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Electrification to reduce or eliminate greenhouse gas emissions is essential to mitigate climate change. However, a substantial portion of our manufacturing and transportation infrastructure will be difficult to electrify and/or will continue to use carbon as a key component, including areas in aviation, heavy-duty and marine transportation, and the chemical industry. In this Roadmap, we explore how multidisciplinary approaches will enable us to close the carbon cycle and create a circular economy by defossilizing these difficult-to-electrify areas and those that will continue to need carbon. We discuss two approaches for this: developing carbon alternatives and improving our ability to reuse carbon, enabled by separations. Furthermore, we posit that co-design and use-driven fundamental science are essential to reach aggressive greenhouse gas reduction targets.

Supported noble metal catalysts, ubiquitous in chemical technology, often undergo dynamic transformations between reduced and oxidized states-which influence the metal nuclearities, oxidation states, and catalytic properties. In this investigation, we report the results of in situ X-ray absorption spectroscopy, scanning transmission electron microscopy, and other physical characterization techniques, bolstered by density functional theory, to elucidate the structural transformations of a set of MgO-supported palladium catalysts under oxidative treatment conditions. As the calcination temperature increased, the as-synthesized supported metallic palladium nanoparticles underwent oxidation to form palladium oxides (at approximately 400 °C), which, at approximately 500 °C, were oxidatively fragmented to form mixtures of atomically dispersed palladium cations. The data indicate two distinct types of atomically dispersed species: palladium cations located at MgO steps and those embedded in the first subsurface layer of MgO. The former exhibit significantly higher (>500 times) catalytic activity for ethylene hydrogenation than the latter. The results pave the way for designing highly active and stable supported palladium hydrogenation catalysts with optimized metal utilization.

The reduction of CO2 is known to promote increased alkene yields from alkane dehydrogenations when the reactions are cocatalyzed. The mechanism of this promotion is not understood in the context of catalyst active-site environments because CO2 is amphoteric, and even general aspects of the chemistry, including the significance of competing side reactions, differ significantly across catalysts. Atomically dispersed chromium cations stabilized in highly siliceous MFI zeolite are shown here to enable the study of the role of parallel CO2 reduction during ethylene-selective ethane dehydrogenation. Based on infrared spectroscopy and X-ray absorption spectroscopy data interpreted through calculations using density functional theory (DFT), the synthesized catalyst contains atomically dispersed Cr cations stabilized by silanol nests in micropores. Reactor studies show that cofeeding CO2 increases stable ethylene-selective ethane dehydrogenation rates over a wide range of partial pressures. Operando X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine-structure (EXAFS) spectra indicate that during reaction at 650 °C the Cr cations maintain a nominal 2+ charge and a total Cr-O coordination number of approximately 2. However, CO2 reduction induces a change, correlated with the CO2 partial pressure, in the population of two distinct Cr-O scattering paths. This indicates that the promotional effect of parallel CO2 reduction can be attributed to a subtle change in Cr-O bond lengths in the local coordination environment of the active site. These insights are made possible by simultaneously fitting multiple EXAFS spectra recorded in different reaction conditions; this novel procedure is expected to be generally applicable for interpreting operando catalysis EXAFS data.

Soft-oxidant-assisted methane coupling has emerged as a promising pathway to upgrade methane from natural gas sources to high-value commodity chemicals, such as ethylene, at selectivities higher than those associated with oxidative (O2) methane coupling (OCM). To date, few studies have reported investigations into the electronic structure and the microscopic physical structure of catalytic active sites present in the binary metal oxide catalyst systems that are known to be effective for this reaction. Correlating the catalyst activity to specific active site structures and electronic properties is an essential aspect of catalyst design. Here, we used X-ray absorption spectroscopy at the Ca K-edge to ascertain the most probable local environment of Ca in the ZnO-supported Ca oxide catalysts. These catalysts are shown here to be active for N2O-assisted methane coupling (N2O-OCM) and have previously been reported to be active for CO2-assisted methane coupling (CO2-OCM). X-ray absorption near edge structure features at multiple Ca loadings are interpreted through simulated spectra derived from ab initio full multiple scattering calculations. These simulations included consideration of CaO structures organized in multiple spatial arrangements-linear, planar, and cubic-with separate analyses of Ca atoms in the surfaces and bulk of the three-dimensional structures. The morphology of the oxide clusters was found to influence the various regions of the X-ray absorption spectrum differently. Experiment and theory show that for low-Ca-loading catalysts (≤1 mol %), which contain sites particularly active for methane coupling, Ca primarily exists in an oxidized state that is consistent with the coordination environment of Ca ions in one- and two-dimensional clusters. In addition to their unique nanoscale structures, the spectra also indicate that these clusters have varying degrees of undercoordinated surface Ca atoms that could further influence their catalytic activities. The local Ca structure was correlated to methane coupling activity from N2O-OCM and previously reported CO2-OCM reactor studies. This study provides a unique perspective on the relationship between the catalyst physical and electronic structure and active sites for soft-oxidant-assisted methane coupling, which can be used to inform future catalyst development.

