A Pan-Respiratory Antiviral Chemotype Targeting a Host Multi-Protein Complex

We present a novel small molecule antiviral chemotype that was identified by an unconventional cell-free protein synthesis and assembly-based phenotypic screen for modulation of viral capsid assembly. Activity of PAV-431, a representative compound from the series, has been validated against infectious virus in multiple cell culture models for all six families of viruses causing most respiratory disease in humans. In animals this chemotype has been demonstrated efficacious for Porcine Epidemic Diarrhea Virus (a coronavirus) and Respiratory Syncytial Virus (a paramyxovirus). PAV-431 is shown to bind to the protein 14-3-3, a known allosteric modulator. However, it only appears to target the small subset of 14-3-3 which is present in a dynamic multi-protein complex whose components include proteins implicated in viral lifecycles and in innate immunity. The composition of this target multi-protein complex appears to be modified upon viral infection and largely restored by PAV-431 treatment. Our findings suggest a new paradigm for understanding, and drugging, the host-virus interface, which leads to a new clinical therapeutic strategy for treatment of respiratory viral disease.

Influence of fluorescent dopants on the vat photopolymerization of acrylate-based plastic scintillators for application in neutron/gamma pulse shape discrimination

Plastic scintillators, a class of solid-state materials used for radiation detection, were additively manufactured with vat photopolymerization. The photopolymer resins consisted of a primary dopant and a secondary dopant dissolved in a bisphenol A ethoxylate diacrylate-based matrix. The absorptive dopants significantly influence important print parameters, for example, secondary dopants decrease the light penetration depth by a factor > 12 ×. The primary dopant 2,5-diphenyloxazole had minimal impact on the printing process even when loaded at 25 % by mass of the resin. Working curve measurements, which relate energy dose to cure depth, were performed as a function of feature size to further assess the influence of dopants. Photopatterns smaller than 150 μm width had apparent increases in critical energy dose compared to larger photopatterns, while all resins maintained printed features in line gratings with 50 μm of separation. Printed scintillator monoliths were compared to scintillators cast by traditional molding, demonstrating that the layer-by-layer printing process does not decrease scintillation response. A maximum light output of 31 % of a benchmark plastic scintillator (EJ-200) and successful pulse shape discrimination were achieved with 20 % by mass 2,5-diphenyloxazole as the primary dopant and 0.1 % by mass 9,9-dimethyl-2,7-distyrylfluorene as the secondary dopant in printed scintillator samples.

Reconfigurable Electrical Networks within a Conductive Hydrogel Composite

Soft materials that exhibit compliance, programmability, and reconfigurability can have a transformative impact as electronic skin for applications in wearable electronics/soft robotics. There has been significant progress in soft conductive materials; however, achieving electrically controlled and reversible changes in conductivity and circuit connectivity remains challenging. To overcome this limitation, a soft material architecture with reconfigurable conductive networks of silver flakes embedded within a hydrogel matrix is presented. The conductive networks can be reversibly created/disconnected through various stimuli, including current, humidity, or temperature. Such stimuli affect electrical connectivity of the hydrogel by controlling its water content, which can be modulated by evaporation under ambient conditions (passive dehydration), evaporation through electrical Joule heating (active dehydration), or absorption of additional water (rehydration). The resulting change in electrical conductivity is reversible and repeatable, endowing the composite with on-demand reconfigurable conductivity. To highlight this material's unique properties, it is shown that conductive traces can be reconfigured after severe damage and revert to lower conductivity after rehydration. Additionally, a quadruped robot is demonstrated that can respond to stimuli by changing direction following exposure to excess water, thereby achieving reprogrammable locomotion behaviors.

Inbreeding depression explains killer whale population dynamics

Understanding the factors that cause endangered populations to either grow or decline is crucial for preserving biodiversity. Conservation efforts often address extrinsic threats, such as environmental degradation and overexploitation, that can limit the recovery of endangered populations. Genetic factors such as inbreeding depression can also affect population dynamics but these effects are rarely measured in the wild and thus often neglected in conservation efforts. Here we show that inbreeding depression strongly influences the population dynamics of an endangered killer whale population, despite genomic signatures of purging of deleterious alleles via natural selection. We find that the 'Southern Residents', which are currently endangered despite nearly 50 years of conservation efforts, exhibit strong inbreeding depression for survival. Our population models suggest that this inbreeding depression limits population growth and predict further decline if the population remains genetically isolated and typical environmental conditions continue. The Southern Residents also had more inferred homozygous deleterious alleles than three other, growing, populations, further suggesting that inbreeding depression affects population fitness. These results demonstrate that inbreeding depression can substantially limit the recovery of endangered populations. Conservation actions focused only on extrinsic threats may therefore fail to account for key intrinsic genetic factors that also limit population growth.

New Methods for Evaluating Energy Infrastructure Development Risks

Many energy technologies that can provide reliable, low-carbon electricity generation are confined to nations that have access to robust technical and economic capabilities, either on their own or through geopolitical alliances. Equally important, these nations maintain a degree of institutional capacity that could lower the risks associated with deploying emergent energy technologies such as advanced nuclear or carbon capture and storage. The complexity, expense, and scrutiny that come with building these facilities make them infeasible choices for most nations. This paradigm is slowly changing, as the pressing need for low-carbon electricity generation and ongoing efforts to develop modular nuclear and carbon capture technologies have opened the door for potentially wider markets, including in nations without substantial institutional capacity. Here, using advanced nuclear technologies as our testbed, we develop new methods to evaluate national readiness for deploying complex energy infrastructure. Specifically, we use Data Envelopment Analysis-a method that eliminates the need for expert judgment-to benchmark performance across nations. We find that approximately 80% of new nuclear deployment occurs in nations that are in the top two quartiles of institutional and economic performance. However, 85% of potential low-carbon electricity demand growth is in nations that are in the bottom two quartiles of performance. We offer iconic paradigms for deploying nuclear power in each of these clusters of nations if the goal is to mitigate risk. Our research helps redouble efforts by industry, regulators, and international development agencies to focus on areas where readiness is low and risk correspondingly higher.

