AMX - the highly automated macromolecular crystallography (17-ID-1) beamline at the NSLS-II.

The highly automated macromolecular crystallography beamline AMX/17-ID-1 is an undulator-based high-intensity (>5 × 1012 photons s-1), micro-focus (7 µm × 5 µm), low-divergence (1 mrad × 0.35 mrad) energy-tunable (5-18 keV) beamline at the NSLS-II, Brookhaven National Laboratory, Upton, NY, USA. It is one of the three life science beamlines constructed by the NIH under the ABBIX project and it shares sector 17-ID with the FMX beamline, the frontier micro-focus macromolecular crystallography beamline. AMX saw first light in March 2016 and started general user operation in February 2017. At AMX, emphasis has been placed on high throughput, high capacity, and automation to enable data collection from the most challenging projects using an intense micro-focus beam. Here, the current state and capabilities of the beamline are reported, and the different macromolecular crystallography experiments that are routinely performed at AMX/17-ID-1 as well as some plans for the near future are presented.

Serial crystallography with multi-stage merging of thousands of images.

KAMO and BLEND provide particularly effective tools to automatically manage the merging of large numbers of data sets from serial crystallography. The requirement for manual intervention in the process can be reduced by extending BLEND to support additional clustering options such as the use of more accurate cell distance metrics and the use of reflection-intensity correlation coefficients to infer `distances' among sets of reflections. This increases the sensitivity to differences in unit-cell parameters and allows clustering to assemble nearly complete data sets on the basis of intensity or amplitude differences. If the data sets are already sufficiently complete to permit it, one applies KAMO once and clusters the data using intensities only. When starting from incomplete data sets, one applies KAMO twice, first using unit-cell parameters. In this step, either the simple cell vector distance of the original BLEND or the more sensitive NCDist is used. This step tends to find clusters of sufficient size such that, when merged, each cluster is sufficiently complete to allow reflection intensities or amplitudes to be compared. One then uses KAMO again using the correlation between reflections with a common hkl to merge clusters in a way that is sensitive to structural differences that may not have perturbed the unit-cell parameters sufficiently to make meaningful clusters. Many groups have developed effective clustering algorithms that use a measurable physical parameter from each diffraction still or wedge to cluster the data into categories which then can be merged, one hopes, to yield the electron density from a single protein form. Since these physical parameters are often largely independent of one another, it should be possible to greatly improve the efficacy of data-clustering software by using a multi-stage partitioning strategy. Here, one possible approach to multi-stage data clustering is demonstrated. The strategy is to use unit-cell clustering until the merged data are sufficiently complete and then to use intensity-based clustering. Using this strategy, it is demonstrated that it is possible to accurately cluster data sets from crystals that have subtle differences.

Robotic sample changers for macromolecular X-ray crystallography and biological small-angle X-ray scattering at the National Synchrotron Light Source II. Corrigendum.

A correction in the paper by Lazo et al. [(2021). J. Synchrotron Rad. 28, 1649-1661] is made.

Robotic sample changers for macromolecular X-ray crystallography and biological small-angle X-ray scattering at the National Synchrotron Light Source II.

Here we present two robotic sample changers integrated into the experimental stations for the macromolecular crystallography (MX) beamlines AMX and FMX, and the biological small-angle scattering (bioSAXS) beamline LiX. They enable fully automated unattended data collection and remote access to the beamlines. The system designs incorporate high-throughput, versatility, high-capacity, resource sharing and robustness. All systems are centered around a six-axis industrial robotic arm coupled with a force torque sensor and in-house end effectors (grippers). They have the same software architecture and the facility standard EPICS-based BEAST alarm system. The MX system is compatible with SPINE bases and Unipucks. It comprises a liquid nitrogen dewar holding 384 samples (24 Unipucks) and a stay-cold gripper, and utilizes machine vision software to track the sample during operations and to calculate the final mount position on the goniometer. The bioSAXS system has an in-house engineered sample storage unit that can hold up to 360 samples (20 sample holders) which keeps samples at a user-set temperature (277 K to 300 K). The MX systems were deployed in early 2017 and the bioSAXS system in early 2019.

FMX - the Frontier Microfocusing Macromolecular Crystallography Beamline at the National Synchrotron Light Source II.

