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  1. Free, publicly-accessible full text available August 1, 2024
  2. Mamyshev oscillators produce high-performance pulses, but technical and practical issues render them unsuitable for widespread use. Here we present a Mamyshev oscillator with several key design features that enable self-starting operation and unprecedented performance and simplicity from an all-fiber laser. The laser generates 110 nJ pulses that compress to 40 fs and 80 nJ with a grating pair. The pulse energy and duration are both the best achieved by a femtosecond all-fiber laser to date, to our knowledge, and the resulting peak power of 1.5 MW is 20 times higher than that of prior all-fiber, self-starting lasers. The simplicity of the design, ease of use, and pulse performance make this laser an attractive tool for practical applications.

     
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  3. Based on work by Dubochet and others in the 1980s and 1990s, samples for single-particle cryo-electron microscopy (cryo-EM) have been vitrified using ethane, propane or ethane/propane mixtures. These liquid cryogens have a large difference between their melting and boiling temperatures and so can absorb substantial heat without formation of an insulating vapor layer adjacent to a cooling sample. However, ethane and propane are flammable, they must be liquified in liquid nitrogen immediately before cryo-EM sample preparation, and cryocooled samples must be transferred to liquid nitrogen for storage, complicating workflows and increasing the chance of sample damage during handling. Experiments over the last 15 years have shown that cooling rates required to vitrify pure water are only ∼250 000 K s −1 , at the low end of earlier estimates, and that the dominant factor that has limited cooling rates of small samples in liquid nitrogen is sample precooling in cold gas present above the liquid cryogen surface, not the Leidenfrost effect. Using an automated cryocooling instrument developed for cryocrystallography that combines high plunge speeds with efficient removal of cold gas, we show that single-particle cryo-EM samples on commercial grids can be routinely vitrified using only boiling nitrogen and obtain apoferritin datasets and refined structures with 2.65 Å resolution. The use of liquid nitrogen as the primary coolant may allow manual and automated workflows to be simplified and may reduce sample stresses that contribute to beam-induced motion. 
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  4. Abstract A precise knowledge of the quark and gluon structure of the proton, encoded by the parton distribution functions (PDFs), is of paramount importance for the interpretation of high-energy processes at present and future lepton–hadron and hadron–hadron colliders. Motivated by recent progress in the PDF determinations carried out by the CT, MSHT, and NNPDF groups, we present an updated combination of global PDF fits: PDF4LHC21. It is based on the Monte Carlo combination of the CT18, MSHT20, and NNPDF3.1 sets followed by either its Hessian reduction or its replica compression. Extensive benchmark studies are carried out in order to disentangle the origin of the differences between the three global PDF sets. In particular, dedicated fits based on almost identical theory settings and input datasets are performed by the three groups, highlighting the role played by the respective fitting methodologies. We compare the new PDF4LHC21 combination with its predecessor, PDF4LHC15, demonstrating their good overall consistency and a modest reduction of PDF uncertainties for key LHC processes such as electroweak gauge boson production and Higgs boson production in gluon fusion. We study the phenomenological implications of PDF4LHC21 for a representative selection of inclusive, fiducial, and differential cross sections at the LHC. The PDF4LHC21 combination is made available via the LHAPDF library and provides a robust, user-friendly, and efficient method to estimate the PDF uncertainties associated to theoretical calculations for the upcoming Run III of the LHC and beyond. 
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  5. The statistical models used to derive the results of experimental analyses are of incredible scientific value andare essential information for analysis preservation and reuse. In this paper, we make the scientific case for systematically publishing the full statistical models and discuss the technical developments that make this practical. By means of a variety of physics cases -including parton distribution functions, Higgs boson measurements, effective field theory interpretations, direct searches for new physics, heavy flavor physics, direct dark matter detection, world averages, and beyond the Standard Model global fits -we illustrate how detailed information on the statistical modelling can enhance the short- and long-term impact of experimental results. 
