VerSoX B07-B: a high-throughput XPS and ambient pressure NEXAFS beamline at Diamond Light Source.

The beamline optics and endstations at branch B of the Versatile Soft X-ray (VerSoX) beamline B07 at Diamond Light Source are described. B07-B provides medium-flux X-rays in the range 45-2200 eV from a bending magnet source, giving access to local electronic structure for atoms of all elements from Li to Y. It has an endstation for high-throughput X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine-structure (NEXAFS) measurements under ultrahigh-vacuum (UHV) conditions. B07-B has a second endstation dedicated to NEXAFS at pressures from UHV to ambient pressure (1 atm). The combination of these endstations permits studies of a wide range of interfaces and materials. The beamline and endstation designs are discussed in detail, as well as their performance and the commissioning process.

Ambient-pressure endstation of the Versatile Soft X-ray (VerSoX) beamline at Diamond Light Source.

The ambient-pressure endstation and branchline of the Versatile Soft X-ray (VerSoX) beamline B07 at Diamond Light Source serves a very diverse user community studying heterogeneous catalysts, pharmaceuticals and biomaterials under realistic conditions, liquids and ices, and novel electronic, photonic and battery materials. The instrument facilitates studies of the near-surface chemical composition, electronic and geometric structure of a variety of samples using X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine-structure (NEXAFS) spectroscopy in the photon energy range from 170 eV to 2800 eV. The beamline provides a resolving power hν/Δ(hν) > 5000 at a photon flux > 1010 photons s-1 over most of its energy range. By operating the optical elements in a low-pressure oxygen atmosphere, carbon contamination can be almost completely eliminated, which makes the beamline particularly suitable for carbon K-edge NEXAFS. The endstation can be operated at pressures up to 100 mbar, whereby XPS can be routinely performed up to 30 mbar. A selection of typical data demonstrates the capability of the instrument to analyse details of the surface composition of solid samples under ambient-pressure conditions using XPS and NEXAFS. In addition, it offers a convenient way of analysing the gas phase through X-ray absorption spectroscopy. Short XPS spectra can be measured at a time scale of tens of seconds. The shortest data acquisition times for NEXAFS are around 0.5 s per data point.

1 m long multilayer-coated deformable piezoelectric bimorph mirror for adjustable focusing of high-energy X-rays.

The Diamond Light Source (DLS) beamline I15-1 measures atomic pair distribution functions (PDF) using scattering of 40-80 keV X-rays. A unique focusing element was needed to condense these X-rays from an initial large cross section (11.0 mm H × 4.2 mm V) into a required spot size of FWHM ≈680 µm (H) × 20 µm (V) at a variable position between the sample and the detector. The large numerical aperture is achieved by coating a silicon substrate over 1 m long with three multilayer stripes of Bragg angle 4.2 mrad. One stripe selects X-rays of each energy 40.0, 65.4, and 76.6 keV. Sixteen piezoelectric bimorph actuators attached to the sides of the mirror substrate adjusted the reflecting surface's shape. Focal spots of vertical width < 15 µm were obtained at three positions over a 0.92 m range, with fast, easy switching from one focal position to another. Minimized root mean square slope errors were close to 0.5 µrad after subtraction of a uniform curvature. Reflectivity curves taken along each stripe showed consistent high peaks with generally small angular variation of peak positions. This is the first application of a 1 m long multilayer-coated bimorph mirror at a synchrotron beamline. Data collected with its help on a slice of a lithium ion battery's cathode are presented.

Temporal deletion of Arl13b reveals that a mispatterned neural tube corrects cell fate over time.

Cilia are necessary for sonic hedgehog (Shh) signaling, which is required to pattern the neural tube. We know that ventral neural cell fates are defined by a specific cohort of transcription factors that are induced by distinct thresholds of Shh activity mediated by opposing gradients of Gli activator (GliA) and Gli repressor (GliR). Despite this understanding, the role of Shh as an instructive morphogen is viewed as increasingly complex, with current models integrating positive inputs in terms of ligand concentration and time, along with negative feedback via the downstream gene regulatory network. To investigate the relative contributions of the positive and negative inputs from Shh signaling in neural patterning, we took advantage of a protein that uncouples the regulation of GliA and GliR: the cilia protein ADP-ribosylation factor-like 13b (Arl13b). By deleting Arl13b in mouse, we induced low-level constitutive GliA function at specific developmental stages and defined a crucial period prior to E10.5 when shifts in the level of GliA cause cells to change their fate. Strikingly, we found that improperly patterned cells in these mice converted to the wild-type pattern by E12.5. We further showed that the recovery of patterning did not occur when we also deleted Gli3, the primary GliR in the neural tube, revealing a crucial role of Gli3 in the maintenance of neural patterning.