Hexagonal boron nitride (hBN) is a highly selective catalyst for the oxidative dehydrogenation of propane (ODHP) to propylene. Using a variety of ex situ characterization techniques, the activity of the catalyst has been attributed to the formation of an amorphous boron oxyhydroxide surface layer. The ODHP reaction mechanism proceeds via a combination of surface mediated and gas phase propagated radical reactions with the relative importance of both depending on the surface-to-void-volume ratio. Here we demonstrate the unique capability of operando X-ray Raman spectroscopy (XRS) to investigate the oxyfunctionalization of the catalyst under reaction conditions (1 mm outer diameter reactor, 500 to 550 °C, P = 30 kPa C3H8, 15 kPa O2, 56 kPa He). We probe the effect of a water cofeed on the surface of the activated catalyst and find that water removes boron oxyhydroxide from the surface, resulting in a lower reaction rate when the surface reaction dominates and an enhanced reaction rate when the gas phase contribution dominates. Computational description of the surface transformations at an atomic-level combined with high precision XRS spectra simulations with the OCEAN code rationalize the experimental observations. This work establishes XRS as a powerful technique for the investigation of light element-containing catalysts under working conditions.

Stable catalysts are essential to address energy and environmental challenges, especially for applications in harsh environments (for example, high temperature, oxidizing atmosphere and steam). In such conditions, supported metal catalysts deactivate due to sintering-a process where initially small nanoparticles grow into larger ones with reduced active surface area-but strategies to stabilize them can lead to decreased performance. Here we report stable catalysts prepared through the encapsulation of platinum nanoparticles inside an alumina framework, which was formed by depositing an alumina precursor within a separately prepared porous organic framework impregnated with platinum nanoparticles. These catalysts do not sinter at 800 °C in the presence of oxygen and steam, conditions in which conventional catalysts sinter to a large extent, while showing similar reaction rates. Extending this approach to Pd-Pt bimetallic catalysts led to the small particle size being maintained at temperatures as high as 1,100 °C in air and 10% steam. This strategy can be broadly applied to other metal and metal oxides for applications where sintering is a major cause of material deactivation.

β-adrenergic receptor (β-AR) signaling in cardiac myocytes is central to cardiac function, but spatiotemporal activation within myocytes is unresolved. In rabbit ventricular myocytes, β-AR agonists or high extracellular [Ca] were applied locally at one end, to measure β-AR signal propagation as Ca-transient (CaT) amplitude and sarcoplasmic reticulum (SR) Ca uptake. High local [Ca]o, increased CaT amplitude under the pipette faster than did ISO, but was also more spatially restricted. Local isoproterenol (ISO) or norepinephrine (NE) increased CaT amplitude and SR Ca uptake, that spread along the myocyte to the unexposed end. Thus, local [Ca]i decline kinetics reflect spatio-temporal progression of β-AR end-effects in myocytes. To test whether intracellular β-ARs contribute to this response, we used β-AR-blockers that are membrane permeant (propranolol) or not (sotalol). Propranolol completely blocked NE-dependent CaT effects. However, blocking surface β-ARs only (sotalol) suppressed only ∼50% of the NE-induced increase in CaT peak and rate of [Ca]i decline, but these changes spread more gradually than NE alone. We also tested whether A-kinase anchoring protein 7γ (AKAP7γ; that interacts with phospholamban) is mobile, such that it might contribute to intracellular spatial propagation of β-AR signaling. We found AKAP7γ to be highly mobile using fluorescence recovery after photobleach of GFP tagged AKAP7γ, and that PKA activation accelerated AKAP7γ-GFP wash-out upon myocyte saponin-permeabilization, suggesting increased AKAP7γ mobility. We conclude that local β-AR activation can activate SR Ca uptake at remote myocyte sites, and that intracellular β-AR and AKAP7γ mobility may play a role in this spread of activation.