Two new macromolecular crystallography (MX) beamlines at the National Synchrotron Light Source II, FMX and AMX, opened for general user operation in February 2017 [Schneider et al. (2013). J. Phys. Conf. Ser. 425, 012003; Fuchs et al. (2014). J. Phys. Conf. Ser. 493, 012021; Fuchs et al. (2016). AIP Conf. Proc. SRI2015, 1741, 030006]. FMX, the micro-focusing Frontier MX beamline in sector 17-ID-2 at NSLS-II, covers a 5-30 keV photon energy range and delivers a flux of 4.0 × 1012 photons s-1 at 1 Šinto a 1 µm × 1.5 µm to 10 µm × 10 µm (V × H) variable focus, expected to reach 5 × 1012 photons s-1 at final storage-ring current. This flux density surpasses most MX beamlines by nearly two orders of magnitude. The high brightness and microbeam capability of FMX are focused on solving difficult crystallographic challenges. The beamline's flexible design supports a wide range of structure determination methods - serial crystallography on micrometre-sized crystals, raster optimization of diffraction from inhomogeneous crystals, high-resolution data collection from large-unit-cell crystals, room-temperature data collection for crystals that are difficult to freeze and for studying conformational dynamics, and fully automated data collection for sample-screening and ligand-binding studies. FMX's high dose rate reduces data collection times for applications like serial crystallography to minutes rather than hours. With associated sample lifetimes as short as a few milliseconds, new rapid sample-delivery methods have been implemented, such as an ultra-high-speed high-precision piezo scanner goniometer [Gao et al. (2018). J. Synchrotron Rad. 25, 1362-1370], new microcrystal-optimized micromesh well sample holders [Guo et al. (2018). IUCrJ, 5, 238-246] and highly viscous media injectors [Weierstall et al. (2014). Nat. Commun. 5, 3309]. The new beamline pushes the frontier of synchrotron crystallography and enables users to determine structures from difficult-to-crystallize targets like membrane proteins, using previously intractable crystals of a few micrometres in size, and to obtain quality structures from irregular larger crystals.

First on-line detection of radioactive fission isotopes produced by laser-accelerated protons.

The on-going developments in laser acceleration of protons and light ions, as well as the production of strong bursts of neutrons and multi-[Formula: see text] photons by secondary processes now provide a basis for novel high-flux nuclear physics experiments. While the maximum energy of protons resulting from Target Normal Sheath Acceleration is presently still limited to around [Formula: see text], the generated proton peak flux within the short laser-accelerated bunches can already today exceed the values achievable at the most advanced conventional accelerators by orders of magnitude. This paper consists of two parts covering the scientific motivation and relevance of such experiments and a first proof-of-principle demonstration. In the presented experiment pulses of [Formula: see text] at [Formula: see text] duration from the PHELIX laser produced more than [Formula: see text] protons with energies above [Formula: see text] in a bunch of sub-nanosecond duration. They were used to induce fission in foil targets made of natural uranium. To make use of the nonpareil flux, these targets have to be very close to the laser acceleration source, since the particle density within the bunch is strongly affected by Coulomb explosion and the velocity differences between ions of different energy. The main challenge for nuclear detection with high-purity germanium detectors is given by the strong electromagnetic pulse caused by the laser-matter interaction close to the laser acceleration source. This was mitigated by utilizing fast transport of the fission products by a gas flow to a carbon filter, where the [Formula: see text]-rays were registered. The identified nuclides include those that have half-lives down to [Formula: see text]. These results demonstrate the capability to produce, extract, and detect short-lived reaction products under the demanding experimental condition imposed by the high-power laser interaction. The approach promotes research towards relevant nuclear astrophysical studies at conditions currently only accessible at nuclear high energy density laser facilities.

Characterization of vertigo and hearing loss in patients with Fabry disease.