The 'Necksafe' head articulation control system: a novel cervical immobilisation device.

INTRODUCTION: The early application of a semirigid disposable cervical collar following trauma is considered a routine practice. The aim of these devices is to immobilise the cervical spine and minimise the risk of additional neurological damage. However, these collars provide only partial immobilisation, are uncomfortable and are associated with a number of complications. Our team designed and tested a novel cervical immobilisation device that aims to improve immobilisation with reduced complications: the 'Necksafe'. METHODS: Human volunteers were recruited and consented to test the novel Necksafe device in comparison with a conventional collar (the AMBU Perfit ACE) in a range of evaluations. These included assessments of the cervical range of movement (CROM) that occurred during scripted movements of the head and neck, and the effect of the new and conventional devices on jugular vein dimensions, assessed using ultrasound scanning. RESULTS: CROM analysis showed that, under standardised testing conditions, the Necksafe device offers cervical immobilisation that is at least equivalent to a conventional collar, and is superior in the planes of extension, lateral flexion and rotation. Ultrasound examination of the jugular veins was inconclusive and did not reveal any differences in jugular venous diameter or flow. Qualitative feedback from ambulance paramedics was highly supportive of the new design, suggesting that it is more comfortable, easier to fit, less confining and better tolerated than a conventional collar, with improved immobilisation effectiveness. CONCLUSIONS: The results of quantitative and qualitative testing are highly supportive of the new Necksafe design, with improved cervical immobilisation, comfort and access to the airway.

Mitochondrial retention of Opa1 is required for mouse embryogenesis.

Mitochondria are dynamic cellular organelles that balance fission and fusion to regulate organelle morphology, distribution, and activity, and Opa1 is one of three GTPases known to regulate mitochondrial fusion. In humans, loss of a single Opa1 allele causes dominant optic atrophy, a degenerative condition that leads to loss of vision. Here we demonstrate that the lilR3 mutant mouse phenotype is due to a point mutation in the Opa1 gene resulting in mislocalized Opa1 protein from the mitochondria to the cytosol. Importantly, the mutation is in the middle domain of the Opa1 protein, for which no function had been described. Lack of mitochondrial retention of Opa1 is sufficient to cause the cellular Opa1 loss-of-function phenotype as the mitochondria are fragmented, indicating an inability to fuse. Despite the normally ubiquitous expression of Opa1 and the essential nature of mitochondria, embryos with aberrant Opa1 survived through midgestation and died at E11.5. These mutants displayed growth retardation, exencephaly, and abnormal patterning along the anterior-posterior axis, although the A-P axis itself was intact. The complex relationship between mitochondrial dynamics and cell death is emphasized by apoptosis in specific cell populations of lilR3 embryos. Our results define, for the first time, a function of the middle domain of the Opa1 protein and demonstrate that mitochondrial retention of Opa1 protein is essential for normal embryogenesis.

Inter-comparison of Low-cost Sensors for Measuring the Mass Concentration of Occupational Aerosols.

Low-cost sensors are effective for measuring the mass concentration of ambient aerosols and secondhand smoke in homes, but their use at concentrations relevant to occupational settings has not been demonstrated. We measured the concentrations of four aerosols (salt, Arizona road dust, welding fume, and diesel exhaust) with three types of low-cost sensors (a DC1700 from Dylos and two commodity sensors from Sharp), an aerosol photometer, and reference instruments at concentrations up to 6500 µg/m3. Raw output was used to assess sensor precision and develop equations to compute mass concentrations. EPA and NIOSH protocols were used to assess the mass concentrations estimated with low-cost sensors compared to reference instruments. The detection efficiency of the DC1700 ranged from 0.04% at 0.1 µm to 108% at 5 µm, as expected, although misclassification of fine and coarse particles was observed. The raw output of the DC1700 had higher precision (lower coefficient of variation, CV = 7.4%) than that of the two sharp devices (CV = 25% and 17%), a finding attributed to differences in manufacturer calibration. Aerosol type strongly influenced sensor response, indicating the need for on-site calibration to convert sensor output to mass concentration. Once calibrated, however, the mass concentration estimated with low-cost sensors was highly correlated with that of reference instruments (R2=0.99). These results suggest that the DC1700 and Sharp sensors are useful in estimating aerosol mass concentration for aerosols at concentrations relevant to the workplace.

