SDU - software for high-throughput automated data collection at the Swiss Light Source.

Recent advances in automation have fostered the development of unattended data collection services at a handful of synchrotron facilities worldwide. At the Swiss Light Source, the installation of new high-throughput sample changers at all three macromolecular crystallography beamlines and the commissioning of the Fast Fragment and Compound Screening pipeline created a unique opportunity to automate data acquisition. Here, the DA+ microservice software stack upgrades, implementation of an automatic loop-centering service and deployment of the Smart Digital User (SDU) software for unattended data collection are reported. The SDU software is the decision-making software responsible for communications between services, sample and device safety, sample centering, sample alignment with grid based X-ray diffraction and, finally, data collection.

Fast fragment- and compound-screening pipeline at the Swiss Light Source.

Over the last two decades, fragment-based drug discovery (FBDD) has emerged as an effective and efficient method to identify new chemical scaffolds for the development of lead compounds. X-ray crystallography can be used in FBDD as a tool to validate and develop fragments identified as binders by other methods. However, it is also often used with great success as a primary screening technique. In recent years, technological advances at macromolecular crystallography beamlines in terms of instrumentation, beam intensity and robotics have enabled the development of dedicated platforms at synchrotron sources for FBDD using X-ray crystallography. Here, the development of the Fast Fragment and Compound Screening (FFCS) platform, an integrated next-generation pipeline for crystal soaking, handling and data collection which allows crystallography-based screening of protein crystals against hundreds of fragments and compounds, at the Swiss Light Source is reported.

3D-printed holders for in meso in situ fixed-target serial X-ray crystallography.

The in meso in situ serial X-ray crystallography method was developed to ease the handling of small fragile crystals of membrane proteins and for rapid data collection on hundreds of microcrystals directly in the growth medium without the need for crystal harvesting. To facilitate mounting of these in situ samples on a goniometer at cryogenic or at room temperatures, two new 3D-printed holders have been developed. They provide for cubic and sponge phase sample stability in the X-ray beam and are compatible with sample-changing robots. The holders can accommodate a variety of window material types, as well as bespoke samples for diffraction screening and data collection at conventional macromolecular crystallography beamlines. They can be used for convenient post-crystallization treatments such as ligand and heavy-atom soaking. The design, assembly and application of the holders for in situ serial crystallography are described. Files for making the holders using a 3D printer are included as supporting information.

The TELL automatic sample changer for macromolecular crystallography.

In this paper, the design and functionalities of the high-throughput TELL sample exchange system for macromolecular crystallography is presented. TELL was developed at the Paul Scherrer Institute with a focus on speed, storage capacity and reliability to serve the three macromolecular crystallography beamlines of the Swiss Light Source, as well as the SwissMX instrument at SwissFEL.

High-intensity x-ray microbeam for macromolecular crystallography using silicon kinoform diffractive lenses.

Macromolecular crystallography often requires focused high-intensity x-ray beams for solving challenging protein structures from micrometer-sized crystals using current synchrotron radiation sources. The design of optical focusing schemes for hard x-rays showing high efficiency and flexibility in beam size is therefore continuously pursued. Here, we present an innovative solution based on a two-stage demagnification of the undulator source for photon energies from 6 keV to 19 keV, commissioned at the X10SA beamline of the Swiss Light Source, where a secondary source is imaged by two crossed silicon kinoform x-ray diffractive lenses with 75 nm outermost zone width. A source-size limited spot with a size of 4.8 µm×1.7 µm(h×v,FWHM) and flux of 7.5×1010 photons/s at 12.4 keV is demonstrated at the sample position.

Correlates of diagnostic accuracy in patients with nonspecific complaints.

OBJECTIVE: To investigate diagnostic accuracy in patient histories involving nonspecific complaints and the extent to which characteristics of physicians and structural properties of patient histories are associated with accuracy. METHODS: Six histories of patients presenting to the emergency department (ED) with nonspecific complaints were provided to 112 physicians: 36 ED physicians, 50 internists, and 26 family practitioners. Physicians listed the 3 most likely diagnoses for each history and indicated which cue(s) they considered crucial. Four weeks later, a subset of 20 physicians diagnosed the same 6 histories again. For each history, experts had previously determined the correct diagnoses and the diagnostic cues. RESULTS: Accuracy ranged from 14% to 64% correct diagnoses (correct diagnosis listed as the most likely) and from 29% to 87% correct differential diagnoses (correct diagnosis listed in the differential). Acute care physicians (ED physicians and internists) included the correct diagnosis in the differential in, on average, 3.4 histories, relative to 2.6 for the family practitioners (P = 0.001, d = .75). Diagnostic performance was fairly reliable (r = .61, P < 0.001). Clinical experience was negatively correlated with diagnostic accuracy (r = -.25, P = 0.008). Two structural properties of patient histories-cue consensus and cue substitutability-were significantly associated with diagnostic accuracy, whereas case difficulty was not. Finally, prevalence of diagnosis also proved significantly correlated with accuracy. CONCLUSIONS: Average diagnostic accuracy in cases with nonspecific complaints far exceeds chance performance, and accuracy varies with medical specialty. Analyzing cue properties in patient histories can help shed light on determinants of diagnostic performance and thus suggest ways to enhance physicians' ability to accurately diagnose cases with nonspecific complaints.