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Opinion statement: Prostate cancer (PCa) is the second most diagnosed malignant neoplasm and is one of the leading causes of cancer-related death in men worldwide. Despite significant advances in screening and treatment of PCa, given the heterogeneity of this disease, optimal personalized therapeutic strategies remain limited. However, emerging predictive and prognostic biomarkers based on individual patient profiles in combination with computer-assisted diagnostics have the potential to guide precision medicine, where patients may benefit from therapeutic approaches optimally suited to their disease. Also, the integration of genotypic and phenotypic diagnostic methods is supporting better informed treatment decisions. Focusing on advanced PCa, this review discusses polygenic risk scores for screening of PCa and common genomic aberrations in androgen receptor (AR), PTEN-PI3K-AKT, and DNA damage response (DDR) pathways, considering clinical implications for diagnosis, prognosis, and treatment prediction. Furthermore, we evaluate liquid biopsy, protein biomarkers such as serum testosterone levels, SLFN11 expression, total alkaline phosphatase (tALP), neutrophil-to-lymphocyte ratio (NLR), tissue biopsy, and advanced imaging tools, summarizing current phenotypic biomarkers and envisaging more effective utilization of diagnostic and prognostic biomarkers in advanced PCa. We conclude that prognostic and treatment predictive biomarker discovery can improve the management of patients, especially in metastatic stages of advanced PCa. This will result in decreased mortality and enhanced quality of life and help design a personalized treatment regimen. [ABSTRACT FROM AUTHOR]

Periodic subwavelength apertures have the ability to passively detect variations in the dielectric properties of the local sample environment through modification of the plasmon resonances associated with these structures. The resulting resonance peak can effectively provide a 'fingerprint' indicative of the dielectric properties of the medium within the near-surface region. Here we report on the use of bimodal silver-based plasmonic colour filters for molecular sensing. Firstly, by exploring the optical output of these devices as a function of the incident polarisation for a range of different analytes of known refractive index, we were able to both maximise and quantify their sensitivity. We then apply this concept to the real-time monitoring of the formation of self-assembled monolayers based on detection of the optical output using a spectrometer. This highlights the potential for bimodal plasmonic devices to be able to dynamically monitor variations in the local environment down to the level of single molecules without the need for specific functionalisation or labelling. Advantages of using this technique include the ability for these devices to be miniaturised and to dynamically tailor their optical output permitting the analysis of very small sample volumes and maximise their dynamic range for a specific analyte. [ABSTRACT FROM AUTHOR]

MyD88 and MAL are Toll-like receptor (TLR) adaptors that signal to induce pro-inflammatory cytokine production. We previously observed that the TIR domain of MAL (MALTIR) forms filaments in vitro and induces formation of crystalline higher-order assemblies of the MyD88 TIR domain (MyD88TIR). These crystals are too small for conventional X-ray crystallography, but are ideally suited to structure determination by microcrystal electron diffraction (MicroED) and serial femtosecond crystallography (SFX). Here, we present MicroED and SFX structures of the MyD88TIR assembly, which reveal a two-stranded higher-order assembly arrangement of TIR domains analogous to that seen previously for MALTIR. We demonstrate via mutagenesis that the MyD88TIR assembly interfaces are critical for TLR4 signaling in vivo, and we show that MAL promotes unidirectional assembly of MyD88TIR. Collectively, our studies provide structural and mechanistic insight into TLR signal transduction and allow a direct comparison of the MicroED and SFX techniques. MAL and MyD88 are downstream adaptors of Toll-like receptors (TLR) and the MAL TIR domain forms filaments in vitro, which in turn nucleate the assembly of crystalline arrays of the MyD88 TIR domain. Here, the authors present the structure of these MyD88 TIR crystalline arrays solved by both microcrystal electron diffraction and serial femtosecond crystallography, and they show with mutagenesis experiments that MyD88 interface residues are important for TLR4 signaling in vivo. [ABSTRACT FROM AUTHOR]