A novel instrument for generating angular increments of 1 nanoradian.

Accurate generation of small angles is of vital importance for calibrating angle-based metrology instruments used in a broad spectrum of industries including mechatronics, nano-positioning, and optic fabrication. We present a novel, piezo-driven, flexure device capable of reliably generating micro- and nanoradian angles. Unlike many such instruments, Diamond Light Source's nano-angle generator (Diamond-NANGO) does not rely on two separate actuators or rotation stages to provide coarse and fine motion. Instead, a single Physik Instrumente NEXLINE "PiezoWalk" actuator provides millimetres of travel with nanometre resolution. A cartwheel flexure efficiently converts displacement from the linear actuator into rotary motion with minimal parasitic errors. Rotation of the flexure is directly measured via a Magnescale "Laserscale" angle encoder. Closed-loop operation of the PiezoWalk actuator, using high-speed feedback from the angle encoder, ensures that the Diamond-NANGO's output drifts by only ∼0.3 nrad rms over ∼30 min. We show that the Diamond-NANGO can reliably move with unprecedented 1 nrad (∼57 ndeg) angular increments over a range of >7000 µrad. An autocollimator, interferometer, and capacitive displacement sensor are used to independently confirm the Diamond-NANGO's performance by simultaneously measuring the rotation of a reflective cube.

Relative impact of covariates in prescribing warfarin according to CYP2C9 genotype.

Patients on warfarin anticoagulant therapy demonstrate wide variation in maintenance dose. Patients possessing variants (*2 and *3) of the cytochrome P450 2C9 gene require reduced maintenance doses compared to those having wild-type alleles (*1). Many other clinical factors have been shown to affect warfarin dose as well. To determine the relative impact of CYP2C9 genotype, age, gender, body surface area, concomitant medication, treatment indication and comorbidity, we conducted a retrospective cohort study in 453 patients managed by the anticoagulation service of a large, horizontally integrated, multispecialty group practice. In this largely Caucasian patient population, the CYP2C9 gene frequencies for *1/*1, *1/*2, *1/*3, *2/*2, *2/*3 and *3/*3 were 65.1%, 19.0%, 12.1%, 1.6%, 1.8% and 0.4%, respectively, approximating Hardy-Weinberg equilibrium. Mean maintenance doses for these genotypes were 36.5, 29.1, 23.5, 28.0, 18.1 and 5.5 mg/week, respectively. In univariate analyses, genotype alone accounted for 19.8% of the variability in maintenance dose. Age, body surface area and male gender accounted for 14.6%, 7.5% and 4.7%, respectively, while cardiac valve replacement as the indication for warfarin accounted for 5.4% of the variability. Collectively, these factors accounted for 33.7% of all dosing variability according to multiple regression. These results will help strengthen the mathematical models that are currently being developed for prospective gene-based warfarin dosing.

Death receptor 5 regulation during selenium-mediated apoptosis in human prostate cancer cells.

Selenium is an essential micronutrient that is currently being tested for prostate cancer chemoprevention. In spite of its significant promise as a chemopreventive agent, the molecular mechanisms of selenium-mediated effects remain to be elucidated. Recent evidence suggests that selenium may mediate its chemopreventive effects by inducing apoptosis in human prostate cancer cells. Here we report that selenium-mediated apoptosis appears to involve membrane death receptor, DR5-dependent pathway in human prostate cancer cells. Selenium specifically upregulated DR5 expression but not that of DR4. Selenium upregulation of DR5 was coupled with caspase 8 activation and Bid cleavage thereby suggesting the existence of a potential cross-talk between the DR5 and the mitochondrial pathways. Thus, our results suggest that DR5 is specifically regulated by selenium and its activation may play an important role in selenium-mediated chemoprevention.

Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans.