Atomically dispersed metals on metal oxide supports are a rapidly growing class of catalysts. Developing an understanding of where and how the metals are bonded to the supports is challenging because support surfaces are heterogeneous, and most reports lack a detailed consideration of these points. Herein, we report two atomically dispersed CO oxidation catalysts having markedly different metal-support interactions: platinum in the first layer of crystalline MgO powder and platinum in the second layer of this support. Structural models have been determined on the basis of data and computations, including those determined by extended X-ray absorption fine structure and X-ray absorption near edge structure spectroscopies, infrared spectroscopy of adsorbed CO, and scanning transmission electron microscopy. The data demonstrate the transformation of surface to subsurface platinum as the temperature of sample calcination increased. Catalyst performance data demonstrate the lower activity but greater stability of the subsurface platinum than of the surface platinum.

Elucidation of reaction mechanisms and the geometric and electronic structure of the active sites themselves is a challenging, yet essential task in the design of new heterogeneous catalysts. Such investigations are best implemented via a multipronged approach that comprises ambient pressure catalysis, surface science, and theory. Herein, we employ this strategy to understand the workings of NiAu single-atom alloy (SAA) catalysts for the selective nonoxidative dehydrogenation of ethanol to acetaldehyde and hydrogen. The atomic dispersion of Ni is paramount for selective ethanol to acetaldehyde conversion, and we show that even the presence of small Ni ensembles in the Au surface results in the formation of undesirable byproducts via C-C scission. Spectroscopic, kinetic, and theoretical investigations of the reaction mechanism reveal that both C-H and O-H bond cleavage steps are kinetically relevant and single Ni atoms are confirmed as the active sites. X-ray absorption spectroscopy studies allow us to follow the charge of the Ni atoms in the Au host before, under, and after a reaction cycle. Specifically, in the pristine state the Ni atoms carry a partial positive charge that increases upon coordination to the electronegative oxygen in ethanol and decreases upon desorption. This type of oxidation state cycling during reaction is similar to the behavior of single-site homogeneous catalysts. Given the unique electronic structure of many single-site catalysts, such a combined approach in which the atomic-scale catalyst structure and charge state of the single atom dopant can be monitored as a function of its reactive environment is a key step toward developing structure-function relationships that inform the design of new catalysts.

Atomically dispersed noble metal catalysts have drawn wide attention as candidates to replace supported metal clusters and metal nanoparticles. Atomic dispersion can offer unique chemical properties as well as maximum utilization of the expensive metals. Addition of a second metal has been found to help reduce the size of Pt ensembles in bimetallic clusters; however, the stabilization of isolated Pt atoms in small nests of nonprecious metal atoms remains challenging. We now report a novel strategy for the design, synthesis, and characterization of a zeolite-supported propane dehydrogenation catalyst that incorporates predominantly isolated Pt atoms stably bonded within nests of Zn atoms located within the nanoscale pores of dealuminated zeolite Beta. The catalyst is stable in long-term operation and exhibits high activity and high selectivity to propene. Atomic resolution images, bolstered by X-ray absorption spectra, demonstrate predominantly atomic dispersion of the Pt in the nests and, with complementary infrared and nuclear magnetic resonance spectra, determine a structural model of the nested Pt.