BACKGROUND: Fabry Disease (FD) is an X-linked hereditary lysosomal storage disorder which leads to a multisystemic intralysosomal accumulation of globotriaosylceramid (Gb3). Besides prominent renal and cardiac organ involvement, patients commonly complain about vestibulocochlear symptoms like high-frequency hearing loss, tinnitus and vertigo. However, comprehensive data especially on vertigo remain scarce. The aim of this study was to examine the prevalence and characteristics of vertigo and hearing loss in patients with FD, depending on renal and cardiac parameters and get hints about the site and the pattern of the lesions. METHODS: Single-center study with 57 FD patients. Every patient underwent an oto-rhino-laryngological examination as well as videonystagmography and vestibular evoked myogenic potentials (VEMPs) and audiological measurements using pure tone audiometry and auditory brainstem response audiometry (ABR). Renal function was measured by eGFR, cardiac impairment was graduated by NYHA class. RESULTS: More than one out of three patients (35.1%) complained about hearing loss, 54.4% about vertigo and 28.1% about both symptom. In 74% a sensorineural hearing loss of at least 25 dB was found, ABR could exclude any retrocochlear lesion. Caloric testing showed abnormal values in 71.9%, VEMPs were pathological in 68%. A correlation between the side or the shape of hearing loss and pathological vestibular testing could not be revealed. CONCLUSIONS: Hearing loss and vertigo show a high prevalence in FD. While hearing loss seems due to a cochlear lesion, peripheral vestibular as well as central nervous pathologies cause vertigo. Thus, both the site of lesion and the pathophysiological patterns seem to differ.

Macromolecular crystallography beamline X25 at the NSLS.

Beamline X25 at the NSLS is one of the five beamlines dedicated to macromolecular crystallography operated by the Brookhaven National Laboratory Macromolecular Crystallography Research Resource group. This mini-gap insertion-device beamline has seen constant upgrades for the last seven years in order to achieve mini-beam capability down to 20 µm × 20 µm. All major components beginning with the radiation source, and continuing along the beamline and its experimental hutch, have changed to produce a state-of-the-art facility for the scientific community.

Effect of pore structure of nanometer scale porous films on the measured elastic modulus.

The impact of pore structure of nanoporous films on the measured elastic modulus is demonstrated for silica-based nanoporous low-k films that are fabricated using an alternative manufacturing sequence which allows a separate control of porosity and matrix properties. For this purpose, different experimental techniques for measuring the elastic properties were compared, including nanoindentation, laser-induced surface acoustic wave spectroscopy (LAwave), and ellipsometric porosimetry (EP). The link between the elastic response of these nanoporous materials and their internal pore structure was investigated using positronium annihilation lifetime spectroscopy (PALS), EP, and diffusion experiments. It is shown that the absolute value of the Berkovich indentation modulus is very sensitive to the local pore structure and stiffness of the substrate and can be influenced by densification and/or anisotropic elasticity upon indentation, while on the other hand spherical indentation results are less sensitive to the local pore structure. The comparison of Berkovich and spherical indentation results combined with finite element simulations can potentially reveal changes in the internal structure of the film. For nanoporous films with porosity above the percolation threshold, the elastic modulus results obtained with LAwave and EP agree very well with spherical indentation results. On the other hand, below the percolation threshold, the elastic modulus values determined by these techniques deviate from the spherical indentation results. This was explained in terms of specific technique related effects that appear to be sensitive to the specific arrangement and morphology of the pores.

Correlated single-crystal electronic absorption spectroscopy and X-ray crystallography at NSLS beamline X26-C.

The research philosophy and new capabilities installed at NSLS beamline X26-C to support electronic absorption and Raman spectroscopies coupled with X-ray diffraction are reviewed. This beamline is dedicated full time to multidisciplinary studies with goals that include revealing the relationship between the electronic and atomic structures in macromolecules. The beamline instrumentation has been fully integrated such that optical absorption spectra and X-ray diffraction images are interlaced. Therefore, optical changes induced by X-ray exposure can be correlated with X-ray diffraction data collection. The installation of Raman spectroscopy into the beamline is also briefly reviewed. Data are now routinely generated almost simultaneously from three complementary types of experiments from the same sample. The beamline is available now to the NSLS general user population.

Single-crystal Raman spectroscopy and X-ray crystallography at beamline X26-C of the NSLS.

