Prevalence of mutations in common tumour types in Northern England and comparable utility of national and international Trial Finders.

PURPOSE: Tumour genomic profiling is of increasing importance in early phase trials to match patients to targeted therapeutics. Mutations vary by demographic group; however, regional differences are not characterised. This was investigated by comparing mutation prevalence for common cancers presenting to Newcastle Experimental Cancer Medicine Centre (ECMC) to The Cancer Genome Atlas (TCGA) and utility of trial matching modalities. METHODS: Detailed clinicogenomic data were obtained for patients presenting September 2017-December 2020. Prevalence of mutations in lung, colorectal, breast and prostate cancer was compared to TCGA GDC Data Portal. Experimental Cancer (EC) Trial Finder utility in matching trials was compared to a Molecular Tumour Board (MTB) and commercial sequencing reports. RESULTS: Of 311 patients with advanced cancer, this consisted of lung (n = 131, 42.1%), colorectal (n = 44, 14.1%), breast (n = 36, 11.6%) and prostate (n = 18, 5.6%). More than one mutation was identified in the majority (n = 260, 84%). Significant prevalence differences compared to TCGA were identified, including a high prevalence of EGFR in lung (P = 0.001); RB1 in breast (P = 0.0002); and multiple mutations in prostate cancer. EC Trial Finder demonstrated significantly different utility than sequencing reports in identifying trials (P = 0.007). CONCLUSIONS: Regional differences in mutations may exist with advanced stage accounting for prevalence of specific mutations. A national Trial Finder shows utility in finding targeted trials whilst commercial sequencing reports may over-report 'actionable' mutations. Understanding local prevalence and trial availability could increase enrolment onto matched early phase trials.

Nanoscale LiZnN - Luminescent Half-Heusler Quantum Dots.

Colloidal semiconductor quantum dots are a well-established technology, with numerous materials available either commercially or through the vast body of literature. The prevalent materials are cadmium-based and are unlikely to find general acceptance in most applications. While the III-V family of materials is a likely substitute, issues remain about its long-term suitability, and other earth-abundant materials are being explored. In this report, we highlight a nanoscale half-Heusler semiconductor, LiZnN, composed of readily available elements as a potential alternative system to luminescent II-VI and III-V nanoparticle quantum dots.

Capillary condensation under atomic-scale confinement.

Capillary condensation of water is ubiquitous in nature and technology. It routinely occurs in granular and porous media, can strongly alter such properties as adhesion, lubrication, friction and corrosion, and is important in many processes used by microelectronics, pharmaceutical, food and other industries1-4. The century-old Kelvin equation5 is frequently used to describe condensation phenomena and has been shown to hold well for liquid menisci with diameters as small as several nanometres1-4,6-14. For even smaller capillaries that are involved in condensation under ambient humidity and so of particular practical interest, the Kelvin equation is expected to break down because the required confinement becomes comparable to the size of water molecules1-22. Here we use van der Waals assembly of two-dimensional crystals to create atomic-scale capillaries and study condensation within them. Our smallest capillaries are less than four ångströms in height and can accommodate just a monolayer of water. Surprisingly, even at this scale, we find that the macroscopic Kelvin equation using the characteristics of bulk water describes the condensation transition accurately in strongly hydrophilic (mica) capillaries and remains qualitatively valid for weakly hydrophilic (graphite) ones. We show that this agreement is fortuitous and can be attributed to elastic deformation of capillary walls23-25, which suppresses the giant oscillatory behaviour expected from the commensurability between the atomic-scale capillaries and water molecules20,21. Our work provides a basis for an improved understanding of capillary effects at the smallest scale possible, which is important in many realistic situations.

Large magnetoelectric coupling in multiferroic oxide heterostructures assembled via epitaxial lift-off.

