X-ray diffraction at the National Ignition Facility.

We report details of an experimental platform implemented at the National Ignition Facility to obtain in situ powder diffraction data from solids dynamically compressed to extreme pressures. Thin samples are sandwiched between tamper layers and ramp compressed using a gradual increase in the drive-laser irradiance. Pressure history in the sample is determined using high-precision velocimetry measurements. Up to two independently timed pulses of x rays are produced at or near the time of peak pressure by laser illumination of thin metal foils. The quasi-monochromatic x-ray pulses have a mean wavelength selectable between 0.6 Å and 1.9 Å depending on the foil material. The diffracted signal is recorded on image plates with a typical 2θ x-ray scattering angle uncertainty of about 0.2° and resolution of about 1°. Analytic expressions are reported for systematic corrections to 2θ due to finite pinhole size and sample offset. A new variant of a nonlinear background subtraction algorithm is described, which has been used to observe diffraction lines at signal-to-background ratios as low as a few percent. Variations in system response over the detector area are compensated in order to obtain accurate line intensities; this system response calculation includes a new analytic approximation for image-plate sensitivity as a function of photon energy and incident angle. This experimental platform has been used up to 2 TPa (20 Mbar) to determine the crystal structure, measure the density, and evaluate the strain-induced texturing of a variety of compressed samples spanning periods 2-7 on the periodic table.

Proteomic profiling of rectal cancer reveals acid ceramidase is implicated in radiation response.

BACKGROUND: Neoadjuvant chemoradiotherapy (CRT) is used in locally advanced rectal cancer when tumours threaten the circumferential resection margin, with varying response to treatment. This experimental study aimed to identify significantly differentially expressed proteins between patients responding and not responding to CRT, and to validate any proteins of interest. METHODS: Mass spectrometry (with isobaric tagging for relative quantification) analysis of rectal cancers pre- and post-CRT, and at resection. Validation of proteins of interest was performed by assessing tissue microarray (TMA) immunohistochemistry expression in a further 111 patients with rectal cancer. RESULTS: Proteomic data are available via ProteomeXchange with identifier PXD008436. Reduced abundance of contributing peptide ions for acid ceramidase (AC) (log fold change -1.526, p = 1.17E-02) was observed in CRT responders. Differential expression of AC was confirmed upon analysis of the TMAs. Cancer site expression of AC in stromal cells from post-CRT resection specimens was observed to be relatively low in pathological complete response (p = 0.003), and relatively high with no response to CRT (p = 0.017). CONCLUSION: AC may be implicated in the response of rectal cancer to CRT. We propose its further assessment as a novel potential biomarker and therapeutic target. SIGNIFICANCE: There is a need for biomarkers to guide the use of chemoradiotherapy in rectal cancer, as none are in routine clinical use. We have determined acid ceramidase may have a role in radiation response, based on novel proteomic profiling and validation in a wider dataset using tissue microarrays. The ability to predict or improve response would positively select those patients who will derive benefit, prevent delays in the local and systemic management of disease in non-responders, and reduce morbidity associated with chemoradiotherapy.

Multiconfigurational nature of 5f orbitals in uranium and plutonium intermetallics.

Uranium and plutonium's 5f electrons are tenuously poised between strongly bonding with ligand spd-states and residing close to the nucleus. The unusual properties of these elements and their compounds (e.g., the six different allotropes of elemental plutonium) are widely believed to depend on the related attributes of f-orbital occupancy and delocalization for which a quantitative measure is lacking. By employing resonant X-ray emission spectroscopy (RXES) and X-ray absorption near-edge structure (XANES) spectroscopy and making comparisons to specific heat measurements, we demonstrate the presence of multiconfigurational f-orbital states in the actinide elements U and Pu and in a wide range of uranium and plutonium intermetallic compounds. These results provide a robust experimental basis for a new framework toward understanding the strongly-correlated behavior of actinide materials.

Emergence of strong exchange interaction in the actinide series: the driving force for magnetic stabilization of curium.

Using electron energy-loss spectroscopy, many-electron atomic spectral calculations, and density functional theory, we show that angular-momentum coupling in the 5f states plays a decisive role in the formation of the magnetic moment in Cm metal. The 5f states of Cm in intermediate coupling are strongly shifted towards the LS coupling limit due to exchange interaction, unlike most actinide elements where the effective spin-orbit interaction prevails. Hund's rule coupling is the key to producing the large spin polarization that dictates the newly found crystal structure of Cm under pressure.

