Inter-Bragg crystallographic phase retrieval from shape transforms, stacking faults and substitutional disorder.

One of the brilliant ideas of John Spence when he saw the first diffraction patterns from the Linac Coherent Light Source was that one could solve the crystallographic phase problem by utilising the intensities between Bragg peaks. Because these intensities are due to the Fourier transform of the shape of the crystal, the approach came to be known as "shape-transform phasing." Shape-transform phasing was developed over the next ten years and formed the basis for many other interesting ideas and pursuits. Here we describe the current best implementation of the original idea using a lattice occupancy formalism and show that certain types of crystal defects can also be modelled via this approach, allowing the molecular structure to be recovered from the additional information offered by the inter-Bragg intensities from these crystal defects.

The serial millisecond crystallography instrument at the Australian Synchrotron incorporating the "Lipidico" injector.

A serial millisecond crystallography (SMX) facility has recently been implemented at the macromolecular crystallography beamline, MX2 at the Australian Synchrotron. The setup utilizes a combination of an EIGER X 16M detector system and an in-house developed high-viscosity injector, "Lipidico." Lipidico uses a syringe needle to extrude the microcrystal-containing viscous media and it is compatible with commercially available syringes. The combination of sample delivery via protein crystals suspended in a viscous mixture and a millisecond frame rate detector enables high-throughput serial crystallography at the Australian Synchrotron. A hit-finding algorithm, based on the principles of "robust-statistics," is employed to rapidly process the data. Here we present the first SMX experimental results with a detector frame rate of 100 Hz (10 ms exposures) and the Lipidico injector using a mixture of lysozyme microcrystals embedded in high vacuum silicon grease. Details of the experimental setup, sample injector, and data analysis pipeline are designed and developed as part of the Australian Synchrotron SMX instrument and are reviewed here.

Is radiation damage the limiting factor in high-resolution single particle imaging with X-ray free-electron lasers?

The prospect of single particle imaging with atomic resolution is one of the scientific drivers for the development of X-ray free-electron lasers. The assumption since the beginning has been that damage to the sample caused by intense X-ray pulses is one of the limiting factors for achieving subnanometer X-ray imaging of single particles and that X-ray pulses need to be as short as possible. Based on the molecular dynamics simulations of proteins in X-ray fields of various durations (5 fs, 25 fs, and 50 fs), we show that the noise in the diffracted signal caused by radiation damage is less than what can be expected from other sources, such as sample inhomogeneity and X-ray shot-to-shot variations. These findings show a different aspect of the feasibility of high-resolution single particle imaging using free-electron lasers, where employing X-ray pulses of longer durations could still provide a useful diffraction signal above the noise due to the Coulomb explosion.

Esophageal hypermotility: cause or effect?

Nutcracker esophagus (NE), Jackhammer esophagus (JHE), distal esophageal spasm (DES), and hypertensive lower esophageal sphincter (HTLES) are defined by esophageal manometric findings. Some patients with these esophageal motility disorders also have abnormal gastroesophageal reflux. It is unclear to what extent these patients' symptoms are caused by the motility disorder, the acid reflux, or both. The aim of this study was to determine the effectiveness of laparoscopic Nissen fundoplication (LNF) on esophageal motility disorders, gastroesophageal reflux, and patient symptoms. Between 2007 and 2013, we performed high-resolution esophageal manometry on 3400 patients, and 221 patients were found to have a spastic esophageal motility disorder. The medical records of these patients were reviewed to determine the manometric abnormality, presence of gastroesophageal symptoms, and amount of esophageal acid exposure. In those patients that underwent LNF, we compared pre- and postoperative esophageal motility, gastroesophageal symptom severity, and esophageal acid exposure. Of the 221 patients with spastic motility disorders, 77 had NE, 2 had JHE, 30 had DES, and 112 had HTLES. The most frequently reported primary and secondary symptoms among all patients were: heartburn and/or regurgitation, 69.2%; respiratory, 39.8%; dysphagia, 35.7%; and chest pain, 22.6%. Of the 221 patients, 192 underwent 24-hour pH monitoring, and 103 demonstrated abnormal distal esophageal acid exposure. Abnormal 24-hour pH monitoring was detected in 62% of patients with heartburn and regurgitation, 49% of patients with respiratory symptoms, 36.8 % of patients with dysphagia, and 32.6% of patients with chest pain. Sixty-six of the 103 patients with abnormal 24-hour pH monitoring underwent LNF. Thirty-eight (13NE, 2JHE, 6 DES, and 17 HTLES) of these 66 patients had a minimum of 6-month postoperative follow-up that included clinical evaluation, esophageal manometry, and 24-hour pH monitoring. Postoperatively, all 38 patients had normal distal esophageal acid exposure. Of these 38 patients, symptoms resolved in 28 and improved in 10. Of six patients (one with NE, two JHE, and three with HTLES) that underwent postoperative esophageal manometry, five exhibited normal motility. Typical reflux symptoms are common among patients with esophageal hypermotility disorders. Abnormal 24-hour pH monitoring is present in the majority of patients with who report typical reflux symptoms and almost half of patients who report respiratory symptoms. Conversely, the majority of patients who report dysphagia or chest pain have normal distal esophageal acid exposure. Based on a small number of patients in this study, it also appears that motility disorders often improve after LNF. LNF is associated with resolution or improvement in reflux related symptoms and esophageal motility parameters in patients exhibiting abnormal esophageal acid exposure. This suggests that patient symptoms are due to abnormal acid exposure and not the motility disorder.