The invention of phase contrast microscopy revolutionized optics, enabling the visualization of highly optically transparent samples without the need for staining. The technique utilizes phase shifts within the sample and is routinely employed in the characterization of biological material and other weakly interacting objects. However, the demand for increased contrast and quantification has continued to drive research into more advanced approaches to phase imaging. Here, we demonstrate that the combination of ptychographic coherent diffractive imaging with plasmonically active metamaterials yields a massive enhancement of both the reconstructed phase and amplitude by exploiting near-field interactions at the metamaterial surface. We present results from nanofabricated samples and tissue sections with thickness ranging from 4 nm to 4 μm. In addition to enabling quantitative phase imaging of metamaterials, this approach opens the way to imaging a wide range of extremely thin or highly transparent objects previously inaccessible to optical microscopy. Plasmonics and metamaterials enable ptychographic coherent diffractive imaging with improved reconstructed phase and amplitude. The approach may be particularly useful for imaging of extremely thin or highly transparent objects. [ABSTRACT FROM AUTHOR]

Single Particle Imaging (SPI) with intense coherent X-ray pulses from X-ray free-electron lasers (XFELs) has the potential to produce molecular structures without the need for crystallization or freezing. Here we present a dataset of 285,944 diffraction patterns from aerosolized Coliphage PR772 virus particles injected into the femtosecond X-ray pulses of the Linac Coherent Light Source (LCLS). Additional exposures with background information are also deposited. The diffraction data were collected at the Atomic, Molecular and Optical Science Instrument (AMO) of the LCLS in 4 experimental beam times during a period of four years. The photon energy was either 1.2 or 1.7 keV and the pulse energy was between 2 and 4 mJ in a focal spot of about 1.3 μm x 1.7 μm full width at half maximum (FWHM). The X-ray laser pulses captured the particles in random orientations. The data offer insight into aerosolised virus particles in the gas phase, contain information relevant to improving experimental parameters, and provide a basis for developing algorithms for image analysis and reconstruction. Measurement(s) X-ray diffraction data Technology Type(s) free electron laser Sample Characteristic - Organism Enterobacteria phage PR772 Sample Characteristic - Location contiguous United States of America Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.13070546 [ABSTRACT FROM AUTHOR]

This review summarizes the literature describing recent advances in the coherent x-ray sciences for the high-resolution characterization of materials. The principles and some of the main experimental techniques as well as their applications are discussed. The advantages of x-ray methods for characterizing 3D microstructures as well as for characterizing plasticity in the bulk become clear from the examples presented. Materials that exhibit size effects within the 0.1-10- μm range benefit enormously from these techniques, and development of the relevant x-ray methods will add to our fundamental understanding of these phenomena. Many of the ideas that have developed in the coherent x-ray science literature have been enabled through advances in x-ray source and detection technology, which has occurred over the past 10 years or so. It is a topic of considerable importance to consider how these techniques, which have matured rapidly, may be best applied to materials imaging in order to meet the growing needs of the community. As coherent x-ray methods for characterizing materials at multiple length scales have developed, several key applications for these techniques have emerged. The key breakthroughs that have been enabled by these new methods are discussed throughout this review, together with an examination of some of the problems that will be addressed by these techniques within the next few years. [ABSTRACT FROM AUTHOR]

X-ray tomography can provide structural information of whole cells in close to their native state. Radiation-induced damage, however, imposes a practical limit to image resolution, and as such, a choice between damage, image contrast, and image resolution must be made. New coherent diffractive imaging techniques, such Fresnel Coherent Diffractive Imaging (FCDI), allows quantitative phase information with exceptional dose efficiency, high contrast, and nano-scale resolution. Here we present three-dimensional quantitative images of a whole eukaryotic cell by FCDI at a spatial resolution below 70 nm with sufficient phase contrast to distinguish major cellular components. From our data, we estimate that the minimum dose required for a similar resolution is close to that predicted by the Rose criterion, considerably below accepted estimates of the maximum dose a frozen-hydrated cell can tolerate. Based on the dose efficiency, contrast, and resolution achieved, we expect this technique will find immediate applications in tomographic cellular characterisation. [ABSTRACT FROM AUTHOR]

