An X-ray ptycho-tomography model of ‘Seeing order in “amorphous” materials’

The nature of the atomic structure of many non-crystalline materials remains a long-standing open question. We use X-ray scattering to model electron images of amorphous materials, where the analogue ‘atoms’ consist of 1μm diameter glass beads. The beads form a substantially random close-packed structure, but are partially ordered in places. X-ray ptycho-tomography reveals the exact position of the beads in 3D and so can be used to compare the modelled electron image with full knowledge of the underlying real structure. Using this, we repeat an experiment reported by Archie Howie and colleagues in 1978 that sought to test for real structure in bright-field electron images of amorphous materials; we demonstrate the validity of the technique, at least in the case of the resolution of the microscopes available at that time and the first Born approximation. We also illustrate how extremely demanding it would have been to infer 3D structure of amorphous material from pairs of stereoscopic images obtained with the same experimental kit: an approach that Archie proposed in the 1970s. We briefly discuss the possibility of using electron ptycho-tomography to solve the amorphous structure problem

Near-field multi-slice ptychography: quantitative phase imaging of optically thick samples with visible light and X-rays

Ptychography is a form of lens-free coherent diffractive imaging now used extensively in electron and synchrotron-based X-ray microscopy. In its near-field implementation, it offers a route to quantitative phase imaging at an accuracy and resolution competitive with holography, with the added advantages of extended field of view and blind deconvolution of the illumination beam profile from the sample image. In this paper we show how near-field ptychography can be combined with a multi-slice model, adding to this list of advantages the unique ability to recover high-resolution phase images of larger samples, whose thickness places them beyond the depth of field of alternative methods

Factors associated with severity of hepatic fibrosis in people with chronic hepatitis C infection

The document attached has been archived with permission from the editor of the Medical Journal of Australia. An external link to the publisher’s copy is included.OBJECTIVE: To determine factors associated with hepatic fibrosis development in people with chronic hepatitis C virus (HCV) infection. METHODS: As a requirement for access to interferon therapy through the S100 scheme in Australia, individual pretreatment demographic and clinical information was collected on 2986 patients from 61 hospital-based liver clinics from 1 October 1994 through 31 December 1996. Patients with both a hepatic fibrosis score and an estimated duration of HCV infection (910) were divided into 540 with no or minimal hepatic fibrosis (stage 0–1) and 370 with moderate to severe hepatic fibrosis (stage 2–3). Seven factors were examined: age at HCV infection, sex, ethnicity, source of infection, duration of infection, alcohol intake, and mean ALT level. A further analysis was performed for all 1135 patients with a hepatic fibrosis score disregarding age at and duration of HCV infection. RESULTS: In multivariate analysis, four factors were significantly associated with moderate to severe hepatic fibrosis: age at infection (OR, 2.33 for age 31–40 years, 5.27 for age > 40 years, and 0.20 for age 30 years, compared with 3 times, compared with 1.5–2 times the upper limit of normal). In the analysis disregarding age at HCV infection and duration of HCV infection, older age was strongly associated with moderate to severe hepatic fibrosis (OR, 2.32 for age 36–40 years, 2.46 for age 41–50 years, 7.87 for age 51–60 years, and 7.15 for age > 60 years, compared with 16–30 years). There was no association in either analysis with sex or source of HCV infection. CONCLUSION: These factors may assist in targeting patients for both liver biopsy-based investigation and therapeutic intervention.Mark Danta, Gregory J Dore, Lisa Hennessy, Yueming Li, Chris R Vickers, Hugh Harley, Meng Ngu, William Reed, Paul V Desmond, William Sievert, Geoff C Farrell, John M Kaldor and Robert G Bate

Operando and High-throughput multicscale-tomography

We report about multiscale tomography with high throughput at the Diamond beamline I13L. The beamline has the purpose of multi-scale and operando imaging and consists of two independent branchlines operating in real and reciprocal space. The imaging branch -called Diamond-Manchester branchline- hosts micro-tomography, grating interferometry and a full-field microscope. For rapid recording a broad spectrum of the undulator radiation is used either with band-passing the light with a combination of a filter and a deflecting mirror or using a multilayer monochromator. For all the methods similar recording times can be achieved, with typical scanning times of some minutes and covering the resolution range from microns to the 100nm range. Most recently a robot arm has been installed to increase the throughput to 300 samples per day. The system is now implemented for user operation in remote operation mode for the micro-tomography setup and can be expanded to the two other experiments. The instrumental capabilities are applied on various topics such as the study of biodiversity of insects or the structural variations of electrode materials in batteries. Fast recording with dedicated sample environments (not using the sample changing robot) enables operando studies in many areas, the charging/discharging cycles on batteries, the degradation of teeth enamel under various conditions or loading brine sandstone mixtures with CO2, to name some examples. For imaging with highest spatial resolution we managed to improve significantly the recording speed of ptycho-tomography, which is now in the order of hours and will be reduced further. We demonstrated in the past 2-D recording with 10kHz and expand the instrumental capability with specific hardware dependent triggering and scanning schemes. We expand the research program for multi-scale imaging across both branchlines (imaging and coherence branchlines) with first studies such as batteries, brain research, concrete

Optical autocollimator for vibration measurements at Diamond I13 beamline

I13 is a 250 m long hard X ray beamline for imaging and coherence experiments at the Diamond Light Source. The beamline comprises two independent experimental branches one for imaging in direct space using X ray microscopy and one for imaging in reciprocal space using coherent imaging techniques. The mechanical stability is very important for implementation of increased capabilities at latest generation of long beamlines. Therefore, the beam stability monitoring is essential part of the day to day operation of the beamlines as well as for analysis of mechanical instability sources for the Diamond II upgrade. In this paper we present the setup developed to measure mechanical stability of beamline based on optical autocollimato

The Structure of a Rigorously Conserved RNA Element within the SARS Virus Genome

We have solved the three-dimensional crystal structure of the stem-loop II motif (s2m) RNA element of the SARS virus genome to 2.7-Å resolution. SARS and related coronaviruses and astroviruses all possess a motif at the 3′ end of their RNA genomes, called the s2m, whose pathogenic importance is inferred from its rigorous sequence conservation in an otherwise rapidly mutable RNA genome. We find that this extreme conservation is clearly explained by the requirement to form a highly structured RNA whose unique tertiary structure includes a sharp 90° kink of the helix axis and several novel longer-range tertiary interactions. The tertiary base interactions create a tunnel that runs perpendicular to the main helical axis whose interior is negatively charged and binds two magnesium ions. These unusual features likely form interaction surfaces with conserved host cell components or other reactive sites required for virus function. Based on its conservation in viral pathogen genomes and its absence in the human genome, we suggest that these unusual structural features in the s2m RNA element are attractive targets for the design of anti-viral therapeutic agents. Structural genomics has sought to deduce protein function based on three-dimensional homology. Here we have extended this approach to RNA by proposing potential functions for a rigorously conserved set of RNA tertiary structural interactions that occur within the SARS RNA genome itself. Based on tertiary structural comparisons, we propose the s2m RNA binds one or more proteins possessing an oligomer-binding-like fold, and we suggest a possible mechanism for SARS viral RNA hijacking of host protein synthesis, both based upon observed s2m RNA macromolecular mimicry of a relevant ribosomal RNA fold