Epitaxial films may be released from growth substrates and transferred to structurally and chemically incompatible substrates, but epitaxial films of transition metal perovskite oxides have not been transferred to electroactive substrates for voltage control of their myriad functional properties. Here we demonstrate good strain transmission at the incoherent interface between a strain-released film of epitaxially grown ferromagnetic La0.7Sr0.3MnO3 and an electroactive substrate of ferroelectric 0.68Pb(Mg1/3Nb2/3)O3-0.32PbTiO3 in a different crystallographic orientation. Our strain-mediated magnetoelectric coupling compares well with respect to epitaxial heterostructures, where the epitaxy responsible for strong coupling can degrade film magnetization via strain and dislocations. Moreover, the electrical switching of magnetic anisotropy is repeatable and non-volatile. High-resolution magnetic vector maps reveal that micromagnetic behaviour is governed by electrically controlled strain and cracks in the film. Our demonstration should inspire others to control the physical/chemical properties in strain-released epitaxial oxide films by using electroactive substrates to impart strain via non-epitaxial interfaces.

Direct measurement of TEM lamella thickness in FIB-SEM.

Transmission electron microscope (TEM) specimen preparation by focused ion beam (FIB) milling requires delicate polishing of a thin window of material during the final stages of the procedure. Over or underpolishing is common and requires extra microscope resources to correct. Despite some methods for lamella thickness measurement being available, the majority of users judge the final polishing step subjectively from scanning electron microscope (SEM) images acquired between milling steps. Here we demonstrate successful thickness determination of thin silicon lamellae using calibrated secondary electron detectors in a FIB-SEM dual-beam chamber. Unlike previous thickness measurement methods it does not require long acquisition times, the use of in-chamber scanning transmission electron microscope (STEM) or energy dispersive x-ray spectroscopy detectors. The calibration aligns a SEM image to an electron energy loss spectroscopy (EELS) map of lamella thickness acquired in a TEM. This calibration reveals the greyscale-thickness dependence of two secondary electron SEM detectors: the through-lens detector (TLD) and the in-chamber electron detector (ICE). It was found that lamella thickness estimation for TLD images is accurate for areas thinner than 0.4 t/λ, whilst ICE images are most accurate for areas thicker than 0.5 t/λ up to 1.1 t/λ. The procedure presented here allows objective lamella thickness determination during the final stages of FIB specimen preparation using conventional imaging modes for common secondary electron detectors. LAY DESCRIPTION: Successful analysis of a material in a transmission electron microscope requires very thin windows of the material to be fabricated. Despite the quality of this analysis relying heavily on the thickness of the window, measuring thickness during window fabrication is not common practice. The authors show that it is possible to measure the thickness of the window directly in a focused-ion-beam chamber with a scanning electron microscope without altering the fabrication procedure, and using electron detectors common to most microscopes.

Atomically thin micas as proton-conducting membranes.

Monolayers of graphene and hexagonal boron nitride (hBN) are highly permeable to thermal protons1,2. For thicker two-dimensional (2D) materials, proton conductivity diminishes exponentially, so that, for example, monolayer MoS2 that is just three atoms thick is completely impermeable to protons1. This seemed to suggest that only one-atom-thick crystals could be used as proton-conducting membranes. Here, we show that few-layer micas that are rather thick on the atomic scale become excellent proton conductors if native cations are ion-exchanged for protons. Their areal conductivity exceeds that of graphene and hBN by one to two orders of magnitude. Importantly, ion-exchanged 2D micas exhibit this high conductivity inside the infamous gap for proton-conducting materials3, which extends from ∼100 °C to 500 °C. Areal conductivity of proton-exchanged monolayer micas can reach above 100 S cm-2 at 500 °C, well above the current requirements for the industry roadmap4. We attribute the fast proton permeation to ~5-Å-wide tubular channels that perforate micas' crystal structure, which, after ion exchange, contain only hydroxyl groups inside. Our work indicates that there could be other 2D crystals5 with similar nanometre-scale channels, which could help close the materials gap in proton-conducting applications.

Laser-writable high-k dielectric for van der Waals nanoelectronics.

Similar to silicon-based semiconductor devices, van der Waals heterostructures require integration with high-k oxides. Here, we demonstrate a method to embed and pattern a multifunctional few-nanometer-thick high-k oxide within various van der Waals devices without degrading the properties of the neighboring two-dimensional materials. This transformation allows for the creation of several fundamental nanoelectronic and optoelectronic devices, including flexible Schottky barrier field-effect transistors, dual-gated graphene transistors, and vertical light-emitting/detecting tunneling transistors. Furthermore, upon dielectric breakdown, electrically conductive filaments are formed. This filamentation process can be used to electrically contact encapsulated conductive materials. Careful control of the filamentation process also allows for reversible switching memories. This nondestructive embedding of a high-k oxide within complex van der Waals heterostructures could play an important role in future flexible multifunctional van der Waals devices.