Assortative mating for reproductive timing affects population recruitment and resilience in a quantitative genetic model

Quantitative models that simulate the inheritance and evolution of fitness-linked traits offer a method for predicting how environmental or anthropogenic perturbations can affect the dynamics of wild populations. Random mating between individuals within populations is a key assumption of many such models used in conservation and management to predict the impacts of proposed management or conservation actions. However, recent evidence suggests that non-random mating may be underestimated in wild populations and play an important role in diversity-stability relationships. Here we introduce a novel individual-based quantitative genetic model that incorporates assortative mating for reproductive timing, a defining attribute of many aggregate breeding species. We demonstrate the utility of this framework by simulating a generalized salmonid lifecycle, varying input parameters, and comparing model outputs to theoretical expectations for several eco-evolutionary, population dynamic scenarios. Simulations with assortative mating systems resulted in more resilient and productive populations than those that were randomly mating. In accordance with established ecological and evolutionary theory, we also found that decreasing the magnitude of trait correlations, environmental variability, and strength of selection each had a positive effect on population growth. Our model is constructed in a modular framework so that future components can be easily added to address pressing issues such as the effects of supportive breeding, variable age structure, differential selection by sex or age, and fishery interactions on population growth and resilience. With code published in a public Github repository, model outputs may easily be tailored to specific study systems by parameterizing with empirically generated values from long-term ecological monitoring programs.

A Pan-respiratory Antiviral Chemotype Targeting a Transient Host Multiprotein Complex

We present a small molecule chemotype, identified by an orthogonal drug screen, exhibiting nanomolar activity against members of all the six viral families causing most human respiratory viral disease, with a demonstrated barrier to resistance development. Antiviral activity is shown in mammalian cells, including human primary bronchial epithelial cells cultured to an air-liquid interface and infected with SARS-CoV-2. In animals, efficacy of early compounds in the lead series is shown by survival (for a coronavirus) and viral load (for a paramyxovirus). The drug target is shown to include a subset of the protein 14-3-3 within a transient host multi-protein complex containing components implicated in viral lifecycles and in innate immunity. This multi-protein complex is modified upon viral infection and largely restored by drug treatment. Our findings suggest a new clinical therapeutic strategy for early treatment upon upper respiratory viral infection to prevent progression to lower respiratory tract or systemic disease.

ONE SENTENCE SUMMARY

A host-targeted drug to treat all respiratory viruses without viral resistance development.

Implications of Large-Effect Loci for Conservation: A Review and Case Study with Pacific Salmon

The increasing feasibility of assembling large genomic datasets for non-model species presents both opportunities and challenges for applied conservation and management. A popular theme in recent studies is the search for large-effect loci that explain substantial portions of phenotypic variance for a key trait(s). If such loci can be linked to adaptations, 2 important questions arise: 1) Should information from these loci be used to reconfigure conservation units (CUs), even if this conflicts with overall patterns of genetic differentiation? 2) How should this information be used in viability assessments of populations and larger CUs? In this review, we address these questions in the context of recent studies of Chinook salmon and steelhead (anadromous form of rainbow trout) that show strong associations between adult migration timing and specific alleles in one small genomic region. Based on the polygenic paradigm (most traits are controlled by many genes of small effect) and genetic data available at the time showing that early-migrating populations are most closely related to nearby late-migrating populations, adult migration differences in Pacific salmon and steelhead were considered to reflect diversity within CUs rather than separate CUs. Recent data, however, suggest that specific alleles are required for early migration, and that these alleles are lost in populations where conditions do not support early-migrating phenotypes. Contrasting determinations under the US Endangered Species Act and the State of California's equivalent legislation illustrate the complexities of incorporating genomics data into CU configuration decisions. Regardless how CUs are defined, viability assessments should consider that 1) early-migrating phenotypes experience disproportionate risks across large geographic areas, so it becomes important to identify early-migrating populations that can serve as reliable sources for these valuable genetic resources; and 2) genetic architecture, especially the existence of large-effect loci, can affect evolutionary potential and adaptability.

Density functionals with asymptotic-potential corrections are required for the simulation of spectroscopic properties of materials

Five effects of correction of the asymptotic potential error in density functionals are identified that significantly improve calculated properties of molecular excited states involving charge-transfer character. Newly developed materials-science computational methods are used to demonstrate how these effects manifest in materials spectroscopy. Connection is made considering chlorophyll-a as a paradigm for molecular spectroscopy, 22 iconic materials as paradigms for 3D materials spectroscopy, and the VN - defect in hexagonal boron nitride as an example of the spectroscopy of defects in 2D materials pertaining to nanophotonics. Defects can equally be thought of as being "molecular" and "materials" in nature and hence bridge the relms of molecular and materials spectroscopies. It is concluded that the density functional HSE06, currently considered as the standard for accurate calculations of materials spectroscopy, should be replaced, in most instances, by the computationally similar but asymptotically corrected CAM-B3LYP functional, with some specific functionals for materials-use only providing further improvements.

Vessels and their sounds reduce prey capture effort by endangered killer whales (Orcinus orca)

Vessel traffic is prevalent throughout marine environments. However, we often have a limited understanding of vessel impacts on marine wildlife, particularly cetaceans, due to challenges of studying fully-aquatic species. To investigate vessel and acoustic effects on cetacean foraging behavior, we attached suction-cup sound and movement tags to endangered Southern Resident killer whales in their summer habitat while collecting geo-referenced proximate vessel data. We identified prey capture dives using whale kinematic signatures and found that the probability of capturing prey increased as salmon abundance increased, but decreased as vessel speed increased. When vessels emitted navigational sonar, whales made longer dives to capture prey and descended more slowly when they initiated these dives. Finally, whales descended more quickly when noise levels were higher and vessel approaches were closer. These findings advance a growing understanding of vessel and sound impacts on marine wildlife and inform efforts to manage vessel impacts on endangered populations.