Electronic and geometric interactions between active and support phases are critical in determining the activity of heterogeneous catalysts, but metal-support interactions are challenging to study. Here, it is demonstrated how the combination of the monolayer-controlled formation using atomic layer deposition (ALD) and colloidal nanocrystal synthesis methods leads to catalysts with sub-nanometer precision of active and support phases, thus allowing for the study of the metal-support interactions in detail. The use of this approach in developing a fundamental understanding of support effects in Pd-catalyzed methane combustion is demonstrated. Uniform Pd nanocrystals are deposited onto Al2 O3 /SiO2 spherical supports prepared with control over morphology and Al2 O3 layer thicknesses ranging from sub-monolayer to a ≈4 nm thick uniform coating. Dramatic changes in catalytic activity depending on the coverage and structure of Al2 O3 situated at the Pd/Al2 O3 interface are observed, with even a single monolayer of alumina contributing an order of magnitude increase in reaction rate. By building the Pd/Al2 O3 interface up layer-by-layer and using uniform Pd nanocrystals, this work demonstrates the importance of controlled and tunable materials in determining metal-support interactions and catalyst activity.

RationaleWe recently discovered pivotal contributions of stress kinase JNK2 (c-Jun N-terminal kinase isoform 2) in increased risk of atrial fibrillation through enhanced diastolic sarcoplasmic reticulum (SR) calcium (Ca2+) leak via RyR2 (ryanodine receptor isoform 2). However, the role of JNK2 in the function of the SERCA2 (SR Ca2+-ATPase), essential in maintaining SR Ca2+ content cycling during each heartbeat, is completely unknown.ObjectiveTo test the hypothesis that JNK2 increases SERCA2 activity SR Ca2+ content and exacerbates an arrhythmic SR Ca2+ content leak-load relationship.Methods and resultsWe used confocal Ca2+ imaging in myocytes and HEK-RyR2 (ryanodine receptor isoform 2-expressing human embryonic kidney 293 cells) cells, biochemistry, dual Ca2+/voltage optical mapping in intact hearts from alcohol-exposed or aged mice (where JNK2 is activated). We found that JNK2, but not JNK1 (c-Jun N-terminal kinase isoform 1), increased SERCA2 uptake and consequently elevated SR Ca2+ content load. JNK2 also associates with and phosphorylates SERCA2 proteins. JNK2 causally enhances SERCA2-ATPase activity via increased maximal rate, without altering Ca2+ affinity. Unlike the CaMKII (Ca2+/calmodulin-dependent kinase II)-dependent JNK2 action in SR Ca2+ leak, JNK2-driven SERCA2 function was CaMKII independent (not prevented by CaMKII inhibition). With CaMKII blocked, the JNK2-driven SR Ca2+ loading alone did not significantly raise leak. However, with JNK2-CaMKII-driven SR Ca2+ leak present, the JNK2-enhanced SR Ca2+ uptake limited leak-induced reduction in SR Ca2+, normalizing Ca2+ transient amplitude, but at a higher arrhythmogenic SR Ca2+ leak. JNK2-specific inhibition completely normalized SR Ca2+ handling, attenuated arrhythmic Ca2+ activities, and alleviated atrial fibrillation susceptibility in aged and alcohol-exposed myocytes and intact hearts.ConclusionsWe have identified a novel JNK2-induced activation of SERCA2. The dual action of JNK2 in CaMKII-dependent arrhythmic SR Ca2+ leak and a CaMKII-independent uptake exacerbates atrial arrhythmogenicity, while helping to maintain normal levels of Ca2+ transients and heart function. JNK2 modulation may be a novel therapeutic target for atrial fibrillation prevention and treatment.

An understanding of the fundamentals of the reaction between CuO with trace amounts of H2S to form CuS products is critical for the optimal utilization of this process in sulfur removal applications. Unfortunately, CuS is a complex material, featuring various Cu2-xS compounds (with 0 ≤ x ≤ 1), distorted crystal phases, and varying electronic structures and coordination environments of Cu and S ions. In this work, we combine ex situ and in situ X-ray absorption spectroscopy (XAS) at S and Cu K edges, fixed bed sorption experiments, DFT simulations, and other characterization techniques to speciate the CuS products formed at different temperatures (298-383 K) and from CuO sorbents with different crystallite sizes (2.8-40 nm). The results of our analysis identify the formation of a distorted CuS layer at the surface of CuO crystals with disulfide groups with shorter Cu-S bonds and higher delocalization of the positive charge of the Cu center into (S1-)2. This distorted CuS layer dominates the XAS signal at lower temperatures (298-323 K) and at the initial stages of sulfidation at higher temperatures (353 and 383 K) where conversion is low (