Anomalous twin boundaries in two dimensional materials.

Twin boundary defects form in virtually all crystalline materials as part of their response to applied deformation or thermal stress. For nearly six decades, graphite has been used as a textbook example of twinning with illustrations showing atomically sharp interfaces between parent and twin. Using state-of-the-art high-resolution annular dark-field scanning transmission electron microscopy, we have captured atomic resolution images of graphitic twin boundaries and find that these interfaces are far more complex than previously supposed. Density functional theory calculations confirm that the presence of van der Waals bonding eliminates the requirement for an atomically sharp interface, resulting in long-range bending across multiple unit cells. We show these remarkable structures are common to other van der Waals materials, leading to extraordinary microstructures, Raman-active stacking faults, and sub-surface exfoliation within bulk crystals.

Ballistic molecular transport through two-dimensional channels.

Gas permeation through nanoscale pores is ubiquitous in nature and has an important role in many technologies1,2. Because the pore size is typically smaller than the mean free path of gas molecules, the flow of the gas molecules is conventionally described by Knudsen theory, which assumes diffuse reflection (random-angle scattering) at confining walls3-7. This assumption holds surprisingly well in experiments, with only a few cases of partially specular (mirror-like) reflection known5,8-11. Here we report gas transport through ångström-scale channels with atomically flat walls12,13 and show that surface scattering can be either diffuse or specular, depending on the fine details of the atomic landscape of the surface, and that quantum effects contribute to the specularity at room temperature. The channels, made from graphene or boron nitride, allow helium gas flow that is orders of magnitude faster than expected from theory. This is explained by specular surface scattering, which leads to ballistic transport and frictionless gas flow. Similar channels, but with molybdenum disulfide walls, exhibit much slower permeation that remains well described by Knudsen diffusion. We attribute the difference to the larger atomic corrugations at molybdenum disulfide surfaces, which are similar in height to the size of the atoms being transported and their de Broglie wavelength. The importance of this matter-wave contribution is corroborated by the observation of a reversed isotope effect, whereby the mass flow of hydrogen is notably higher than that of deuterium, in contrast to the relation expected for classical flows. Our results provide insights into the atomistic details of molecular permeation, which previously could be accessed only in simulations10,14, and demonstrate the possibility of studying gas transport under controlled confinement comparable in size to the quantum-mechanical size of atoms.

Transport of hydrogen isotopes through interlayer spacing in van der Waals crystals.

Atoms start behaving as waves rather than classical particles if confined in spaces commensurate with their de Broglie wavelength. At room temperature this length is only about one ångström even for the lightest atom, hydrogen. This restricts quantum-confinement phenomena for atomic species to the realm of very low temperatures1-5. Here, we show that van der Waals gaps between atomic planes of layered crystals provide ångström-size channels that make quantum confinement of protons apparent even at room temperature. Our transport measurements show that thermal protons experience a notably higher barrier than deuterons when entering van der Waals gaps in hexagonal boron nitride and molybdenum disulfide. This is attributed to the difference in the de Broglie wavelengths of the isotopes. Once inside the crystals, transport of both isotopes can be described by classical diffusion, albeit with unexpectedly fast rates comparable to that of protons in water. The demonstrated ångström-size channels can be exploited for further studies of atomistic quantum confinement and, if the technology can be scaled up, for sieving hydrogen isotopes.

Chromaticity separation and the alpha response.