Biochemical and functional characterization of mutant KRAS epitopes validates this oncoprotein for immunological targeting

Activating RAS missense mutations are among the most prevalent genomic alterations observed in human cancers and drive oncogenesis in the three most lethal tumor types. Emerging evidence suggests mutant KRAS (mKRAS) may be targeted immunologically, but mKRAS epitopes remain poorly defined. Here we employ a multi-omics approach to characterize HLA class I-restricted mKRAS epitopes. We provide proteomic evidence of mKRAS epitope processing and presentation by high prevalence HLA class I alleles. Select epitopes are immunogenic enabling mKRAS-specific TCRαβ isolation. TCR transfer to primary CD8⁺ T cells confers cytotoxicity against mKRAS tumor cell lines independent of histologic origin, and the kinetics of lytic activity correlates with mKRAS peptide-HLA class I complex abundance. Adoptive transfer of mKRAS-TCR engineered CD8⁺ T cells leads to tumor eradication in a xenograft model of metastatic lung cancer. This study validates mKRAS peptides as bona fide epitopes facilitating the development of immune therapies targeting this oncoprotein.

KRAS is commonly mutated at codon 12 in several cancer types, offering a unique opportunity for the development of neoantigen-targeted immunotherapy. Here the authors present a pipeline for the prediction, identification and validation of HLA class-I restricted mutant KRAS G12 peptides, leading to the generation of mutant KRAS-specific T cell receptors for adoptive T cell immunotherapy.

Accurate prediction of the properties of materials using the CAM-B3LYP density functional

Density functionals with asymptotic corrections to the long-range potential provide entry-level methods for calculations on molecules that can sustain charge transfer, but similar applications in materials science are rare. We describe an implementation of the CAM-B3LYP range-separated functional within the Vienna Ab-initio Simulation Package (VASP) framework, together with its analytical functional derivatives. Results obtained for eight representative materials: aluminum, diamond, graphene, silicon, NaCl, MgO, 2D h-BN, and 3D h-BN, indicate that CAM-B3LYP predictions embody mean-absolute deviations (MAD) compared to HSE06 that are reduced by a factor of six for lattice parameters, four for quasiparticle band gaps, three for the lowest optical excitation energies, and six for exciton binding energies. Further, CAM-B3LYP appears competitive compared to ab initio G₀ W₀ and Bethe-Salpeter equation approaches. The CAM-B3LYP implementation in VASP was verified by comparison of optimized geometries and reaction energies for isolated molecules taken from the ACCDB database, evaluated in large periodic unit cells, to analogous results obtained using Gaussian basis sets. Using standard GW pseudopotentials and energy cutoffs for the plane-wave calculations and the aug-cc-pV5Z basis set for the atomic-basis ones, the MAD in energy for 1738 chemical reactions was 0.34 kcal mol^-1 , while for 480 unique bond lengths this was 0.0036 Å; these values reduced to 0.28 kcal mol^-1 (largest error 0.94 kcal mol^-1 ) and 0.0009 Å by increasing the plane-wave cutoff energy to 850 eV.

4D-Printable Liquid Metal-Liquid Crystal Elastomer Composites

Soft actuators that undergo programmable shape change in response to a stimulus are enabling components of future soft robots and other soft machines. Strategies to power these actuators often require the incorporation of rigid, electrically conductive materials into the soft actuator, thus limiting the compliance and shape change of the material. In this study, we develop a 4D-printable composite composed of liquid crystal elastomer (LCE) matrix with dispersed droplets of eutectic gallium indium alloy (EGaIn). Using deformable EGaIn droplets in place of rigid conductive fillers preserves the compliance and shape-morphing properties of the LCE. The process enables 4D-printed LCE actuators capable of photothermal and electrothermal actuation. At low liquid metal (LM) concentrations (71 wt %), the composite actuator exhibits a photothermal response upon irradiation of near-IR light. Printed actuators with a twisted nematic configuration are capable of bending angles of 150° at 800 mW cm^-2. At higher LM concentrations (88 wt %), the embedded LM droplets can form percolating networks that conduct electricity and enable electrical Joule heating of the LCE. Actuation strain ranging from 5 to 12% is controlled by the amount of electrical power that is delivered to the composite. We also introduce a method for multimaterial printing of monolithic structures where the LM filler loading is spatially varied. These multifunctional materials exhibit innate responsivity where the actuator behaves as an electrical switch and can report one of two states (on/off). These multiresponsive, 4D-printable composites enable multifunctional, mechanically active structures that can be powered with IR light or low DC voltages.

Endangered predators and endangered prey: Seasonal diet of Southern Resident killer whales

Understanding diet is critical for conservation of endangered predators. Southern Resident killer whales (SRKW) (Orcinus orca) are an endangered population occurring primarily along the outer coast and inland waters of Washington and British Columbia. Insufficient prey has been identified as a factor limiting their recovery, so a clear understanding of their seasonal diet is a high conservation priority. Previous studies have shown that their summer diet in inland waters consists primarily of Chinook salmon (Oncorhynchus tshawytscha), despite that species' rarity compared to some other salmonids. During other times of the year, when occurrence patterns include other portions of their range, their diet remains largely unknown. To address this data gap, we collected feces and prey remains from October to May 2004-2017 in both the Salish Sea and outer coast waters. Using visual and genetic species identification for prey remains and genetic approaches for fecal samples, we characterized the diet of the SRKWs in fall, winter, and spring. Chinook salmon were identified as an important prey item year-round, averaging ~50% of their diet in the fall, increasing to 70-80% in the mid-winter/early spring, and increasing to nearly 100% in the spring. Other salmon species and non-salmonid fishes, also made substantial dietary contributions. The relatively high species diversity in winter suggested a possible lack of Chinook salmon, probably due to seasonally lower densities, based on SRKW's proclivity to selectively consume this species in other seasons. A wide diversity of Chinook salmon stocks were consumed, many of which are also at risk. Although outer coast Chinook samples included 14 stocks, four rivers systems accounted for over 90% of samples, predominantly the Columbia River. Increasing the abundance of Chinook salmon stocks that inhabit the whales' winter range may be an effective conservation strategy for this population.

Identifying carbon as the source of visible single-photon emission from hexagonal boron nitride

Single-photon emitters (SPEs) in hexagonal boron nitride (hBN) have garnered increasing attention over the last few years due to their superior optical properties. However, despite the vast range of experimental results and theoretical calculations, the defect structure responsible for the observed emission has remained elusive. Here, by controlling the incorporation of impurities into hBN via various bottom-up synthesis methods and directly through ion implantation, we provide direct evidence that the visible SPEs are carbon related. Room-temperature optically detected magnetic resonance is demonstrated on ensembles of these defects. We perform ion-implantation experiments and confirm that only carbon implantation creates SPEs in the visible spectral range. Computational analysis of the simplest 12 carbon-containing defect species suggest the negatively charged [Formula: see text] defect as a viable candidate and predict that out-of-plane deformations make the defect environmentally sensitive. Our results resolve a long-standing debate about the origin of single emitters at the visible range in hBN and will be key to the deterministic engineering of these defects for quantum photonic devices.