Toward atomic resolution diffractive imaging of isolated molecules with X-ray free-electron lasers.

We give a detailed account of the theoretical analysis and the experimental results of an X-ray-diffraction experiment on quantum-state selected and strongly laser-aligned gas-phase ensembles of the prototypical large asymmetric rotor molecule 2,5-diiodobenzonitrile, performed at the Linac Coherent Light Source [Phys. Rev. Lett.112, 083002 (2014)]. This experiment is the first step toward coherent diffractive imaging of structures and structural dynamics of isolated molecules at atomic resolution, i.e., picometers and femtoseconds, using X-ray free-electron lasers.

Ultrafast X-ray probing of water structure below the homogeneous ice nucleation temperature.

Water has a number of anomalous physical properties, and some of these become drastically enhanced on supercooling below the freezing point. Particular interest has focused on thermodynamic response functions that can be described using a normal component and an anomalous component that seems to diverge at about 228 kelvin (refs 1-3). This has prompted debate about conflicting theories that aim to explain many of the anomalous thermodynamic properties of water. One popular theory attributes the divergence to a phase transition between two forms of liquid water occurring in the 'no man's land' that lies below the homogeneous ice nucleation temperature (TH) at approximately 232 kelvin and above about 160 kelvin, and where rapid ice crystallization has prevented any measurements of the bulk liquid phase. In fact, the reliable determination of the structure of liquid water typically requires temperatures above about 250 kelvin. Water crystallization has been inhibited by using nanoconfinement, nanodroplets and association with biomolecules to give liquid samples at temperatures below TH, but such measurements rely on nanoscopic volumes of water where the interaction with the confining surfaces makes the relevance to bulk water unclear. Here we demonstrate that femtosecond X-ray laser pulses can be used to probe the structure of liquid water in micrometre-sized droplets that have been evaporatively cooled below TH. We find experimental evidence for the existence of metastable bulk liquid water down to temperatures of 227(-1)(+2) kelvin in the previously largely unexplored no man's land. We observe a continuous and accelerating increase in structural ordering on supercooling to approximately 229 kelvin, where the number of droplets containing ice crystals increases rapidly. But a few droplets remain liquid for about a millisecond even at this temperature. The hope now is that these observations and our detailed structural data will help identify those theories that best describe and explain the behaviour of water.

The extraction of single-particle diffraction patterns from a multiple-particle diffraction pattern.

The structures of biological molecules may soon be determined with X-ray free-electron lasers without crystallization by recording the coherent diffraction patterns of many identical copies of a molecule. Most analysis methods require a measurement of each molecule individually. However, current injection methods deliver particles to the X-ray beam stochastically and the maximum yield of single particle measurements is 37% at optimal concentration. The remaining 63% of pulses intercept no particles or multiple particles. We demonstrate that in the latter case single particle diffraction patterns can be extracted provided the particles are sufficiently separated. The technique has the potential to greatly increase the amount of data available for three-dimensional imaging of identical particles with X-ray lasers.

Single-particle structure determination by correlations of snapshot X-ray diffraction patterns.

Diffractive imaging with free-electron lasers allows structure determination from ensembles of weakly scattering identical nanoparticles. The ultra-short, ultra-bright X-ray pulses provide snapshots of the randomly oriented particles frozen in time, and terminate before the onset of structural damage. As signal strength diminishes for small particles, the synthesis of a three-dimensional diffraction volume requires simultaneous involvement of all data. Here we report the first application of a three-dimensional spatial frequency correlation analysis to carry out this synthesis from noisy single-particle femtosecond X-ray diffraction patterns of nearly identical samples in random and unknown orientations, collected at the Linac Coherent Light Source. Our demonstration uses unsupported test particles created via aerosol self-assembly, and composed of two polystyrene spheres of equal diameter. The correlation analysis avoids the need for orientation determination entirely. This method may be applied to the structural determination of biological macromolecules in solution.

A scheme for lensless X-ray microscopy combining coherent diffraction imaging and differential corner holography.