High-resolution X-ray imaging techniques using optical elements such as zone plates are widely used for viewing the internal structure of samples in exquisite detail. The resolution attainable is ultimately limited by the manufacturing tolerances for the optics. Combining ideas from crystallography and holography, this limit may be surpassed by the method of coherent diffractive imaging (CDI). Although CDI shows particular promise in applications involving X-ray free-electron lasers, it is also emerging as an important new technique for imaging at third-generation synchrotrons. The limited coherent output of these sources, however, is a significant barrier to obtaining shorter exposure times. A fundamental assumption of coherent diffractive imaging is that the incident light is well-approximated by a single optical frequency. In this Letter, we demonstrate the first experimental realization of 'polyCDI', using a broadband source to achieve a factor of 60 reduction in the exposure time over quasi-monochromatic coherent diffractive imaging. [ABSTRACT FROM AUTHOR]

The availability of third-generation synchrotrons and ultimately X-ray free-electron lasers is driving the development of many new methods of microscopy. Among these techniques, coherent diffractive imaging (CDI) is one of the most promising, offering nanometre-scale imaging of non-crystallographic samples. Image reconstruction from a single diffraction pattern has hitherto been possible only for small, isolated samples, presenting a fundamental limitation on the CDI method. Here we report on a form of imaging we term ‘keyhole’ CDI, which can reconstruct objects of arbitrary size. We demonstrate the technique using visible light and X-rays, with the latter producing images of part of an extended object with a detector-limited resolution of better than 20 nm. Combining the improved resolution of modern X-ray optics with the wavelength-limited resolution of CDI, the method paves the way for detailed imaging of a single quantum dot or of a small virus within a complex host environment. [ABSTRACT FROM AUTHOR]

The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a β-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reliable structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source. The new European X-Ray Free-Electron Laser (EuXFEL) is the first XFEL that generates X-ray pulses with a megahertz inter-pulse spacing. Here the authors demonstrate that high-quality and damage-free protein structures can be obtained with the currently available 1.1 MHz repetition rate pulses using lysozyme as a test case and furthermore present a β-lactamase structure. [ABSTRACT FROM AUTHOR]

Focussed Ion Beam (FIB) milling is a mainstay of nano-scale machining. By manipulating a tightly focussed beam of energetic ions, often gallium (Ga+), FIB can sculpt nanostructures via localised sputtering. This ability to cut solid matter on the nano-scale revolutionised sample preparation across the life, earth and materials sciences. Despite its widespread usage, detailed understanding of the FIB-induced structural damage, intrinsic to the technique, remains elusive. Here we examine the defects caused by FIB in initially pristine objects. Using Bragg Coherent X-ray Diffraction Imaging (BCDI), we are able to spatially-resolve the full lattice strain tensor in FIB-milled gold nano-crystals. We find that every use of FIB causes large lattice distortions. Even very low ion doses, typical of FIB imaging and previously thought negligible, have a dramatic effect. Our results are consistent with a damage microstructure dominated by vacancies, highlighting the importance of free-surfaces in determining which defects are retained. At larger ion fluences, used during FIB-milling, we observe an extended dislocation network that causes stresses far beyond the bulk tensile strength of gold. These observations provide new fundamental insight into the nature of the damage created and the defects that lead to a surprisingly inhomogeneous morphology. [ABSTRACT FROM AUTHOR]

The Fourier transform (FT), a cornerstone of optical processing, enables rapid evaluation of fundamental mathematical operations, such as derivatives and integrals. Conventionally, a converging lens performs an optical FT in free space when light passes through it. The speed of the transformation is limited by the thickness and the focal length of the lens. By using the wave nature of surface plasmon polaritons (SPPs), here we demonstrate that the FT can be implemented in a planar configuration with a minimal propagation distance of around 10 μm, resulting in an increase of speed by four to five orders of magnitude. The photonic FT was tested by synthesizing intricate SPP waves with their Fourier components. The reduced dimensionality in the minuscule device allows the future development of an ultrafast on-chip photonic information processing platform for large-scale optical computing.