Chromatic gratings can be uncomfortable to view and can evoke a large haemodynamic response. Both the discomfort and the amplitude of the haemodynamic response increase monotonically with the perceptual difference in the colour of the component bars of the grating, as registered by the separation in their chromaticity in the CIE 1976 UCS diagram. Individuals with photosensitive epilepsy exhibit epileptiform EEG activity in response to flickering light of alternate colours. The probability of the epileptiform response again increases monotonically with the separation of the colours in the CIE UCS diagram. We investigated whether alpha power, which is known to reflect the excitation of large populations of neurons, is similarly affected by the separation in chromaticity. Chromatic square-wave gratings with bars that differed in CIE UCS chromaticity were presented, together with a central fixation cross. In 18 non-clinical participants, alpha responses were recorded over the visual cortex (O1, Oz, O2, PO3, POz, PO4, P1, P2) and compared to responses in prefrontal cortex (F1, F2). Gratings comprised bars of two alternate colours that either had a small difference in chromaticity (mean CIE UCS separation of 0.03), a medium difference (mean separation of 0.19), or a large difference (mean separation of 0.43). The colour pairs had chromaticities that lay on the red-green, red-blue, or blue-green borders of the screen gamut. Regardless of the hue, the larger the separation in chromaticity, the greater the alpha desynchronization and the lower the alpha power (p = 0.004), but only in posterior electrodes (p < 0.001). Together this indicates that differences in colour evoke a cortical excitation that increases monotonically with the colour difference. In this respect the alpha response resembles the haemodynamic response.

Multiscale correlative tomography: an investigation of creep cavitation in 316 stainless steel.

Creep cavitation in an ex-service nuclear steam header Type 316 stainless steel sample is investigated through a multiscale tomography workflow spanning eight orders of magnitude, combining X-ray computed tomography (CT), plasma focused ion beam (FIB) scanning electron microscope (SEM) imaging and scanning transmission electron microscope (STEM) tomography. Guided by microscale X-ray CT, nanoscale X-ray CT is used to investigate the size and morphology of cavities at a triple point of grain boundaries. In order to understand the factors affecting the extent of cavitation, the orientation and crystallographic misorientation of each boundary is characterised using electron backscatter diffraction (EBSD). Additionally, in order to better understand boundary phase growth, the chemistry of a single boundary and its associated secondary phase precipitates is probed through STEM energy dispersive X-ray (EDX) tomography. The difference in cavitation of the three grain boundaries investigated suggests that the orientation of grain boundaries with respect to the direction of principal stress is important in the promotion of cavity formation.

High magnetic relaxivity in a fluorescent CdSe/CdS/ZnS quantum dot functionalized with MRI contrast molecules.

Light emitting semiconducting quantum dots show great promise as solar cells, optoelectronic devices and multimodal imaging probes. Here we demonstrate successful grafting of a thiol-functionalised GdIII MRI contrast agent onto the surface of core-multishell CdSe/CdS/ZnS quantum dots. The resulting nanoprobe exhibits intense photoluminescence and unprecedentedly large T1 relaxivity of 6800 mM-1 s-1 per nanoparticle due to secure implanting of ca. 620 magnetic centers per quantum dot unit.

Substrate Induced Strain Field in FeRh Epilayers Grown on Single Crystal MgO (001) Substrates.

Equi-atomic FeRh is highly unusual in that it undergoes a first order meta-magnetic phase transition from an antiferromagnet to a ferromagnet above room temperature (Tr ≈ 370 K). This behavior opens new possibilities for creating multifunctional magnetic and spintronic devices which can utilise both thermal and applied field energy to change state and functionalise composites. A key requirement in realising multifunctional devices is the need to understand and control the properties of FeRh in the extreme thin film limit (tFeRh < 10 nm) where interfaces are crucial. Here we determine the properties of FeRh films in the thickness range 2.5-10 nm grown directly on MgO substrates. Our magnetometry and structural measurements show that a perpendicular strain field exists in these thin films which results in an increase in the phase transition temperature as thickness is reduced. Modelling using a spin dynamics approach supports the experimental observations demonstrating the critical role of the atomic layers close to the MgO interface.

The application of in situ analytical transmission electron microscopy to the study of preferential intergranular oxidation in Alloy 600.

In situ analytical transmission electron microscopy (TEM) can provide a unique perspective on dynamic reactions in a variety of environments, including liquids and gases. In this study, in situ analytical TEM techniques have been applied to examine the localised oxidation reactions that occur in a Ni-Cr-Fe alloy, Alloy 600, using a gas environmental cell at elevated temperatures. The initial stages of preferential intergranular oxidation, shown to be an important precursor phenomenon for intergranular stress corrosion cracking in pressurized water reactors (PWRs), have been successfully identified using the in situ approach. Furthermore, the detailed observations correspond to the ex situ results obtained from bulk specimens tested in hydrogenated steam and in high temperature PWR primary water. The excellent agreement between the in situ and ex situ oxidation studies demonstrates that this approach can be used to investigate the initial stages of preferential intergranular oxidation relevant to nuclear power systems.