Probing the population of the spin-orbit split levels in the actinide 5f states.

Spin-orbit interaction in the 5f states is believed to strongly influence exotic behaviors observed in actinide metals and compounds. Understanding these interactions and how they relate to the actinide series is of considerable importance. To address this issue, the branching ratio of the white-line peaks of the N4,5 edge for the light actinide metals, alpha-Th, alpha-U, and alpha-Pu were recorded using electron energy-loss spectroscopy (EELS) in a transmission electron microscope (TEM) and synchrotron-radiation-based X-ray absorption spectroscopy (XAS). Using the spin-orbit sum rule and the branching ratios from both experimental spectra and many-electron atomic spectral calculations, accurate values of the spin-orbit interaction, and thus the relative occupation of the j = 5/2 and 7/2 levels, are determined for the actinide 5f states. Results show that the spin-orbit sum rule works very well with both EELS and XAS spectra, needing little or no correction. This is important, since the high spatial resolution of a TEM can be used to overcome the problems of single-crystal growth often encountered with actinide metals, allowing acquisition of EELS spectra, and subsequent spin-orbit analysis, from nm-sized regions. The relative occupation numbers obtained by our method have been compared with recent theoretical results and they show a good agreement in their trend.

Caesarean section delivery and the risk of allergic disorders in childhood.

BACKGROUND: The composition of the intestinal flora in young children, if unfavourable, may increase the susceptibility to allergic disorders. Beneficial intestinal microbes originate from the maternal vaginal tract and thus are more likely to be transferred during vaginal births than during Caesarean sections (C-sections). OBJECTIVE: To determine whether children born by C-section have a different risk of allergic disorders compared with those delivered vaginally. We also tested the hypothesis that the risk of allergic disorders is highest for children born after 'repeat C-sections'. METHODS: A retrospective cohort study of 8,953 children aged 3-10 years. Children diagnosed with allergic rhinoconjunctivitis (AR), asthma, atopic dermatitis (AD), or food allergies were identified from the Kaiser Permanente Northwest Region electronic records. The children's sex, birth weight, birth order, postnatal exposure to antibiotics as well as the mothers' age, ethnicity, education, marital status, smoking status during pregnancy, and use of asthma or hayfever medications were identified through the mothers' medical records or through the Oregon Birth Registry. RESULTS: The risk of being diagnosed with AR was significantly higher in the children born by C-section than in those delivered vaginally: adjusted odds ratio (OR)=1.37%, 95% confidence interval (CI)=1.14-1.63. Delivery by C-section was also associated with the subsequent diagnosis of asthma (OR=1.24%, 95% CI=1.01-1.53); this association was gender specific, with a positive association restricted to girls (OR for asthma in girls: OR=1.53%, 95% CI=1.11-2.10; in boys: OR=1.08%, 95% CI=0.81-1.43). There was no significant association between mode of delivery and AD. If children born in a 'repeat C-section' were considered separately the risk of being diagnosed with AR increased further (OR=1.78%, 95% CI=1.34-2.37). The same increase was noted for asthma in girls (OR=1.83%, 95% CI=1.13-2.97) but not in boys. CONCLUSION: Caesarean sections may be associated with an increased risk of developing AR in childhood.

Applicability of the spin-orbit sum rule for the actinide 5f states.

The branching ratio of core-valence transitions in electron energy-loss spectroscopy and x-ray absorption spectroscopy is linearly related to the expectation value of the spin-orbit operator of the valence states. Here, we analyze the branching ratio of the N(4,5) edges in the actinides and find that the spin-orbit sum rule gives an accurate result without the need to include the core-valence interactions. The branching ratio is not only useful to study the variations in the 5f spin-orbit interaction, it also allows us to constrain the 5f count for given angular-momentum coupling conditions.

Failure of Russell-Saunders coupling in the 5f states of plutonium.

Using high energy-electron energy loss spectroscopy, transmission electron microscopy, and synchrotron-radiation-based x-ray absorption spectroscopy, we provide the first experimental evidence that Russell-Saunders (LS) coupling fails for the 5f states of Pu. These results support the assumption that only the use of jj or intermediate coupling is appropriate for the 5f states of Pu. High energy-electron energy loss spectroscopy experiments were performed by use of a transmission electron microscope and are coupled with image and diffraction data; therefore, the measurements are completely phase specific.

