNAs was faithfully reproduced by the RTC in this in vitro system. Mainly positive-strand RNAs were synthesized and protein synthesis was not required for RTC activity in vitro. All RTC activity, enzymatic and putative membrane-spanning nsps, and viral RNA cosedimented with heavy membrane structures. Furthermore, the pelleted RTC required the addition of a cytoplasmic host factor for reconstitution of its in vitro activity. Newly synthesized subgenomic RNA appeared to be released, while genomic RNA remained predominantly associated with the RTC-containing fraction. RTC activity was destroyed by detergent treatment, suggesting an important role for membranes. The RTC appeared to be protected by membranes, as newly synthesized viral RNA and several replicase/transcriptase subunits were protease- and nuclease-resistant and became susceptible to degradation only upon addition of a non-ionic detergent. Our data establish a vital functional dependence of SARS-CoV RNA synthesis on virus-induced membrane structures

The Cryogenic System for the LHC Test String 2: Design, Commissioning and Operation

A 107-m long superconducting magnet string representing a full-cell of the LHC machine was designed for assembly and commissioning at CERN in order to validate the final design choices. This new facility, thereafter called Test String 2, and its cryogenic infrastructure cons ist of feed and return boxes coupled via transfer lines to a 6 kW @ 4.5 K refrigerator and to a low pressure pumping group, a separate cryogenic distribution line, an electrical feed box with HTS current leads, 2 quadrupole and 6 dipole prototype and pre-series superconducting magnets

Local Soft Tissue and Bone Displacements Following Midfacial Bipartition Distraction in Apert Syndrome – Quantification Using a Semi-Automated Method

ABSTRACT: Patients with Apert syndrome experience midfacial hypoplasia, hypertelorism, and downslanting palpebral fissures which can be corrected by midfacial bipartition distraction with rigid external distraction device. Quantitative studies typically focus on quantifying rigid advancement and rotation postdistraction, but intrinsic shape changes of bone and soft tissue remain unknown. This study presents a method to quantify these changes. Pre- and post-operative computed tomography scans from patients with Apert syndrome undergoing midfacial bipartition distraction with rigid external distraction device were collected. Digital Imaging and Communications in Medicine files were converted to three-dimensional bone and soft tissue reconstructions. Postoperative reconstructions were aligned on the preoperative maxilla, followed by nonrigid iterative closest point transformation to determine local shape changes. Anatomical point-to-point displacements were calculated and visualized using a heatmap and arrow map. Nine patients were included.Zygomatic arches and frontal bone demonstrated the largest changes. Mid-lateral to supra-orbital rim showed an upward, inward motion. Mean bone displacements ranged from 3.3 to 12.8 mm. Soft tissue displacements were relatively smaller, with greatest changes at the lateral canthi. Midfacial bipartition distraction with rigid external distraction device results in upward, inward rotation of the orbits, upward rotation of the zygomatic arch, and relative posterior motion of the frontal bone. Local movements were successfully quantified using a novel method, which can be applied to other surgical techniques/syndromes

Plasmodium berghei NK65 in Combination with IFN-γ Induces Endothelial Glucocorticoid Resistance via Sustained Activation of p38 and JNK.

Malaria-associated acute respiratory distress syndrome (MA-ARDS) is an often lethal complication of malaria. Currently, no adequate therapy for this syndrome exists. Although glucocorticoids (GCs) have been used to improve clinical outcome of ARDS, their therapeutic benefits remain unclear. We previously developed a mouse model of MA-ARDS, in which dexamethasone treatment revealed GC resistance. In the present study, we investigated GC sensitivity of mouse microvascular lung endothelial cells stimulated with interferon-γ (IFN-γ) and Plasmodium berghei NK65 (PbNK65). Upon challenge with IFN-γ alone, dexamethasone inhibited the expression of CCL5 (RANTES) by 90% and both CCL2 (MCP-1) and CXCL10 (IP-10) by 50%. Accordingly, whole transcriptome analysis revealed that dexamethasone differentially affected several gene clusters and in particular inhibited a large cluster of IFN-γ-induced genes, including chemokines. In contrast, combined stimulation with IFN-γ and PbNK65 extract impaired inhibitory actions of GCs on chemokine release, without affecting the capacity of the GC receptor to accumulate in the nucleus. Subsequently, we investigated the effects of GCs on two signaling pathways activated by IFN-γ. Dexamethasone left phosphorylation and protein levels of signal transducer and activator of transcription 1 (STAT1) unhampered. In contrast, dexamethasone inhibited the IFN-γ-induced activation of two mitogen-activated protein kinases (MAPK), JNK, and p38. However, PbNK65 extract abolished the inhibitory effects of GCs on MAPK signaling, inducing GC resistance. These data provide novel insights into the mechanisms of GC actions in endothelial cells and show how malaria may impair the beneficial effects of GCs

Insights into metazoan evolution from <i>Alvinella pompejana</i> cDNAs

BackgroundAlvinella pompejana is a representative of Annelids, a key phylum for evo-devo studies that is still poorly studied at the sequence level. A. pompejana inhabits deep-sea hydrothermal vents and is currently known as one of the most thermotolerant Eukaryotes in marine environments, withstanding the largest known chemical and thermal ranges (from 5 to 105°C). This tube-dwelling worm forms dense colonies on the surface of hydrothermal chimneys and can withstand long periods of hypo/anoxia and long phases of exposure to hydrogen sulphides. A. pompejana specifically inhabits chimney walls of hydrothermal vents on the East Pacific Rise. To survive, Alvinella has developed numerous adaptations at the physiological and molecular levels, such as an increase in the thermostability of proteins and protein complexes. It represents an outstanding model organism for studying adaptation to harsh physicochemical conditions and for isolating stable macromolecules resistant to high temperatures.ResultsWe have constructed four full length enriched cDNA libraries to investigate the biology and evolution of this intriguing animal. Analysis of more than 75,000 high quality reads led to the identification of 15,858 transcripts and 9,221 putative protein sequences. Our annotation reveals a good coverage of most animal pathways and networks with a prevalence of transcripts involved in oxidative stress resistance, detoxification, anti-bacterial defence, and heat shock protection. Alvinella proteins seem to show a slow evolutionary rate and a higher similarity with proteins from Vertebrates compared to proteins from Arthropods or Nematodes. Their composition shows enrichment in positively charged amino acids that might contribute to their thermostability. The gene content of Alvinella reveals that an important pool of genes previously considered to be specific to Deuterostomes were in fact already present in the last common ancestor of the Bilaterian animals, but have been secondarily lost in model invertebrates. This pool is enriched in glycoproteins that play a key role in intercellular communication, hormonal regulation and immunity.ConclusionsOur study starts to unravel the gene content and sequence evolution of a deep-sea annelid, revealing key features in eukaryote adaptation to extreme environmental conditions and highlighting the proximity of Annelids and Vertebrates