Industry-relevant magnetron sputtering and cathodic arc ultra-high vacuum deposition system for in situ x-ray diffraction studies of thin film growth using high energy synchrotron radiation.

We present an industry-relevant, large-scale, ultra-high vacuum (UHV) magnetron sputtering and cathodic arc deposition system purposefully designed for time-resolved in situ thin film deposition/annealing studies using high-energy (>50 keV), high photon flux (>10(12) ph/s) synchrotron radiation. The high photon flux, combined with a fast-acquisition-time (<1 s) two-dimensional (2D) detector, permits time-resolved in situ structural analysis of thin film formation processes. The high-energy synchrotron-radiation based x-rays result in small scattering angles (<11°), allowing large areas of reciprocal space to be imaged with a 2D detector. The system has been designed for use on the 1-tonne, ultra-high load, high-resolution hexapod at the P07 High Energy Materials Science beamline at PETRA III at the Deutsches Elektronen-Synchrotron in Hamburg, Germany. The deposition system includes standard features of a typical UHV deposition system plus a range of special features suited for synchrotron radiation studies and industry-relevant processes. We openly encourage the materials research community to contact us for collaborative opportunities using this unique and versatile scientific instrument.

Hydrogenation of O and OH on Pt(111): a comparison between the reaction rates of the first and the second hydrogen addition steps.

The formation of water through hydrogenation of oxygen on platinum occurs at a surprisingly low reaction rate. The reaction rate limited process for this catalytic reaction is, however, yet to be settled. In the present work, the reaction rates of the first and the second hydrogen addition steps are compared when hydrogen is obtained through intense synchrotron radiation that induces proton production in a water overlayer on top of the adsorbed oxygen species. A substantial amount of the produced hydrogen diffuses to the platinum surface and promotes water formation at the two starting conditions O/Pt(111) and (H2O+OH)/Pt(111). The comparison shows no significant difference in the reaction rate between the first and the second hydrogen addition steps, which indicates that the rate determining process of the water formation from oxygen on Pt(111) is neither the first nor the second H addition step or, alternatively, that both H addition steps exert rate control.

Low O2 dissociation barrier on Pt(111) due to adsorbate-adsorbate interactions.

O(2) dissociation on Pt(111) has been followed at low and saturation coverage using temperature-programmed x-ray photoelectron spectroscopy and simulated with mean-field kinetic modeling, yielding dissociation (E(a)) and desorption (E(d)) barriers of 0.32 and 0.36 eV, respectively. Density functional theory calculations show that E(a) is strongly influenced by the O-O interatomic potential in the atomic final state: of the supercells considered, that which maximizes attractive third-nearest-neighbor interactions in the atomic final state yields both the lowest computed dissociation barrier (0.24 eV) and the best agreement with experiment. It is proposed that the effect of adsorbate-adsorbate interactions must be considered when modeling catalytic processes involving dissociative steps.

Geometric and electronic structure of methane adsorbed on a Pt surface.

The electronic structure of methane adsorbed on Pt(977) is investigated using angle-resolved x-ray absorption spectroscopy (XAS) in combination with density functional theory spectrum calculations. XAS, which probes the unoccupied states atom specifically, shows the appearance of the symmetry-forbidden gas-phase lowest unoccupied molecular orbital due to s-p rehybridization. In addition new adsorption-induced states appear just above the Fermi level. A systematic investigation, where computed XA spectra are compared with the experiment, indicates elongation of the C-H bond pointing toward the surface to 1.18+/-0.05 A. The bond elongation arises due to mixing between bonding and antibonding C-H orbitals. Computed charge density difference plots show that no covalent chemical bond is formed between the adsorbate and substrate upon adsorption. The changes in electronic structure arise in order to minimize the Pauli repulsion by polarizing charge away from the surface toward the carbon atom of the methane molecule.

Transcriptional profiling of the peripheral blood response during tularemia.

Tularemia is a febrile disease caused by the highly contagious bacterium Francisella tularensis. We undertook an analysis of the transcriptional response in peripheral blood during the course of ulceroglandular tularemia by use of Affymetrix microarrays comprising 14,500 genes. Samples were obtained from seven individuals at five occasions during 2 weeks after the first hospital visit and convalescent samples 3 months later. In total, 265 genes were differentially expressed, 95 of which at more than one time point. The differential expression was verified with real-time quantitative polymerase chain reaction for 36 genes (R(2)=0.590). The most prominent changes were noted in samples drawn on days 2-3 and a considerable proportion of the upregulated genes appeared to represent an interferon-gamma-induced response and also a proapoptotic response. Genes involved in the generation of innate and acquired immune responses were found to be downregulated, presumably a pathogen-induced event. A logistic regression analysis revealed that seven genes were good predictors of the early phase of tularemia. This is the first description of the transcriptional host response to ulceroglandular tularemia and the study has identified gene subsets relevant to the pathogenesis of the disease and subsets that may serve as early diagnostic biomarkers.

Biomarker selection for detection of occult tumour cells in lymph nodes of colorectal cancer patients using real-time quantitative RT-PCR.