A high-resolution serial sectioning specimen preparation technique for application to electron backscatter diffraction.

A high-resolution serial sectioning specimen preparation technique is described for acquisition of electron backscatter diffraction (EBSD) data. The primary objective is to develop a method to reproducibly remove a controlled thickness of material from a polycrystalline Ta sample while producing quality surfaces for EBSD orientation imaging. This is integrated with the ability to accurately measure the amount of material removed with each iteration and experimentally register the ensuing EBSD scans. To facilitate enhanced accuracy of this method, a metrology device containing high-precision etching patterns is fabricated using standard lithographic techniques. This metrology device allows for the sub-micron measurement of the serial section slice thickness and approximately 1 microm registration accuracy of each EBSD scan.

The structural basis for red fluorescence in the tetrameric GFP homolog DsRed.

Green fluorescent protein (GFP) has rapidly become a standard tool for investigating a variety of cellular activities, and has served as a model system for understanding spectral tuning in chromophoric proteins. Distant homologs of GFP in reef coral and anemone display two new properties of the fluorescent protein family: dramatically red-shifted spectra, and oligomerization to form tetramers. We now report the 1.9 A crystal structure of DsRed, a red fluorescent protein from Discosoma coral. DsRed monomers show similar topology to GFP, but additional chemical modification to the chromophore extends the conjugated pi-system and likely accounts for the red-shifted spectra. Oligomerization of DsRed occurs at two chemically distinct protein interfaces to assemble the tetramer. The DsRed structure reveals the chemical basis for the functional properties of red fluorescent proteins and provides the basis for rational engineering of this subfamily of GFP homologs.

Mo/Si and Mo/Be multilayer thin films on Zerodur substrates for extreme-ultraviolet lithography.

Multilayer-coated Zerodur optics are expected to play a pivotal role in an extreme-ultraviolet (EUV) lithography tool. Zerodur is a multiphase, multicomponent material that is a much more complicated substrate than commonly used single-crystal Si or fused-silica substrates. We investigate the effect of Zerodur substrates on the performance of high-EUV reflectance Mo/Si and Mo/Be multilayer thin films. For Mo/Si the EUV reflectance had a nearly linear dependence on substrate roughness for roughness values of 0.06-0.36 nm rms, and the FWHM of the reflectance curves (spectral bandwidth) was essentially constant over this range. For Mo/Be the EUV reflectance was observed to decrease more steeply than Mo/Si for roughness values greater than approximately 0.2-0.3 nm. Little difference was observed in the EUV reflectivity of multilayer thin films deposited on different substrates as long as the substrate roughness values were similar.

A G protein gamma subunit-like domain shared between RGS11 and other RGS proteins specifies binding to Gbeta5 subunits.

Regulators of G protein signaling (RGS) proteins act as GTPase-activating proteins (GAPs) toward the alpha subunits of heterotrimeric, signal-transducing G proteins. RGS11 contains a G protein gamma subunit-like (GGL) domain between its Dishevelled/Egl-10/Pleckstrin and RGS domains. GGL domains are also found in RGS6, RGS7, RGS9, and the Caenorhabditis elegans protein EGL-10. Coexpression of RGS11 with different Gbeta subunits reveals specific interaction between RGS11 and Gbeta5. The expression of mRNA for RGS11 and Gbeta5 in human tissues overlaps. The Gbeta5/RGS11 heterodimer acts as a GAP on Galphao, apparently selectively. RGS proteins that contain GGL domains appear to act as GAPs for Galpha proteins and form complexes with specific Gbeta subunits, adding to the combinatorial complexity of G protein-mediated signaling pathways.

An in situ nanoindentation specimen holder for a high voltage transmission electron microscope.

We describe in detail, the design, construction, and testing of a specimen holder that allows for the nanoindentation of surfaces while viewing in cross-section in a high voltage transmission electron microscope (TEM). This nanoindentation specimen holder, having three-axis position control of a diamond indenter in combination with micromachined specimens, allows for the first time the dynamic observation of subsurface microstructure evolution under an indenter tip. Additionally, the sample design techniques that have been developed for these procedures may eliminate the need for TEM specimen preparation for additional ex situ nanoindentation experiments. Initial experimental results from in situ indentation of Si samples in the high voltage electron microscope are reported here to demonstrate the capability of this new specimen holder.