A mobile sex-determining region, male-specific haplotypes and rearing environment influence age at maturity in Chinook salmon

Variation in age at maturity is an important contributor to life history and demographic variation within and among species. The optimal age at maturity can vary by sex, and the ability of each sex to evolve towards its fitness optimum depends on the genetic architecture of maturation. Using GWAS of RAD sequencing data, we show that age at maturity in Chinook salmon exhibits sex-specific genetic architecture, with age at maturity in males influenced by large (up to 20 Mb) male-specific haplotypes. These regions showed no such effect in females. We also provide evidence for translocation of the sex-determining gene between two different chromosomes. This has important implications for sexually antagonistic selection, particularly that sex linkage of adaptive genes may differ within and among populations based on chromosomal location of the sex-determining gene. Our findings will facilitate research into the genetic causes of shifting demography in Chinook salmon as well as a better understanding of sex determination in this species and Pacific salmon in general.

Controlled Assembly of Liquid Metal Inclusions as a General Approach for Multifunctional Composites

Soft composites that use droplets of gallium-based liquid metal (LM) as the dispersion phase have the potential for transformative impact in multifunctional material engineering. However, it is unclear whether percolation pathways of LM can support high electrical conductivity in a wide range of matrix materials. This issue is addressed through an approach to LM composite synthesis that focuses on the interrelated effects of matrix curing/solidification and droplet formation. The combined influence of LM concentration, particle size, and sedimentation is explored. By developing this approach, the functionalities that have been demonstrated with LM composites can be generalized to other matrix materials that impart additional functionality. Specifically, composites are synthesized using a biodegradable/reprocessable plastic (polycaprolactone), a hydrogel (poly(vinyl alcohol)), and a processable rubber (a styrene-ethylene-butylene-styrene derivative) to demonstrate wide applicability. This method enables synthesis of composites: i) with high stretchability and negligible electromechanical coupling (>600% strain); ii) with Joule-heated healing and reprocessability; iii) with electrical and mechanical self-healing; and iv) that can be printed. This approach to controlled assembly represents a widely applicable technique for creating new classes of LM composites with unprecedented multifunctionality.

Network topologies dictate electromechanical coupling in liquid metal-elastomer composites

Elastomers embedded with micro- and nanoscale droplets of liquid metal (LM) alloys like eutectic gallium-indium (EGaIn) can exhibit unique combinations of elastic, thermal, and electrical properties that are difficult to achieve using rigid filler. For composites with sufficient concentrations of liquid metal, the LM droplets can form percolating networks that conduct electricity and deform with the surrounding elastomer as the composite is stretched. Surprisingly, experimental measurements performed on LM-embedded elastomers (LMEEs) show that the total electrical resistance of the composite increases only slightly even as the elastomer is stretched to several times its natural length. In contrast, Pouillet's law would predict an exponential increase in resistance (Ω) with stretch (λ) due to the incompressibility of liquid metal and elastomer. In this manuscript, we perform a computational analysis to examine the unique electromechanical properties of conductive LMEE composites. Our analysis suggests that the gauge factor that quantifies electromechanical coupling (i.e. G = {ΔΩ/Ω0}/λ) decreases with increasing tortuosity of the conductive pathways formed by the connected LM droplets. A dimensionless parameter for path tortuosity can be used to estimate G for statistically homogeneous LMEE composites. These results rationalize experimental observations and provide insight into the influence of liquid metal droplet assembly on the functionality of the composite.

Size of liquid metal particles influences actuation properties of a liquid crystal elastomer composite

Composites of liquid crystal elastomer (LCE) that are electrically conductive have the potential to function as soft "artificial muscle" actuators that can be reversibly stimulated with electrical Joule-heating. Conductivity can be achieved by embedding the LCE with droplets of an alloy of gallium and indium that is liquid at room temperature. These soft artificial muscles are capable of >50% reversible actuation with an applied load. The key to actuation at high loadings of liquid metal (LM) is that the droplets deform with the surrounding matrix. By controlling the size of LM droplets through simple processing techniques, we show that the actuator properties of the LM-LCE muscle can be tuned. For example, composites with smaller liquid metal particles (ca. 10 μm or less) are stiffer than those with larger liquid metal particles (ca. >100 μm) and are capable of greater force output. However, smaller particles reduce actuation strain and composites with large particles exhibit significantly greater stroke length. Such tunability in actuation properties permits the fabrication of specialized soft artificial muscles, where processing of the composite controls actuation strain and actuation force.

Single-photon emitters in hexagonal boron nitride: a review of progress

This report summarizes progress made in understanding properties such as zero-phonon-line energies, emission and absorption polarizations, electron-phonon couplings, strain tuning and hyperfine coupling of single photon emitters in hexagonal boron nitride. The primary aims of this research are to discover the chemical nature of the emitting centres and to facilitate deployment in device applications. Critical analyses of the experimental literature and data interpretation, as well as theoretical approaches used to predict properties, are made. In particular, computational and theoretical limitations and challenges are discussed, with a range of suggestions made to overcome these limitations, striving to achieve realistic predictions concerning the nature of emitting centers. A symbiotic relationship is required in which calculations focus on properties that can easily be measured, whilst experiments deliver results in a form facilitating mass-produced calculations.