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  6. Serial synchrotron-based crystallography using intense microfocused X-ray beams, fast-framing detectors and protein microcrystals held at 300 K promises to expand the range of accessible structural targets and to increase overall structure-pipeline throughputs. To explore the nature and consequences of X-ray radiation damage under microbeam illumination, the time-, dose- and temperature-dependent evolution of crystal diffraction have been measured with maximum dose rates of 50 MGy s −1 . At all temperatures and dose rates, the integrated diffraction intensity for a fixed crystal orientation shows non-exponential decays with dose. Non-exponential decays are a consequence of non-uniform illumination and the resulting spatial evolution of diffracted intensity within the illuminated crystal volume. To quantify radiation-damage lifetimes and the damage state of diffracting crystal regions, a revised diffraction-weighted dose (DWD) is defined and it is shown that for Gaussian beams the DWD becomes nearly independent of actual dose at large doses. An apparent delayed onset of radiation damage seen in some intensity–dose curves is in fact a consequence of damage. Intensity fluctuations at high dose rates may arise from the impulsive release of gaseous damage products. Accounting for these effects, data collection at the highest dose rates increases crystal radiation lifetimes near 300 K (but not at 100 K) by a factor of ∼1.5–2 compared with those observed at conventional dose rates. Improved quantification and modeling of the complex spatio-temporal evolution of protein microcrystal diffraction in intense microbeams will enable more efficient data collection, and will be essential in improving the accuracy of structure factors and structural models. 
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  7. Small-angle X-ray scattering (SAXS) is an increasingly popular technique that provides low-resolution structural information about biological macromolecules in solution. Many of the practical limitations of the technique, such as minimum required sample volume, and of experimental design, such as sample flow cells, are necessary because the biological samples are sensitive to damage from the X-rays. Radiation damage typically manifests as aggregation of the sample, which makes the collected data unreliable. However, there has been little systematic investigation of the most effective methods to reduce damage rates, and results from previous damage studies are not easily compared with results from other beamlines. Here a methodology is provided for quantifying radiation damage in SAXS to provide consistent results between different experiments, experimenters and beamlines. These methods are demonstrated on radiation damage data collected from lysozyme, glucose isomerase and xylanase, and it is found that no single metric is sufficient to describe radiation damage in SAXS for all samples. The radius of gyration, molecular weight and integrated SAXS profile intensity constitute a minimal set of parameters that capture all types of observed behavior. Radiation sensitivities derived from these parameters show a large protein dependence, varying by up to six orders of magnitude between the different proteins tested. This work should enable consistent reporting of radiation damage effects, allowing more systematic studies of the most effective minimization strategies. 
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  8. The thermal contraction of aqueous cryoprotectant solutions on cooling to cryogenic temperatures is of practical importance in protein cryocrystallography and in biological cryopreservation. In the former case, differential contraction on cooling of protein molecules and their lattice relative to that of the internal and surrounding solvent may lead to crystal damage and the degradation of crystal diffraction properties. Here, the amorphous phase densities of aqueous solutions of glycerol and ethylene glycol at T = 77 K have been determined. Densities with accuracies of <0.5% to concentrations as low as 30%( w / v ) were determined by rapidly cooling drops with volumes as small as 70 pl, assessing their optical clarity and measuring their buoyancy in liquid nitrogen–argon solutions. The use of these densities in contraction matching of internal solvent to the available solvent spaces is complicated by several factors, most notably the exclusion of cryoprotectants from protein hydration shells and the expected deviation of the contraction behavior of hydration water from bulk water. The present methods and results will assist in developing rational approaches to cryoprotection and an understanding of solvent behavior in protein crystals. 
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  9. All evidence to date indicates that at T = 100 K all protein crystals exhibit comparable sensitivity to X-ray damage when quantified using global metrics such as change in scaling B factor or integrated intensity versus dose. This is consistent with observations in cryo-electron microscopy, and results because nearly all diffusive motions of protein and solvent, including motions induced by radiation damage, are frozen out. But how do the sensitivities of different proteins compare at room temperature, where radiation-induced radicals are free to diffuse and protein and lattice structures are free to relax in response to local damage? It might be expected that a large complex with extensive conformational degrees of freedom would be more radiation sensitive than a small, compact globular protein. As a test case, the radiation sensitivity of 70S ribosome crystals has been examined. At T = 100 and 300 K, the half doses are 64 MGy (at 3 Å resolution) and 150 kGy (at 5 Å resolution), respectively. The maximum tolerable dose in a crystallography experiment depends upon the initial or desired resolution. When differences in initial data-set resolution are accounted for, the former half dose is roughly consistent with that for model proteins, and the 100/300 K half-dose ratio is roughly a factor of ten larger. 70S ribosome crystals exhibit substantially increased resolution at 100 K relative to 300 K owing to cooling-induced ordering and not to reduced radiation sensitivity and slower radiation damage. 
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