Structural basis of activity and subunit recognition in G protein heterotrimers.

BACKGROUND: Inactive heterotrimeric G proteins are composed of a GDP-bound alpha subunit (Galpha) and a stable heterodimer of Gbeta and Ggamma subunits. Upon stimulation by a receptor, Galpha subunits exchange GDP for GTP and dissociate from Gbetagamma, both Galpha and Gbetagamma then interact with downstream effectors. Isoforms of Galpha, Gbeta and Ggamma potentially give rise to many heterotrimeric combinations, limited in part by amino acid sequence differences that lead to selective interactions. The mechanism by which GTP promotes Gbetagamma dissociation is incompletely understood. The Gly203-->Ala mutant of Gialpha1 binds and hydrolyzes GTP normally but does not dissociate from Gbetagamma, demonstrating that GTP binding and activation can be uncoupled. Structural data are therefore important for understanding activation and subunit recognition in G protein heterotrimers. RESULTS: The structures of the native (Gialpha1beta1gamma2) heterotrimer and that formed with Gly203-->AlaGialpha1 have been determined to resolutions of 2.3 A and 2.4 A, respectively, and reveal previously unobserved segments at the Ggamma2 C terminus. The Gly203-->Ala mutation alters the conformation of the N terminus of the switch II region (Val201-Ala203), but not the global structure of the heterotrimer. The N termini of Gbeta and Ggamma form a rigid coiled coil that packs at varying angles against the beta propeller of Gbeta. Conformational differences in the CD loop of beta blade 2 of Gbeta mediate isoform-specific contacts with Galpha. CONCLUSIONS: The Gly203-->Ala mutation in Gialpha1 blocks the conformational changes in switch II that are required to release Gbetagamma upon binding GTP. The interface between the ras-like domain of Galpha and the beta propeller of Gbeta appears to be conserved in all G protein heterotrimers. Sequence variation at the Gbeta-Galpha interface between the N-terminal helix of Galpha and the CD loop of beta blade 2 of Gbeta1 (residues 127-135) could mediate isoform-specific contacts. The specificity of Gbeta and Ggamma interactions is largely determined by sequence variation in the contact region between helix 2 of Ggamma and the surface of Gbeta.

Expression of basic fibroblast growth factor in nasal polyps.

Basic fibroblast growth factor (bFGF) is a polypeptide that is mitogenic for a wide variety of cell types. We used Northern blot analysis and immunohistochemistry to determine if bFGF is expressed in the nasal polyp tissue; bFGF messenger RNA was detectable in the polyps examined by Northern blot analysis. Strong immunostaining for bFGF was found in blood vessels and along the basement membrane of the epithelial cell layers. Basal epithelial cells and some infiltrating mononuclear cells also stained for bFGF. Proliferating cell nuclear antigen colocalized with bFGF to basal epithelial cells, endothelial cells, and areas of focal epithelial metaplasia. The polyp tissue was double-labeled with a mouse monoclonal antitryptase, a specific mast cell marker, and anti-bFGF. A significant number (65% +/- 19%) of the bFGF-positive mononuclear cells in the polyp tissues were positive for tryptase. These findings suggest that bFGF may contribute to the endothelial and epithelial proliferation in nasal polyp tissues and that mast cells are one source of this growth factor.

The A326S mutant of Gialpha1 as an approximation of the receptor-bound state.

Agonist-bound heptahelical receptors activate heterotrimeric G proteins by catalyzing exchange of GDP for GTP on their alpha subunits. In search of an approximation of the receptor-alpha subunit complex, we have considered the properties of A326S Gialpha1, a mutation discovered originally in Gsalpha (Iiri, T., Herzmark, P., Nakamoto, J. M., Van Dop, C., and Bourne, H. R. (1994) Nature 371, 164-168) that mimics the effect of receptor on nucleotide exchange. The mutation accelerates dissociation of GDP from the alphai1beta1gamma2 heterotrimer by 250-fold. Nevertheless, affinity of mutant Gialpha1 for GTPgammaS is high in the presence of Mg2+, and the mutation has no effect on the intrinsic GTPase activity of the alpha subunit. The mutation also uncouples two activities of betagamma: stabilization of the GDP-bound alpha subunit (which is retained) and retardation of GDP dissociation from the heterotrimer (which is lost). For wild-type and mutant Gialpha1, beta gamma prevents irreversible inactivation of the alpha subunit at 30 degreesC. However, the mutation accelerates irreversible inactivation of alpha at 37 degreesC despite the presence of beta gamma. Structurally, the mutation weakens affinity for GTPgammaS by steric crowding: a 2-fold increase in the number of close contacts between the protein and the purine ring of the nucleotide. By contrast, we observe no differences in structure at the GDP binding site between wild-type heterotrimers and those containing A326S Gialpha1. However, the GDP binding site is only partially occupied in crystals of G protein heterotrimers containing A326S Gialpha1. In contrast to original speculations about the structural correlates of receptor-catalyzed nucleotide exchange, rapid dissociation of GDP can be observed in the absence of substantial structural alteration of a Galpha subunit in the GDP-bound state.