RhoA S-nitrosylation as a regulatory mechanism influencing endothelial barrier function in response to G+-bacterial toxins.

Disruption of the endothelial barrier in response to Gram positive (G+) bacterial toxins is a major complication of acute lung injury (ALI) and can be further aggravated by antibiotics which stimulate toxin release. The integrity of the pulmonary endothelial barrier is mediated by the balance of disruptive forces such as the small GTPase RhoA, and protective forces including endothelium-derived nitric oxide (NO). How NO protects against the barrier dysfunction is incompletely understood and our goal was to determine whether NO and S-nitrosylation can modulate RhoA activity and whether this mechanism is important for G+ toxin-induced microvascular permeability. We found that the G+ toxin listeriolysin-O (LLO) increased RhoA activity and that NO and S-NO donors inhibit RhoA activity. RhoA was robustly S-nitrosylated as determined by biotin-switch and mercury column analysis. MS revealed that three primary cysteine residues are S-nitrosylated including cys16, cys20 and cys159. Mutation of these residues to serine diminished S-nitrosylation to endogenous NO and mutant RhoA was less sensitive to inhibition by S-NO. G+-toxins stimulated the denitrosylation of RhoA which was not mediated by S-nitrosoglutathione reductase (GSNOR), thioredoxin (TRX) or thiol-dependent enzyme activity but was instead stimulated directly by elevated calcium levels. Calcium-promoted the direct denitrosylation of WT but not mutant RhoA and mutant RhoA adenovirus was more effective than WT in disrupting the barrier integrity of human lung microvascular endothelial cells. In conclusion, we reveal a novel mechanism by which NO and S-nitrosylation reduces RhoA activity which may be of significance in the management of pulmonary endothelial permeability induced by G+-toxins.

Molecular transport through capillaries made with atomic-scale precision.

Nanometre-scale pores and capillaries have long been studied because of their importance in many natural phenomena and their use in numerous applications. A more recent development is the ability to fabricate artificial capillaries with nanometre dimensions, which has enabled new research on molecular transport and led to the emergence of nanofluidics. But surface roughness in particular makes it challenging to produce capillaries with precisely controlled dimensions at this spatial scale. Here we report the fabrication of narrow and smooth capillaries through van der Waals assembly, with atomically flat sheets at the top and bottom separated by spacers made of two-dimensional crystals with a precisely controlled number of layers. We use graphene and its multilayers as archetypal two-dimensional materials to demonstrate this technology, which produces structures that can be viewed as if individual atomic planes had been removed from a bulk crystal to leave behind flat voids of a height chosen with atomic-scale precision. Water transport through the channels, ranging in height from one to several dozen atomic planes, is characterized by unexpectedly fast flow (up to 1 metre per second) that we attribute to high capillary pressures (about 1,000 bar) and large slip lengths. For channels that accommodate only a few layers of water, the flow exhibits a marked enhancement that we associate with an increased structural order in nanoconfined water. Our work opens up an avenue to making capillaries and cavities with sizes tunable to ångström precision, and with permeation properties further controlled through a wide choice of atomically flat materials available for channel walls.

Van der Waals pressure and its effect on trapped interlayer molecules.

Van der Waals assembly of two-dimensional crystals continue attract intense interest due to the prospect of designing novel materials with on-demand properties. One of the unique features of this technology is the possibility of trapping molecules between two-dimensional crystals. The trapped molecules are predicted to experience pressures as high as 1 GPa. Here we report measurements of this interfacial pressure by capturing pressure-sensitive molecules and studying their structural and conformational changes. Pressures of 1.2±0.3 GPa are found using Raman spectrometry for molecular layers of 1-nm in thickness. We further show that this pressure can induce chemical reactions, and several trapped salts are found to react with water at room temperature, leading to two-dimensional crystals of the corresponding oxides. This pressure and its effect should be taken into account in studies of van der Waals heterostructures and can also be exploited to modify materials confined at the atomic interfaces.