Three-dimensional structures derived from X-ray diffraction of protein crystals provide a wealth of information. Features and interactions important for the function of macromolecules can be deduced and catalytic mechanisms postulated. Still, many questions can remain, for example regarding metal oxidation states and the interpretation of `mystery density', i.e. ambiguous or unknown features within the electron density maps, especially at ∼2 Šresolutions typical of most macromolecular structures. Beamline X26-C at the National Synchrotron Light Source (NSLS), Brookhaven National Laboratory (BNL), provides researchers with the opportunity to not only determine the atomic structure of their samples but also to explore the electronic and vibrational characteristics of the sample before, during and after X-ray diffraction data collection. When samples are maintained under cryo-conditions, an opportunity to promote and follow photochemical reactions in situ as a function of X-ray exposure is also provided. Plans are in place to further expand the capabilities at beamline X26-C and to develop beamlines at NSLS-II, currently under construction at BNL, which will provide users access to a wide array of complementary spectroscopic methods in addition to high-quality X-ray diffraction data.

Detection and characterization of carbon contamination on EUV multilayer mirrors.

In this paper, we detect and characterize the carbon contamination layers that are formed during the illumination of extreme ultraviolet (EUV) multilayer mirrors. The EUV induced carbon layers were characterized ex situ using spectroscopic ellipsometry (SE) and laser generated surface acoustic waves (LG-SAW). We show that both LG-SAW and SE are very sensitive for measuring carbon layers, even in the presence of the highly heterogeneous structure of the multilayer. SE has better overall sensitivity, with a detection limit of 0.2 nm, while LG-SAW has an estimated detection limit of 2 nm. In addition, SE reveals that the optical properties of the EUV induced carbon contamination layer are consistent with the presence of a hydrogenated, polymeric like carbon. On the other hand, LG-SAW reveals that the EUV induced carbon contamination layer has a low Young's modulus (<100 GPa), which means that the layer is mechanically soft. We compare the limits of detection and quantification of the two techniques and discuss their prospective for monitoring carbon contamination build up on EUV optics.

Integrated software for macromolecular crystallography synchrotron beamlines II: revision, robots and a database.

This manuscript chronicles the evolution of software used originally to control a diffractometer at a macromolecular crystallography beamline. The system has been augmented and rewritten. A modular and carefully organized suite of programs now handles the whole experimental environment from a single vantage point. It provides automatic logging of the experiment and communication with the user, all the way from an initial proposal to perform the work to the end of data collection. This has included construction of a relational database to organize all details of the experiment and incorporation of a robotic specimen changer to provide automation for high-throughput applications.

Beamline X29: a novel undulator source for X-ray crystallography.

A high-flux insertion device and beamline for macromolecular crystallography has been built at the National Synchrotron Light Source (NSLS) that employs a mini-gap undulator source developed by the NSLS. The mini-gap undulator at beamline X29 is a hybrid-magnet device of period 12.5 mm operating at proven gaps of 3.3-10 mm. The beamline provides hard X-rays for macromolecular crystallography experiments from the second and third harmonics over an energy range of 5-15 keV. The X-ray optics is designed to deliver intense and highly collimated X-rays. Horizontal focusing is achieved by a cryogenically cooled sagittally focusing double-crystal monochromator with approximately 4.1:1 demagnification. A vertical focusing mirror downstream of the monochromator is used for harmonic rejection and vertical focusing. The experimental station hosts an Area Detector Systems Quantum 315 CCD detector with 2.2 s readout time between exposures and Crystal Logic goniostat for crystal rotation and detector positioning. An auto-mounter crystal changer has been installed to facilitate the high-throughput data collection required by the major users, which includes structural genomics projects and the Macromolecular Crystallography Research Resource mail-in program. X29 is 10(3) times brighter than any existing bending-magnet beamline at NSLS with an actual flux of 2.5 x 10(11) photons s(-1) through a 0.12 mm square aperture at 11.271 keV.

Comparison of pre-hospital combination-fibrinolysis plus conventional care with pre-hospital combination-fibrinolysis plus facilitated percutaneous coronary intervention in acute myocardial infarction.