Structure, stability and water adsorption on ultra-thin TiO2 supported on TiN

Interfacial metal-oxide systems with ultra-thin oxide layers are of high interest for their use in catalysis. The chemical activity of ultra-thin metal-oxide layers can be substantially enhanced compared to interfacial models with thicker oxide. In this study, we present a Density Functional Theory (DFT) investigation of the structure of ultra-thin rutile layers (one and two TiO₂ layers) supported on TiN and the stability of water on these interfacial structures. The rutile layers are stabilized on the TiN surface through the formation of interfacial Ti-O bonds. Charge transfer from the TiN substrate leads to the formation of reduced Ti³⁺ cations in TiO₂. The concentration of Ti³⁺ is proportionally higher in the ultra-thin oxide, compared to interfacial models with thicker oxide layers. The structure of the one-layer oxide slab is strongly distorted at the interface while the thicker TiO₂ layer preserves the rutile structure. The energy cost for the formation of a single O vacancy in the one-layer oxide slab is only 0.5 eV with respect to the ideal interface. For the two-layer oxide slab, the introduction of several vacancies in an already non-stoichiometric system becomes progressively more favourable, which indicates the stability of the highly defective interfaces. Isolated water molecules dissociate when adsorbed at the TiO₂ layers. At higher coverages, the preference is for molecular water adsorption. Our ab initio thermodynamics calculations show the fully water covered stoichiometric models as the most stable structure at typical ambient conditions. This behaviour is similar to that observed on thicker oxide in TiO₂-TiN interfaces or pure TiO₂ surfaces. In contrast, interfacial models with multiple vacancies are most stable at low (reducing) oxygen chemical potential values. The high concentration on reduced Ti³⁺ introduces significant distortions in the O-defective slab. Whereas, a water monolayer adsorbs dissociatively on the highly distorted 2-layer TiO_1.75-TiN interface, where the Ti³⁺ states lying above the top of the valence band contribute to a significant reduction of the energy gap compared to the stoichiometric TiO₂-TiN model. Our results provide a guide for the design of novel interfacial systems containing ultra-thin TiO₂ with potential application as photocatalytic water splitting devices.

Silver-Coated Poly(dimethylsiloxane) Beads for Soft, Stretchable, and Thermally Stable Conductive Elastomer Composites

We introduce an elastomer composite filled with silver (Ag) flakes and Ag-coated poly(dimethylsiloxane) (PDMS) beads that exhibits electrical conductivity that is 2 orders of magnitude greater than that of elastomers in which the same concentration of Ag filler is uniformly dispersed. In addition to the dramatic enhancement in conductivity, these composites exhibit high mechanical compliance (strain limit, >100%) and robust thermal stability (conductivity change, <10% at 150 °C). The incorporation of Ag-coated PDMS beads introduces an effective phase segregation in which Ag flakes are confined to the "grain boundaries" between the embedded beads. This morphological control aids in the percolation of the Ag flakes and the formation of conductive bridges between neighboring Ag shells. The confinement of Ag flakes also suppresses thermal expansion and changes in electrical conductivity of the percolating networks when the composite is heated. We demonstrate potential applications of thermally stable elastic conductors in wearable devices and soft robotics by fabricating a highly stretchable antenna for a "smart" furnace glove and a strain sensor for soft gripper operation in hot water.

A multifunctional shape-morphing elastomer with liquid metal inclusions

Natural soft tissue achieves a rich variety of functionality through a hierarchy of molecular, microscale, and mesoscale structures and ordering. Inspired by such architectures, we introduce a soft, multifunctional composite capable of a unique combination of sensing, mechanically robust electronic connectivity, and active shape morphing. The material is composed of a compliant and deformable liquid crystal elastomer (LCE) matrix that can achieve macroscopic shape change through a liquid crystal phase transition. The matrix is dispersed with liquid metal (LM) microparticles that are used to tailor the thermal and electrical conductivity of the LCE without detrimentally altering its mechanical or shape-morphing properties. Demonstrations of this composite for sensing, actuation, circuitry, and soft robot locomotion suggest the potential for versatile, tissue-like multifunctionality.

Abstract 577: Optimization of methods for the analysis of class I MHC peptides by mass spectrometry

Immuno-oncology describes therapeutic approaches exploiting the body's immune system to fight cancer. One approach involves educating the immune-system to recognize and destroy tumor cells by targeting tumor-specific neoantigens. Neoantigens are antigens presented by tumors but not recognized by the immune-system. Identification of Neoantigens is therefore an active area of research and development. The major histocompatibility complex (MHC) plays a crucial role in antigen presentation. Peptides generated by protein degradation in the cytosol are presented, non-covalently bound to MHC Class I molecules, on the surface of cells for inspection by T-lymphocytes. Cytotoxic T lymphocytes (CTL) recognize peptides presented by MHC Class I. The recognition of peptide antigens presented by MHC Class I results in the destruction of the presenting cell by the CTL. Characterization of peptides associated with MHC Class I molecules requires a targeted protein complex enrichment, an unbiased peptide elution and finally a peptide analysis method. Here we present the latest results from our work optimizing and performing a workflow for the analysis of peptides associated with Class I MHC molecules.

Citation Format: Michael J. Ford, Richard C. Jones, Ravi Amunugama, David Allen, Paul Del Rizzo, James Mobley, Michael Pisano. Optimization of methods for the analysis of class I MHC peptides by mass spectrometry [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 577.

van der Waals forces control ferroelectric-antiferroelectric ordering in CuInP2S6 and CuBiP2Se6 laminar materials

We show how van der Waals (vdW) forces outcompete covalent and ionic forces to control ferroelectric ordering in CuInP2S6 nanoflakes as well as in CuInP2S6 and CuBiP2Se6 crystals. While the self-assembly of these 2D layered materials is clearly controlled by vdW effects, this result indicates that the internal layer structure is also similarly controlled. Using up to 14 first-principles computational methods, we predict that the bilayers of both materials should be antiferroelectric. However, antiferroelectric nanoflakes and bulk materials are shown to embody two fundamentally different types of inter-layer interactions, with vdW forces strongly favouring one and strongly disfavouring the other compared to ferroelectric ordering. Strong specific vdW interactions involving the Cu atoms control this effect. Thickness-dependent significant cancellation of these two large opposing vdW contributions results in a small net effect that interacts with weak ionic contributions to control ferroelectric ordering.