Accurate identification of lymph node involvement is critical for successful treatment of patients with colorectal carcinoma (CRC). Real-time quantitative RT-PCR with a specific probe and RNA copy standard for biomarker mRNA has proven very powerful for detection of disseminated tumour cells. Which properties of biomarker mRNAs are important for identification of disseminated CRC cells? Seven biomarker candidates, CEA, CEACAM1-S/L, CEACAM6, CEACAM7-1/2, MUC2, MMP7 and CK20, were compared in a test-set of lymph nodes from 51 CRC patients (Dukes' A-D) and 10 controls. Normal colon epithelial cells, primary tumours, and different immune cells were also analysed. The biomarkers were ranked according to: (1) detection of haematoxylin/eosin positive nodes, (2) detection of Dukes' A and B patients, who developed metastases during a 54 months follow-up period and (3) identification of patients with Dukes' C and D tumours using the highest value of control nodes as cutoff. The following properties appear to be of importance; (a) no expression in immune cells, (b) relatively high and constant expression in tumour tissue irrespective of Dukes' stage and (c) no or weak downregulation in tumours compared to normal tissue. CEA fulfilled these criteria best, followed by CK20 and MUC2.

Physisorption-induced C-H bond elongation in methane.

Physisorption of methane to a Pt surface was studied by x-ray absorption spectroscopy in combination with density functional theory spectrum calculations. The experiment shows new electronic states appearing upon physisorption. We find that these states are due to orbital mixing causing charge polarization as a means to minimize Pauli repulsion. The results can be explained by elongation of 1 C-H bond by 0.09 A in the physisorbed state even though no covalent chemical bond is formed.

X-ray absorption spectroscopy measurements of liquid water.

Recent studies, based on X-ray absorption spectroscopy (XAS) and X-ray Raman scattering (XRS), have shown that the hydrogen bond network in liquid water consists mainly of water molecules with only two strong hydrogen bonds. Since this result is controversial, it is important to demonstrate the reliability of the experimental data, which is the purpose of this paper. Here we compare X-ray absorption spectra of liquid water recorded with five very different techniques sensitive to the local environment of the absorbing molecule. Overall, the spectra obtained with photon detection show a very close similarity and even the observable minor differences can be understood. The comparison demonstrates that XAS and XRS can indeed be applied reliably to study the local bonding of the water molecule and thus to reveal the hydrogen bond situation in bulk water.

The structure of the first coordination shell in liquid water.

X-ray absorption spectroscopy and x-ray Raman scattering were used to probe the molecular arrangement in the first coordination shell of liquid water. The local structure is characterized by comparison with bulk and surface of ordinary hexagonal ice Ih and with calculated spectra. Most molecules in liquid water are in two hydrogen-bonded configurations with one strong donor and one strong acceptor hydrogen bond in contrast to the four hydrogen-bonded tetrahedral structure in ice. Upon heating from 25 degrees C to 90 degrees C, 5 to 10% of the molecules change from tetrahedral environments to two hydrogen-bonded configurations. Our findings are consistent with neutron and x-ray diffraction data, and combining the results sets a strong limit for possible local structure distributions in liquid water. Serious discrepancies with structures based on current molecular dynamics simulations are observed.

Electronic structure effects from hydrogen bonding in the liquid phase and in chemisorption: an integrated theory and experimental effort.

A closely integrated theoretical and experimental effort to understand chemical bonding using X-ray spectroscopic probes is presented. Theoretical techniques to simulate XAS (X-ray absorption spectroscopy), XES (X-ray emission spectroscopy), RIXS (resonant inelastic X-ray scattering) and XPS (X-ray photoelectron spectroscopy) spectra have been developed and implemented within a density functional theory (DFT) framework. In combination with new experimental techniques, such as high-resolution XAS on liquid water under ambient conditions and XES on complicated surface adsorbates, new insight into e.g. hydrogen-bonded systems is obtained. For the (3x2) overlayer structure of glycine/Cu(110), earlier work has been extended to include adsorbate-adsorbate interactions. Structures are optimized for large cluster models and for periodic boundary conditions. It is found that specific features in the spectra arise from hydrogen-bonding interactions, which thus have important effects at the molecular-orbital level. XAS on liquid water shows a pronounced pre-edge feature with significant intensity, while the spectrum of ice shows only little intensity in this region. Theoretical spectrum calculations, based on instantaneous structures obtained from molecular-dynamics (MD) simulations, show that the pre-edge feature in the liquid is caused by water molecules with unsaturated hydrogen bonding. Some aspects of the theoretical simulations will be briefly discussed.

Penetration of loracarbef into the maxillary sinus: a pharmacokinetic assessment.