Since its identification in April 2009, an A(H1N1) virus containing a unique combination of gene segments from both North American and Eurasian swine lineages has continued to circulate in humans. The lack of similarity between the 2009 A(H1N1) virus and its nearest relatives indicates that its gene segments have been circulating undetected for an extended period. Its low genetic diversity suggests that the introduction into humans was a single event or multiple events of similar viruses. Molecular markers predictive of adaptation to humans are not currently present in 2009 A(H1N1) viruses, suggesting that previously unrecognized molecular determinants could be responsible for the transmission among humans. Antigenically the viruses are homogeneous and similar to North American swine A(H1N1) viruses but distinct from seasonal human A(H1N1).

Impact of age, CYP2C9 genotype and concomitant medication on the rate of rise for prothrombin time during the first 30 days of warfarin therapy.

OBJECTIVES: To characterize the impact of several important clinical variables on the rate of anticoagulation during warfarin initiation (i.e., the first 30 days). DESIGN: Retrospective study. SETTING: An anticoagulation service of a large horizontally integrated, multispecialty group practice in central and northern Wisconsin. PARTICIPANTS: Patients with sufficient laboratory data obtained during the initiation phase of warfarin treatment. METHODS: Patients were consented and genotyped for cytochrome P450 (CYP) 2C9 polymorphisms. Anticoagulation laboratory data were then electronically abstracted and fitted to a logistic growth model. Rate of anticoagulation was compared between groups. RESULTS: During warfarin initiation, the mean slope for rise in International Normalized Ratio (INR) of prothrombin time was significantly associated with age (p = 0.03, n = 166). Because a relationship between diabetes and warfarin dosing has been suggested previously, we assessed the impact of this comorbidity in our model as well. Diabetes showed relatively little impact, but concomitant treatment with an anti-diabetic sulfonylurea medication was associated with an increase in slope (3-fold, p < 0.05). Since this drug interaction may occur at the level of CYP2C9, we also assessed the impact of CYP2C9 genotype in our model. The impact of CYP2C9 genotype was marginally significant (p = 0.119, non-pooled dataset; p = 0.053, data pooled for CYP2C9 *2/*2, *2/*3 and *3/*3). CONCLUSIONS: Age and concomitant sulfonylurea therapy alter the rate of anticoagulation during the first 30 days of warfarin therapy.

A prospective, randomized pilot trial of model-based warfarin dose initiation using CYP2C9 genotype and clinical data.

BACKGROUND: Rapid genetic screening for cytochrome P450 (CYP) 2C9 variants may play a role in improving the efficacy and safety of warfarin in individuals with CYP2C9 variants. The feasibility of prospective CYP2C9 model-based warfarin dosing has not yet been assessed. OBJECTIVES: To evaluate the feasibility of applying a CYP2C9 gene-based warfarin dosing model in clinical practice. DESIGN: Prospective, randomized, single-blinded clinical pilot trial. SETTING: Large multispecialty group practice. PATIENTS: Candidates were recruited from a list of clinic patients eligible for warfarin initiation. This included patients with newly diagnosed thromboembolic disease or atrial arrhythmia, as well as patients anticipating elective valvuloplasty or arthroplasty. Patients who previously received warfarin were excluded. INTERVENTIONS: Subjects were randomized to receive either 1) a standard initiation dose of 5 mg warfarin/day, or 2) rapid CYP2C9 genotyping and an initiation dose determined using parameters estimated from a previously published multivariate model [including age, body size, co-morbidity (e.g., diabetes), clinical indication (e.g., valvuloplasty) and CYP2C9 genotype]. MEASUREMENTS: Primary outcome measurements were patient willingness to participate, physician willingness to refer, sample processing time, ability to administer calculated dosage and adequacy of follow-up. LIMITATIONS: This pilot trial was designed to assess the feasibility of model-based warfarin dosing. Power was insufficient for statistical comparison of adverse event rates. RESULTS: Forty-three of 117 patients had no prior warfarin treatment and were eligible. Five declined to participate. Twenty patients were randomized to a standard initiation dose of 5 mg daily. Eighteen patients were randomized to model-based dosing. All but one participant received the assigned initiation dose. Blood draw to dosage calculation time (including genotyping) required approximately 4 hours. Six adverse events occurred within the standard dosing group, and two adverse events occurred within the model-based dosing group. CONCLUSIONS: Prospective application of a multivariate CYP2C9 gene-based warfarin dosing model is feasible.