Ab Initio Investigation of Water Adsorption and Hydrogen Evolution on Co9S8 and Co3S4 Low-Index Surfaces

We used density functional theory approach, with the inclusion of a semiempirical dispersion potential to take into account van der Waals interactions, to investigate the water adsorption and dissociation on cobalt sulfide Co₉S₈ and Co₃S₄(100) surfaces. We first determined the nanocrystal shape and selected representative surfaces to analyze. We then calculated water adsorption and dissociation energies, as well as hydrogen and oxygen adsorption energies, and we found that sulfur vacancies on Co₉S₈(100) surface enhance the catalytic activity toward water dissociation by raising the energy level of unhybridized Co 3d states closer to the Fermi level. Sulfur vacancies, however, do not have a significant impact on the energetics of Co₃S₄(100) surface.

Superconductivity in intercalated buckled two-dimensional materials: KGe2

Germanene has emerged as a novel two-dimensional material with various interesting properties and applications. Here we report the possibility of superconductivity in a stable potassium intercalated germanene compound, KGe2, with a transition temperature Tc ∼ 11 K, and an electron-phonon coupling of 1.9. Applying a 5% tensile strain, which reduces the buckling height by 4.5%, leads to the reduction of the electron-phonon coupling by 11% and a slight increase in Tc ∼ 12 K. That is, strong electron-phonon coupling results from the buckled structure of the germanene layers. Despite being an intercalated van der Waals material similar to intercalated graphite superconductors, it does not possess an occupied interlayer state.

Acceptor Percolation Determines How Electron-Accepting Additives Modify Transport of Ambipolar Polymer Organic Field-Effect Transistors

Organic field-effect transistors (OFETs) that utilize ambipolar polymer semiconductors can benefit from the ability of both electron and hole conduction, which is necessary for complementary circuits. However, simultaneous hole and electron transport in organic field-effect transistors result in poor ON/OFF ratios, limiting potential applications. Solution processing methods have been developed to control charge transport properties and transform ambipolar conduction to hole-only conduction. The electron-acceptor phenyl-C61-butyric acid methyl ester (PC₆₁BM), when mixed in solution with an ambipolar semiconducting polymer, can reduce electron conduction. Unipolar p-type OFETs with high, well-defined ON/OFF ratios and without detrimental effects on hole conduction are achieved for a wide range of blend compositions, from 95:5 to 5:95 wt % semiconductor polymer:PC₆₁BM. When introducing the alternative acceptor N, N'-bis(1-ethylpropyl)-3,4:9,10-perylenediimide (PDI), high ON/OFF ratios are achieved for 95:5 wt % semiconductor polymer:PDI; however, electron conduction increases for 50:50 and 5:95 wt % semiconductor polymer:PDI. As described within, we show that electron conduction is practically eliminated when additive domains do not percolate across the OFET channel, that is, electrons are "morphologically trapped". Morphologies were characterized by optical, electron, and atomic force microscopy as well as X-ray scattering techniques. PC₆₁BM was substituted with an endohedral Lu₃N fullerene, which enhanced contrast in electron microscopy and allowed for more detailed insight into the blend morphologies. Blends with alternative, nonfullerene acceptors further emphasize the importance of morphology and acceptor percolation, providing insights for such blends that control ambipolar transport and ON/OFF ratios.

Investigating the effect of dietary calcium levels on ileal endogenous amino acid losses and standardized ileal amino acid digestibility in broilers and laying hens

Two studies were conducted to evaluate the effect of dietary Ca levels (low, 1% and high, 3%) on ileal endogenous amino acid losses (IEAAL) and standardized ileal amino acid digestibility (SIAAD) in broilers (BR) and laying hens (LH) fed nitrogen-free diets (NFD) and distiller's dried grain with solubles (DDGS)-based diets. A total of 384 male Cobb 500 BR and 288 LH were used in a completely randomized design (CRD) with 16 (BR) or 12 (LH) replicate cages with 6 birds/replicate. IEAAL and apparent ileal digestibility (AID) of AA were analyzed using the GLM procedure of SAS appropriate for a CRD while SIAAD values were analyzed using the GLM procedure of SAS appropriate for a 2 × 2 factorial arrangement of treatments. For BR, IEAAL and N losses (mg/kg of dry matter intake, DMI) were higher (P < 0.05) when NFD with high Ca level was fed (total AA was 39%, N was 35% higher). For most of the AA, AID was higher (P < 0.05) in BR fed DDGS-based diet with high Ca level. High dietary Ca resulted in higher (P < 0.05) SIAAD for all the AA except for Arg, Lys, Met, Cys, and Tyr. For LH, AID of AA was higher (P < 0.05) for the DDGS diet with high Ca level in 13 of the 18 AA evaluated. There was interaction (P < 0.05) between diet Ca level and correction method on LH SIAAD values for Thr, Asp, Gly, and Ser. The SIAAD values for 8 AA were higher (P < 0.05) in birds on high Ca DDGS diet. Correction with low Ca NFD resulted in higher (P < 0.05) SIAAD values for all the AA. Result from this study showed that high Ca increased total IEAAL in BR by 39% but decreased same by 27% in LH. Finally, SIAAD values were increased in BR fed high Ca DDGS-based diet while SIAAD value in LH was lower when correction was done using values from high Ca-NFD fed birds.

Abstract 5717: Mass spectrometry as a tool for MHC class I and II neoantigen discovery

A neoantigen is a patient-specific tumor antigen resulting from mutations during oncogenesis (1). Advances in genome sequencing of cancer tumor tissues combined with bioinformatics have enabled the identification of tumor specific mutations and the prediction of the peptides that will be presented by the MHC complex. The presented peptides are recognized as foreign by the immune system and can be used to discriminate cancerous from normal cells. Neoantigen prediction by gene sequencing and in silico approaches can be strengthened and further supported by mass spectrometry. The molecular level characterization of peptides associated with molecules of the major histocompatibility complex requires a targeted protein complex enrichment, an unbiased peptide elution, and finally a peptide analysis method. We use immunoaffinity to isolate the target complex, elute the peptides under conditions minimizing protein contamination and finally analyze the peptides by mass spectrometry. Here we present a case studies of our recent work applying workflows for the analysis of peptides associated with both Class I and Class II MHC molecules. Combining state-of-the-art mass spectrometry and bioinformatics, we demonstrate the utility of this approach for neoantigen identification and quantitation.

Reference: 1. Sun et al. Cancer Lett 2017;392:17-25.