Loracarbef, a beta-lactam antibiotic of the carbacephem class, is active in vitro against pathogens associated with acute maxillary sinusitis. To study the extent and duration of maxillary sinus fluid penetration after administration of loracarbef, 20 patients (10 men, 10 women; average age, 41 +/- 13 years) with acute sinusitis were treated with loracarbef 400 mg every 12 hours for 10 days. A lavage catheter was inserted into the maxillary sinus, and 150-microL sinus fluid samples were obtained at 0 (baseline), 0.5, 1, 1.5, 2, and 2.5 hours after the first dose and at 24 and 48 hours (12 hours after the second and fourth doses, respectively). Venous blood samples were obtained at the same times. Maxillary fluid and serum samples were frozen immediately at -20 degrees C to -70 degrees C until later bioassay using a direct agar diffusion method. Excluding missing data or inappropriately timed samples, the mean (+/- SD) sinus fluid concentrations were 0.16 +/- 0.12 microgram/mL at baseline, 0.23 +/- 0.17 microgram/mL at 0.5 hour, 1.11 +/- 1.44 micrograms/mL at 1 hour, 1.63 +/- 2.07 micrograms/mL at 1.5 hours, 1.75 +/- 2.01 micrograms/mL at 2 hours, and 1.60 +/- 1.96 micrograms/mL at 2.5 hours after dose. The mean sinus fluid concentration before the third dose (approximately 12 hours after the second dose) was 1.01 +/- 0.89 microgram/mL and before the fifth dose (approximately 12 hours after the fourth dose) was 0.88 +/- 0.90 microgram/mL. Taking the highest sinus fluid concentration measured in each patient, the mean peak sinus fluid concentration was 2.12 +/- 1.98 micrograms/mL (range, 0 to 6.7 micrograms/mL). The pretherapy peripheral leukocyte count appeared to have a statistically significant association (P < 0.01) with loracarbef sinus fluid penetration as estimated by the sinus fluid area under the concentration-time curve at 0 to 2.5 hours. Loracarbef 400 mg twice daily achieved sinus fluid concentrations that appeared to exceed the minimum concentration required to inhibit 90% of relevant acute sinusitis pathogens throughout the 12-hour interdose interval in most patients with acute maxillary sinusitis.

Histidine-rich domain of the knob protein of the human malaria parasite Plasmodium falciparum.

Membranes of erythrocytes infected with the human malaria parasite Plasmodium falciparum develop protrusions called knobs. These structures are essential for the survival of the parasite in the host, and their induction requires the synthesis of the knob protein by the parasite. We describe the isolation of a cDNA clone encoding the amino-terminal half of the knob protein. A cDNA library was constructed from RNA prepared from ring stages of a P. falciparum isolate that has retained its ability to induce knobs (knob+ phenotype). A synthetic oligonucleotide probe encoding polyhistidine was used to isolate the cDNA clone, which encodes the amino-terminal half of a polypeptide with all the known attributes of the knob protein. The gene is not transcribed in variants that do not synthesize the knob protein and thereby cannot induce knobs (knob- phenotype). The apparent lack of transcription in knob- variants is due to different mechanisms: although the gene is present in one knob- isolate, it has been deleted in a cloned knob- variant. The primary structure of the polypeptide deduced from a partial sequence of the cDNA is distinctly different from other malarial histidine-rich polypeptides. The amino-terminal sequence shows the characteristic features of a signal peptide. This is followed by a histidine-rich domain and a subsequent region which contains one histidine. Peptide map analysis of the knob protein is consistent with the structural features deduced from the sequence analysis of the cDNA.

Perceptibility of experimental and clinical lesions in the CT image with and without image processing.

The Ohio-Nuclear Delta 50 FS whole-body CT scanner and image filtering programs FI and SP:SMOOTH provided with the equipment were used to investigate how the perceptibility in the CT image of artificial lesions in a phantom and of liver lesions in patients was influenced by different reconstruction diameters, radiation doses and section thicknesses and by image filtering and different conditions of viewing. The perceptibility of both artificial and clinical lesions was considerably improved, especially in scans with a low radiation dose, when optimum viewing conditions and image filters were used.

Rapid zymogen activation and isolation of serine proteases from an individual mouse pancreas by affinity chromatography: genetical heterogeneity of chymotrypsins of Mus musculus.

A rapid method to prepare homogeneous fractions of the various chymotrypsins and trypsins from a single mouse pancreas (130-150 mg wet weight) is described. The method was applied to investigate intra-species variation on a molecular level using chymotrypsins as biochemical indicators. The conditions for optimal extraction of the zymogens in the homogenized pancreas have been studied. DNA had to be removed from the homogenate to obtain maximum chymotrypsin yields (approximately 1% of the wet weight of the pancreas). The activation was initiated by immobilized bovine trypsin that was removed by filtration. Then chymotrypsinogens in the homogenate were activated by mouse trypsin. After completed activation homogeneous chymotrypsins (one anionic and one cationic form) could be isolated in an one step analytical affinity chromatographic separation, using soybean trypsin inhibitor bound in Sepharose as a protease specific adsorbent. The end products were characterized by isoelectric focussing, amino acid composition, enzymatic parameters, molar extinction coefficient, and the number of polypeptide chains. Hereby, the existence of two chymotrypsinogen loci in the mouse genome could be demonstrated. Differences in structure and function between the corresponding enzymes from the two strains were found. This allelomorphism was verified in the crossing of the off-spring.