AIMS: Early and complete reperfusion is the main treatment goal in ST-elevation myocardial infarction (STEMI). The timely optimal reperfusion strategy might be a pre-hospital initiated pharmacological reperfusion with subsequent facilitated percutaneous coronary intervention (PCI). This approach has been compared with pre-hospital combination-fibrinolysis only to determine whether either one of these methods offer advantages with respect to final infarct size. METHODS AND RESULTS: Patients with STEMI were randomized to either pre-hospital combination-fibrinolysis (half-dose reteplase+abciximab) with standard care (n=82) or pre-hospital combination-fibrinolysis with facilitated PCI (n=82). Primary endpoint was the infarct size assessed by delayed enhancement magnetic resonance. Secondary endpoints were ST-segment resolution at 90 min and a composite of death, re-myocardial infarction, major bleeding, and stroke at 6 months. The infarct size was lower after facilitated PCI with 5.2% [interquartile range (IQR) 1.3-11.2] as opposed to 10.4% (IQR 3.4-16.3) after pre-hospital combination-fibrinolysis (P=0.001). Complete ST-segment resolution was 80.0% after facilitated PCI vs. 51.9% after pre-hospital combination-fibrinolysis (P<0.001). After facilitated PCI, there was a trend towards a lower event rate in the combined clinical endpoint (15 vs. 25%, P=0.10, relative risk 0.57, 95% CI 0.28-1.13). CONCLUSION: In patients with STEMI, additional facilitated PCI after pre-hospital combination-fibrinolysis results in an improved tissue perfusion with subsequent smaller infarct size as opposed to pre-hospital combination-fibrinolysis alone. This translates into a trend towards a better clinical outcome.

Combining Brillouin spectroscopy and laser-SAW technique for elastic property characterization of thick DLC films.

Surface Brillouin spectroscopy (SBS) has been widely used for elastic property characterization of thin films. For films thicker than 500 nm, however, the wavelength of surface acoustic wave in the frequency range available for SBS is smaller than film thickness, and the SBS measures only the Rayleigh wave of the film. The laser-SAW technique, on the other hand, measures only the low-frequency portion of the surface acoustic wave dispersion and can estimate only one elastic modulus of the film (typically Young's modulus). In this work, we have combined the two methods to determine both Young's modulus and Poisson's ratio of a diamond-like carbon (DLC) film. It was found that reasonable estimates can be obtained for the longitudinal wave velocity, shear wave velocity, and Young's modulus of the film. The Poisson's ratio, however, still has a relatively large measurement error.

Three-beam interference is a sensitive measure of the efficacy of macromolecular refinement techniques.

Triplet phases recorded from insulin crystals were used to measure the improvement of phases during model refinement and to quantify the contribution made by each step in the refinement. Conventional amplitude data were recorded to 1.5 A resolution from rhombohedral pig insulin crystals using 1.54 A Cu Kalpha radiation. An initial atomic model and starting phases were obtained from a published structure and the atomic model was refined against the amplitude data using CNS. The refined phases were compared with 800 triplet phases that were measured from similar crystals using a three-beam interference technique and 1.1 A wavelength synchrotron radiation. The solvent region was improved further using a novel density-modification procedure. Calculated triplet phases were obtained from the model after each step in the refinement and were compared with the recorded triplet phases. The average difference between the recorded triplet phases and the calculated triplet phases was used as an unbiased measure of the correctness of the model at each stage in the refinement. The average individual phase error was estimated from discrepancies from triplet phases after each refinement step. Conventional atomic refinement of an approximate starting model reduced the average individual phase error from 21.6 to 14.7 degrees. Improvement of the solvent region, including the difference-map flattening procedure, reduced the individual phase error by a further 2.6 degrees. Modeling the discrete disorder of four amino acids accounted for an additional 0.5 degrees improvement and the final individual phase error was 11.6 degrees.

Neurofeedback and quantitative electroencephalography.

This study was conducted in an attempt to determine the efficacy of neurofeedback (NFB) in the treatment of patients suffering from vertigo or tinnitus. Results indicated that after NFB, power for delta and theta bands was reduced; however, an increase of power was noted for the alpha bands. Furthermore, normalization was observed for the vestibular evoked potentials (VestEP). After NFB, a normalization of the VestEP was also demonstrated in a patient suffering from a bilateral tinnitus. A follow-up study (12 months after NFB) demonstrated that the VestEP were normal.