An understanding of the fundamentals of the reaction between CuO with trace amounts of H2S to form CuS products is critical for the optimal utilization of this process in sulfur removal applications. Unfortunately, CuS is a complex material, featuring various Cu2-xS compounds (with 0 ≤ x ≤ 1), distorted crystal phases, and varying electronic structures and coordination environments of Cu and S ions. In this work, we combine ex situ and in situ X-ray absorption spectroscopy (XAS) at S and Cu K edges, fixed bed sorption experiments, DFT simulations, and other characterization techniques to speciate the CuS products formed at different temperatures (298-383 K) and from CuO sorbents with different crystallite sizes (2.8-40 nm). The results of our analysis identify the formation of a distorted CuS layer at the surface of CuO crystals with disulfide groups with shorter Cu-S bonds and higher delocalization of the positive charge of the Cu center into (S1-)2. This distorted CuS layer dominates the XAS signal at lower temperatures (298-323 K) and at the initial stages of sulfidation at higher temperatures (353 and 383 K) where conversion is low (

Complexes with neighboring metal centers in isolated pairs and their analogues on surfaces are drawing increasing attention as catalysts. These include molecular homogeneous catalysts incorporating various ligands, enzymes, and solids that include pairs of metal atoms mounted on supports. Catalysts in this broad class are active for numerous reactions and offer unexplored opportunities to address challenging reactions, such as oxidation of methane and oxidation of water in artificial photosynthesis. The subject of supported metal pair-site catalysts is in its infancy, facing challenges in (a) precise synthesis, (b) structure determination at the atomic scale, and (c) stabilization in reactive atmospheres. In this Perspective, we summarize key characteristics of molecular and enzymatic catalysts that incorporate neighboring metal centers and build on this foundation to assess the emerging literature of metal pair-site catalysts on various supports. The supported catalysts include those synthesized by anchoring molecular dinuclear precursors to support surfaces and those synthesized by selective formation of dinuclear surface species from mononuclear surface species. Examples of metals in this class are rhodium and iridium, and examples of supports are MgO and Fe2O3. We summarize characterization of these materials by electron microscopy and spectroscopy, emphasizing atomic-resolution aberration-corrected scanning transmission electron microscopy and spectroscopies that provide atomic-scale structural information and allow characterization of functioning catalysts, especially X-ray absorption spectroscopy. We list some opportunities for research, including suggestions that might lead to structurally well-defined supported metal pair-sites with new catalytic properties.

Complexes with neighboring metal centers in isolated pairs and their analogues on surfaces are drawing increasing attention as catalysts. These include molecular homogeneous catalysts incorporating various ligands, enzymes, and solids that include pairs of metal atoms mounted on supports. Catalysts in this broad class are active for numerous reactions and offer unexplored opportunities to address challenging reactions, such as oxidation of methane and oxidation of water in artificial photosynthesis. The subject of supported metal pair-site catalysts is in its infancy, facing challenges in (a) precise synthesis, (b) structure determination at the atomic scale, and (c) stabilization in reactive atmospheres. In this Perspective, we summarize key characteristics of molecular and enzymatic catalysts that incorporate neighboring metal centers and build on this foundation to assess the emerging literature of metal pair-site catalysts on various supports. The supported catalysts include those synthesized by anchoring molecular dinuclear precursors to support surfaces and those synthesized by selective formation of dinuclear surface species from mononuclear surface species. Examples of metals in this class are rhodium and iridium, and examples of supports are MgO and Fe2O3. We summarize characterization of these materials by electron microscopy and spectroscopy, emphasizing atomic-resolution aberration-corrected scanning transmission electron microscopy and spectroscopies that provide atomic-scale structural information and allow characterization of functioning catalysts, especially X-ray absorption spectroscopy. We list some opportunities for research, including suggestions that might lead to structurally well-defined supported metal pair-sites with new catalytic properties.