Citation Format: Michael J. Ford, Richard Jones, David Allen, Ravi Amunugama, Michael Pisano, James Mobley, Paul Domanski, Bill Ho, Daniel Bochar, Melissa Holt. Mass spectrometry as a tool for MHC class I and II neoantigen discovery [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5717.

The effect of drying method temperature, collection method, and marker type on apparent ileal amino acid digestibility in 21-day-old broilers fed corn-soybean meal-barley based diet

For accurate estimation of nutrient digestibility, an ideal drying and sampling method is required to preserve the quality of the digesta. A standard corn-soybean meal (corn-SBM) broiler starter diet was fed from d 0 to 10 before birds were placed on the experimental diets until d 21. One hundred and sixty-eight male Cobb 500 broiler chicks were used to evaluate the effect of two drying methods (freeze-dryer vs. forced air-oven) and two drying temperatures (40 vs. 55°C) (Exp 1), while ninety-six chicks were used to evaluate the effect of flushing and squeezing as well as marker types (titanium vs. chromium) on apparent ileal DM, N, Ca, P, and AA digestibility (Exp 2). There were seven (Exp 1) or eight (Exp 2) replicate cages per treatment with 6 birds/cage. Digesta from the distal two thirds of the ileum was obtained from birds following euthanasia on d 21 by squeezing (Exp 1) and squeezing or flushing (Exp 2). Samples collected were stored in the freezer at -20°C until they were either freeze-dried (FD) or oven-dried (OD) at 40 or 55°C. There were no interactions between the drying methods and drying temperatures (Exp 1) on apparent ileal DM, N, and AA digestibility. Met had the highest (92.3%) while Cys had the lowest (73.8%) digestibility value. In Exp 2, no interaction between sampling methods and marker types was observed. The effect of sampling methods was not significant except for Arg and Met where squeezing resulted in higher (P < 0.05) digestibility values. Furthermore, apparent ileal His, Ile, Cys, Ser, and Tyr digestibility tended to be higher (P < 0.1) in squeezed digesta compared to the flushed digesta. Results from these studies showed that OD ileal digesta at 40 or 55°C had no negative effect on apparent ileal AA digestibility. Likewise, marker type did not influence apparent ileal AA digestibility values.

Examining the effect of dietary electrolyte balance, energy source, and length of feeding of nitrogen-free diets on ileal endogenous amino acid losses in broilers

The effect of dietary electrolyte balance (DEB), energy source (ES), and length of feeding of nitrogen-free diet (NFD) on ileal endogenous amino acid (EAA) loss in mg/kg dry matter intake (DMI) was evaluated in broiler chickens. In Experiment 1, 720 chickens consisting of 15 replicate cages with 6 chickens/replicate were used. Treatments were arranged in a 2 × 2 × 2 factorial and consisted of 4 NFD with 2 levels (low or high) of DEB and 2 ES [corn starch (CS) or dextrose (DX)], and 2 sampling time-points (diets were fed for either 72 h (d 16 to 19) or 120 h (d 16 to 21). Experiment 2 used 360 chickens in a 2 × 2 factorial arrangement of treatments with 2 levels (low or high) of DEB and 2 ES (CS or DX). Diets were fed for 72 h (d 18 to 21). All birds had access to feed and water on an ad libitum basis. Data were analyzed using the GLM procedure of SAS appropriate for a completely randomized design for a factorial arrangement of treatments. For Experiment 1, there were interactions (P < 0.05) between the 3 main factors for nitrogen and all the AA except Trp. Broilers that were fed DX-based NFD with high DEB for 72 h had the highest (P < 0.05) EAA losses. In Experiment 2, there was no interaction between DEB and ES except for His and Lys. When ileal EAA losses from birds fed the low DEB, CS-based NFD were used to standardize apparent ileal digestibility values from a previous study, there was no effect of length of feeding on standardized ileal AA digestibility values. In conclusion, DX-based NFD with high DEB increased endogenous AA loses. Despite differences in ileal EAA losses from CS-based NFD, standardized ileal AA digestibility values were not influenced by the length of feeding of NFD. Based on the results from these studies, NFD could be fed for 72 h without influencing SIAAD values.

Anisotropic functionalization of upconversion nanoparticles

Despite significant advances toward accurate tuning of the size and shape of colloidal nanoparticles, the precise control of the surface chemistry thereof remains a grand challenge. It is desirable to conjugate functional bio-molecules onto the selected facets of nanoparticles owing to the versatile capabilities rendered by the molecules. We report here facet-selective conjugation of DNA molecules onto upconversion nanoparticles via ligand competition reaction. Different binding strengths of phosphodiester bonds and phosphate groups on DNA and the surfactant molecules allow one to create heterogeneous bio-chemistry surface for upconversion nanoparticles. The tailored surface properties lead to the formation of distinct self-assembly structures. Our findings provide insight into the interactions between biomolecules and nanoparticles, unveiling the potential of using nanoparticles as fundamental building blocks for creating self-assembled nano-architectures.

Characterization of Peptides Associated with Molecules of the Major Histocompatibility Complex using Mass Spectrometry

The major histocompatibility complex (MHC) is a region of highly polymorphic genes encoding for glycoproteins (MHC molecules) that form part of the cell-mediated branch of the acquired immune system. In the cytosol, cellular self and foreign (non-self) proteins are constantly being degraded; it is the peptides generated that are presented, non-covalently bound to MHC molecules, on the surface of cells for inspection by cytotoxic T-lymphocytes (CTLs). Non-recognition of the presented peptide ultimately leads to cell destruction.

Characterizing the factors associated with non-recognition is an attractive proposition for anyone interested in generating tools for targeted cell destruction. In the field of oncology the obvious application then is the targeted destruction of cancerous cells. To enable the molecular level characterization of peptides associated with molecules of the major histocompatibility complex requires a targeted protein complex enrichment, an unbiased peptide elution and finally a peptide analysis method. Most frequently an immunoprecipitation is used to isolate the target complex. The peptide elution is performed under conditions minimizing protein contamination and finally peptide analysis is accomplished by mass spectrometry.

Here we present a case study of our recent work optimizing and performing a workflow for the analysis of peptides associated with Class I and Class II MHC molecules.