Variability, reproducibility, and data-collection time of pulmonary bedside monitoring.

Breath-by-breath pulmonary function testing at the bedside is now available both with special-purpose stand-alone equipment and with the new generation of ventilators. The authors studied the variability of, reproducibility of, and ideal length of data collection for nine indices of pulmonary function that may be useful for ventilatory management, weaning, and patient comfort. Work of breathing (as both J/L and J/min), pressure-time product, rapid shallow breathing index, respiratory time fraction, respiratory drive, change in esophageal pressure during inspiration, expiratory airway resistance, and dynamic compliance were measured in ten normal subjects and in eight patients being weaned from mechanical ventilation. All nine indices were reproducible when compared by paired t-test with two separate sets of data collected in normal subjects. Repeated measures in the normal subjects allowed calculation of 95% confidence intervals for the nine variables. There was no statistically significant difference between data collections of 5 minutes compared with those of 10 and 15 minutes. Breath-by-breath variability ranged from a coefficient of variation of 3% for the shallow breathing index in one patient to 131% for the work of breathing in J/min in another. Population variability ranged from values reported previously for other pulmonary parameters to nearly double for some parameters. The authors conclude that a 5-minute data collection time is sufficient to obtain reliable breath-by-breath data at the bedside. While taken together these indices may provide clinically useful information, their usefulness individually remains to be demonstrated because of their large variability.

The "worth" of routine spirometry in a cystic fibrosis clinic.

In our cystic fibrosis clinic, all patients older than 6 years perform spirometry at each visit just before being seen by the health care team. Upon review, we determined that our perceived rationale for this practice was that the medical history fails to detect deterioration in a sizable minority of patients whose pulmonary decline can be detected by spirometry. Furthermore, the literature and our own experience indicates that physical examination frequently will not detect changes in pulmonary status until the changes are advanced. As part of an ongoing quality/cost assessment, we decided to challenge our rationale for performing routine spirometry. Using standard methodology, we developed a six-item Likert style questionnaire, the purpose of which was to assess perceived changes in pulmonary symptoms since the last clinic visit. The questionnaire had an acceptable degree of internal consistency (Cronbach's alpha = 0.92), although the question about sputum production showed the least correlation with responses to other items. We administered the questionnaire to 103 consecutive different patients and examined the association between reported changes in symptoms and actual changes in spirometric outcomes. Overall, there was a statistically significant, but clinically weak association between symptom scores and change in FEV1, r2 = 0.16, P < 0.001. Twenty-three patients had a decline in FEV1 of > or = 10% from one clinic visit to the next. Depending on the method used to place symptom scores into categories indicating that pulmonary symptoms were "worse," "same," or "better" than at the last clinic visit, 40-60% of these 23 patients indicated they felt the "same" or "better." We conclude that spirometry is a justifiable part of all clinic visits for patients with cystic fibrosis, assuming that one would want to detect and treat declines in pulmonary status before they become advanced.

Preparation of multilayered materials in cross-section for in situ TEM tensile deformation studies.

The success of in situ transmission electron microscopy experimentation is often dictated by proper specimen preparation and sample design procedures. We have developed a novel technique permitting the production of tensile specimens of multilayered films in cross-section for in situ deformation studies. Of primary, importance in the development of this technique is the production of an electron transparent micro-gauge section. This micro-gauge section predetermines the position at which plastic deformation, crack nucleation and growth, and failure are observed. In short, we report in detail, a unique combination of specimen preparation procedural steps and the design of a multilayer foil sample. The ability of these procedures to facilitate the success of in situ TEM tensile studies of layered materials in cross-section is demonstrated using a Cu-Zr multilayer foil.