We successfully use the corners of a common silicon nitride supporting window in lensless X-ray microscopy as extended references in differential holography to obtain a real space hologram of the illuminated object. Moreover, we combine this method with the iterative phasing techniques of coherent diffraction imaging to enhance the spatial resolution on the reconstructed object, and overcome the problem of missing areas in the collected data due to the presence of a beam stop, achieving a resolution close to 85 nm.

Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight.

The morphology of micrometre-size particulate matter is of critical importance in fields ranging from toxicology to climate science, yet these properties are surprisingly difficult to measure in the particles' native environment. Electron microscopy requires collection of particles on a substrate; visible light scattering provides insufficient resolution; and X-ray synchrotron studies have been limited to ensembles of particles. Here we demonstrate an in situ method for imaging individual sub-micrometre particles to nanometre resolution in their native environment, using intense, coherent X-ray pulses from the Linac Coherent Light Source free-electron laser. We introduced individual aerosol particles into the pulsed X-ray beam, which is sufficiently intense that diffraction from individual particles can be measured for morphological analysis. At the same time, ion fragments ejected from the beam were analysed using mass spectrometry, to determine the composition of single aerosol particles. Our results show the extent of internal dilation symmetry of individual soot particles subject to non-equilibrium aggregation, and the surprisingly large variability in their fractal dimensions. More broadly, our methods can be extended to resolve both static and dynamic morphology of general ensembles of disordered particles. Such general morphology has implications in topics such as solvent accessibilities in proteins, vibrational energy transfer by the hydrodynamic interaction of amino acids, and large-scale production of nanoscale structures by flame synthesis.

Femtosecond dark-field imaging with an X-ray free electron laser.

The emergence of femtosecond diffractive imaging with X-ray lasers has enabled pioneering structural studies of isolated particles, such as viruses, at nanometer length scales. However, the issue of missing low frequency data significantly limits the potential of X-ray lasers to reveal sub-nanometer details of micrometer-sized samples. We have developed a new technique of dark-field coherent diffractive imaging to simultaneously overcome the missing data issue and enable us to harness the unique contrast mechanisms available in dark-field microscopy. Images of airborne particulate matter (soot) up to two microns in length were obtained using single-shot diffraction patterns obtained at the Linac Coherent Light Source, four times the size of objects previously imaged in similar experiments. This technique opens the door to femtosecond diffractive imaging of a wide range of micrometer-sized materials that exhibit irreproducible complexity down to the nanoscale, including airborne particulate matter, small cells, bacteria and gold-labeled biological samples.

Synopsis of investigations into proposed theories on the etiology of achalasia.

The current state of research into the etiology of achalasia only allows for speculation. To date, several studies have been performed investigating genetic, immune, and infectious disease mechanisms; however, none of these have been conclusive. Further research into this topic is warranted given the severity of the disease, and it may be possible that all of these mechanisms are involved in the pathophysiology of the disease.

Direct exit-wave reconstruction from a single defocused image.

We propose a direct, non-iterative method for the exact recovery of the complex wave in the exit-surface plane of a coherently illuminated object from a single defocused image. The method is applicable for a wide range of illumination conditions. The defocus range is subject to certain conditions, which if satisfied allow the complex exit-surface wave to be directly recovered by solving a set of linear equations. These linear equations, whose coefficients depend on the incident illumination, are obtained by analyzing the autocorrelation function of an auxiliary wave which is related to the exit-surface wave in a simple way. This autocorrelation is constructed by taking the inverse Fourier transform of the defocused image. We present an experimental proof of concept by recovering the exit-surface wave of a microfiber illuminated by a plane wave formed using a HeNe laser.

Theoretical estimation for correlations of diffraction patterns from objects differently oriented in space.

Coherent diffraction imaging of single biomolecules is expected to open unique opportunities for studies of non-crystalline samples. There are, however, still many technical and physical issues that need to be resolved in a more quantitative manner, especially if one aims for structural information at high resolution. Signal recorded from an object after a single shot is low. As primarily proposed in Spence and Doak (2004) and Huldt et al. (2003), averaging over the diffraction patterns from many different shots is necessary, in order to achieve a signal-to-noise ratio sufficient for image reconstruction. The images of the randomly oriented molecules have to be sorted out in order to identify those corresponding to the similar spatial orientations of the objects. This procedure is called the classification of diffraction images. Here we approach the classification in the framework of pattern-to-pattern correlations, and analyse theoretically the correlations between diffraction images of differently oriented objects.

Practical implementation of a direct method for coherent diffractive imaging.

We experimentally implement a direct, non-iterative method for recovering the complex wave in the exit-surface plane of a coherently illuminated object. The form of illumination is subject to certain conditions. By satisfying these conditions, the complex exit-surface wave is directly recovered from a single far-field intensity pattern, by solving a set of linear equations. These linear equations, whose coefficients depend on the incident illumination, are obtained by analyzing the autocorrelation function of the exit-surface wave. This autocorrelation is constructed by taking the inverse Fourier transform of the diffraction pattern. We introduce a preconditioning step, for the system of linear equations, which improves the robustness of the method to noise. While the present experimental proof of concept has been performed using a visible-light laser, the method is applicable to diffractive imaging using coherent X-ray and electron sources.