Doping Polymer Semiconductors by Organic Salts: Toward High-Performance Solution-Processed Organic Field-Effect Transistors

Solution-processed organic field-effect transistors (OFETs) were fabricated with the addition of an organic salt, trityl tetrakis(pentafluorophenyl)borate (TrTPFB), into thin films of donor-acceptor copolymer semiconductors. The performance of OFETs is significantly enhanced after the organic salt is incorporated. TrTPFB is confirmed to p-dope the organic semiconductors used in this study, and the doping efficiency as well as doping physics was investigated. In addition, systematic electrical and structural characterizations reveal how the doping enhances the performance of OFETs. Furthermore, it is shown that this organic salt doping method is feasible for both p- and n-doping by using different organic salts and, thus, can be utilized to achieve high-performance OFETs and organic complementary circuits.

Deterministic Nanopatterning of Diamond Using Electron Beams

Diamond is an ideal material for a broad range of current and emerging applications in tribology, quantum photonics, high-power electronics, and sensing. However, top-down processing is very challenging due to its extreme chemical and physical properties. Gas-mediated electron beam-induced etching (EBIE) has recently emerged as a minimally invasive, facile means to dry etch and pattern diamond at the nanoscale using oxidizing precursor gases such as O₂ and H₂O. Here we explain the roles of oxygen and hydrogen in the etch process and show that oxygen gives rise to rapid, isotropic etching, while the addition of hydrogen gives rise to anisotropic etching and the formation of topographic surface patterns. We identify the etch reaction pathways and show that the anisotropy is caused by preferential passivation of specific crystal planes. The anisotropy can be controlled by the partial pressure of hydrogen and by using a remote RF plasma source to radicalize the precursor gas. It can be used to manipulate the geometries of topographic surface patterns as well as nano- and microstructures fabricated by EBIE. Our findings constitute a comprehensive explanation of the anisotropic etch process and advance present understanding of electron-surface interactions.

The Irritable Bowel Syndrome: A Disease or a Response? Discussion Paper

The irritable bowel syndrome is a problem commonly found in the population as a whole, in general practice and in general hospital and specialist gastroenterological clinical practice. A population survey found that 14% of those interviewed exhibited symptoms of the irritable bowel syndrome but did not present to their general practitioner. In the gastroenterology clinic it is said to represent approximately one-third to one-half of referrals1.

Magnetic properties of stoichiometric and defective Co9S8

Our theoretical investigation confirms the antiferromagnetic nature of pentlandite Co₉S₈ and predicts a change in the local magnetic properties upon sulfur vacancy formation.

Competing tradeoffs between increasing marine mammal predation and fisheries harvest of Chinook salmon

Many marine mammal predators, particularly pinnipeds, have increased in abundance in recent decades, generating new challenges for balancing human uses with recovery goals via ecosystem-based management. We used a spatio-temporal bioenergetics model of the Northeast Pacific Ocean to quantify how predation by three species of pinnipeds and killer whales (Orcinus orca) on Chinook salmon (Oncorhynchus tshawytscha) has changed since the 1970s along the west coast of North America, and compare these estimates to salmon fisheries. We find that from 1975 to 2015, biomass of Chinook salmon consumed by pinnipeds and killer whales increased from 6,100 to 15,200 metric tons (from 5 to 31.5 million individual salmon). Though there is variation across the regions in our model, overall, killer whales consume the largest biomass of Chinook salmon, but harbor seals (Phoca vitulina) consume the largest number of individuals. The decrease in adult Chinook salmon harvest from 1975-2015 was 16,400 to 9,600 metric tons. Thus, Chinook salmon removals (harvest + consumption) increased in the past 40 years despite catch reductions by fisheries, due to consumption by recovering pinnipeds and endangered killer whales. Long-term management strategies for Chinook salmon will need to consider potential conflicts between rebounding predators or endangered predators and prey.

Evaluating the Cost, Safety, and Proliferation Risks of Small Floating Nuclear Reactors

It is hard to see how our energy system can be decarbonized if the world abandons nuclear power, but equally hard to introduce the technology in nonnuclear energy states. This is especially true in countries with limited technical, institutional, and regulatory capabilities, where safety and proliferation concerns are acute. Given the need to achieve serious emissions mitigation by mid-century, and the multidecadal effort required to develop robust nuclear governance institutions, we must look to other models that might facilitate nuclear plant deployment while mitigating the technology's risks. One such deployment paradigm is the build-own-operate-return model. Because returning small land-based reactors containing spent fuel is infeasible, we evaluate the cost, safety, and proliferation risks of a system in which small modular reactors are manufactured in a factory, and then deployed to a customer nation on a floating platform. This floating small modular reactor would be owned and operated by a single entity and returned unopened to the developed state for refueling. We developed a decision model that allows for a comparison of floating and land-based alternatives considering key International Atomic Energy Agency plant-siting criteria. Abandoning onsite refueling is beneficial, and floating reactors built in a central facility can potentially reduce the risk of cost overruns and the consequences of accidents. However, if the floating platform must be built to military-grade specifications, then the cost would be much higher than a land-based system. The analysis tool presented is flexible, and can assist planners in determining the scope of risks and uncertainty associated with different deployment options.

Tunable and high-purity room temperature single-photon emission from atomic defects in hexagonal boron nitride

Two-dimensional van der Waals materials have emerged as promising platforms for solid-state quantum information processing devices with unusual potential for heterogeneous assembly. Recently, bright and photostable single photon emitters were reported from atomic defects in layered hexagonal boron nitride (hBN), but controlling inhomogeneous spectral distribution and reducing multi-photon emission presented open challenges. Here, we demonstrate that strain control allows spectral tunability of hBN single photon emitters over 6 meV, and material processing sharply improves the single photon purity. We observe high single photon count rates exceeding 7 × 106 counts per second at saturation, after correcting for uncorrelated photon background. Furthermore, these emitters are stable to material transfer to other substrates. High-purity and photostable single photon emission at room temperature, together with spectral tunability and transferability, opens the door to scalable integration of high-quality quantum emitters in photonic quantum technologies.Inhomogeneous spectral distribution and multi-photon emission are currently hindering the use of defects in layered hBN as reliable single photon emitters. Here, the authors demonstrate strain-controlled wavelength tuning and increased single photon purity through suitable material processing.