Prevalence of respiratory symptoms in patients with achalasia.

Achalasia is a primary esophageal motor disorder that results in poor clearance of the esophagus. Although an esophagus filled with debris and undigested food should put these patients at risk for aspiration, the frequency with which the latter occurs has never been documented. In this study, we sought to determine the incidence of respiratory symptoms and complaints in patients with achalasia. A comprehensive symptom questionnaire was administered to 110 patients with achalasia presenting to the Swallowing Center at the University of Washington between 1994 and 2008 as part of their preoperative work-up. Questionnaires were analyzed for the frequency of respiratory complaints in addition to the more typical symptoms of dysphagia, regurgitation, and chest pain. Twenty-two achalasia patients with respiratory symptoms who had also undergone Heller myotomy and completed a post-op follow-up questionnaire were analyzed as a subset. Ninety-five patients (86%) complained of at least daily dysphagia. Fifty-one patients (40%) reported the occurrence of at least one respiratory symptom daily, including cough in 41 patients (37%), aspiration (the sensation of inhaling regurgitated esophagogastric material) in 34 patients (31%), hoarseness in 23 patients (21%), wheezing in 17 patients (15%), shortness of breath in 11 patients (10%), and sore throat in 13 patients (12%). Neither age nor gender differed between those with and those without respiratory symptoms. In the subset of patients with respiratory symptoms who had undergone Heller myotomy, respiratory symptoms improved in the majority after the procedure. Patients with achalasia experience respiratory symptoms with much greater frequency than the approximately 10% that was previously believed. Awareness of this association may be important in the workup and ultimate treatment of patients with this uncommon esophageal disorder.

A method for correcting the effect of specimen drift on coherent diffractive imaging.

Coherent diffractive imaging involves the inversion of a diffraction pattern to find the wave function at the exit-surface plane of the specimen. It is a promising technique for imaging, for example, nanoparticles with electrons and biological molecules with X-rays. If the illumination is not a plane wave of infinite extent, then a relative drift between the illumination and the object introduces errors into the diffraction pattern; an issue which is often overlooked. This may be of particular importance for applications with electron microscopes which use nanoscale probes. Here we show that beams which are uniform over a sufficiently large region can be used to pose a phase retrieval problem that is immune from specimen drift, provided suitable analysis of the diffraction data is undertaken. The method only applies to objects contained within a support that is smaller than a uniform region of the beam.

Spatial incoherence in phase retrieval based on focus variation.

We investigate the effect of spatial incoherence on two methods of phase retrieval based on focus variation: the transport of intensity equation and iterative wave function reconstruction. Spatial incoherence provides an upper bound on the defocus step size which should be used in each case. The requirement that phase information manifests itself in sufficient variation in the defocused images provides a lower bound on the defocus step size which should be used in each case. The scaling of these upper and lower bounds with object size and imaging resolution differs in such a way that, given the spatial incoherence properties of the source, for sufficiently low resolutions neither technique can retrieve phase information. The regions of applicability of the two techniques are discussed.

Rupture of abdominal aortic aneurysm with tear of inferior vena cava in a patient with prior endograft.

We report a case of contained rupture of abdominal aortic aneurysm and tear of the inferior vena cava (IVC) 15 months after placement of an aortic endograft (ANEURX graft, Medtronic, Sunnyvale, Calif). A 63-year-old man with significant coronary artery disease underwent endograft exclusion of abdominal aortic aneurysm with Aneurx graft. The patient was seen with a rupture of the aortic aneurysm, probably caused by poor proximal fixation of the graft associated with separation of the left iliac extension limb from the main body of the graft. Angulated right iliac limb of the stent graft penetrated into the Ivc just above the common iliac junction and caused sealed perforation. Successful repair with aortobiiliac graft reconstruction after removal of the endograft was accomplished. The IVC laceration was repaired. Possible mechanisms of failure of endograft are discussed.

[Personal experience with anesthesia of ambulatory patients operated on in odontostomatological offices]. / Notre expérience de l'anesthésie des patients ambulatoires opérés dans les cabinets odonto-stomatologiques

The authors report their experience of anaesthesia of ambulatory patients operated on in dental surgeries; the authors review safety factors, specially, choice of material, drugs and techniques which seem to them essential. They expose in detail their personal techniques, in particular, nasotracheal intubation and open circuit, association of a powerful analgesic drug with a short duration of activity and a mild antiemetic neuroleptic drug completed by inhalation of a mixture of Ethrane and oxygen. The various problems which may occur are considered together with their solutions.