Single-site Ir(CO)2 complexes bonded to high-surface-area metal oxide supports, SiO2, TiO2, Fe2O3, CeO2, MgO, and La2O3, were synthesized by chemisorption of Ir(CO)2(acac) (acac = acetylacetonate) followed by coating with each of the following ionic liquids (ILs): 1-n-butyl-3-methylimidazolium tetrafluoroborate, [BMIM][BF4], 1-n-butyl-3-methylimidazolium acetate, [BMIM][Ac], and 1-(3-cyanopropyl)-3-methylimidazolium dicyanamide, [CPMIM][DCA]. Extended X-ray absorption fine structure spectroscopy showed that site-isolated iridium was bonded to oxygen atoms of the support. Electron densities on the iridium enveloped by each IL sheath/support combination were characterized by carbonyl infrared spectroscopy of the iridium gem-dicarbonyls and by X-ray absorption near-edge structure data. The electron-donor/acceptor tendencies of both the support and IL determine the activity and selectivity of the catalysts for the hydrogenation of 1,3-butadiene, with electron-rich iridium being selective for partial hydrogenation. The results resolve the effects of the IL and support as ligands; for example, the effect of the IL becomes dominant when the support has a weak electron-donor character. The combined effects of supports and ILs as ligands offer broad opportunities for tuning catalytic properties of supported metal catalysts.

Single-site Ir(CO)2 complexes bonded to high-surface-area metal oxide supports, SiO2, TiO2, Fe2O3, CeO2, MgO, and La2O3, were synthesized by chemisorption of Ir(CO)2(acac) (acac = acetylacetonate) followed by coating with each of the following ionic liquids (ILs): 1-n-butyl-3-methylimidazolium tetrafluoroborate, [BMIM][BF4], 1-n-butyl-3-methylimidazolium acetate, [BMIM][Ac], and 1-(3-cyanopropyl)-3-methylimidazolium dicyanamide, [CPMIM][DCA]. Extended X-ray absorption fine structure spectroscopy showed that site-isolated iridium was bonded to oxygen atoms of the support. Electron densities on the iridium enveloped by each IL sheath/support combination were characterized by carbonyl infrared spectroscopy of the iridium gem-dicarbonyls and by X-ray absorption near-edge structure data. The electron-donor/acceptor tendencies of both the support and IL determine the activity and selectivity of the catalysts for the hydrogenation of 1,3-butadiene, with electron-rich iridium being selective for partial hydrogenation. The results resolve the effects of the IL and support as ligands; for example, the effect of the IL becomes dominant when the support has a weak electron-donor character. The combined effects of supports and ILs as ligands offer broad opportunities for tuning catalytic properties of supported metal catalysts.

Characterizing materials at nanoscale resolution to provide new insights into structure property performance relationships continues to be a challenging research target due to the inherently low signal from small sample volumes, and is even more difficult for nonconductive materials, such as zeolites. Herein, we present the characterization of a single Cu-exchanged zeolite crystal, namely Cu-SSZ-13, used for NOX reduction in automotive emissions, that was subject to a simulated 135,000-mile aging. By correlating Atom Probe Tomography (APT), a single atom microscopy method, and Scanning Transmission X-ray Microscopy (STXM), which produces high spatial resolution X-ray Absorption Near Edge Spectroscopy (XANES) maps, we show that a spatially non-uniform proportion of the Al was removed from the zeolite framework. The techniques reveal that this degradation is heterogeneous at length scales from micrometers to tens of nanometers, providing complementary insight into the long-term deactivation of this catalyst system.

Characterizing materials at nanoscale resolution to provide new insights into structure property performance relationships continues to be a challenging research target due to the inherently low signal from small sample volumes, and is even more difficult for nonconductive materials, such as zeolites. Herein, we present the characterization of a single Cu-exchanged zeolite crystal, namely Cu-SSZ-13, used for NOX reduction in automotive emissions, that was subject to a simulated 135,000-mile aging. By correlating Atom Probe Tomography (APT), a single atom microscopy method, and Scanning Transmission X-ray Microscopy (STXM), which produces high spatial resolution X-ray Absorption Near Edge Spectroscopy (XANES) maps, we show that a spatially non-uniform proportion of the Al was removed from the zeolite framework. The techniques reveal that this degradation is heterogeneous at length scales from micrometers to tens of nanometers, providing complementary insight into the long-term deactivation of this catalyst system.

BackgroundTrachoma, a leading cause of blindness, is targeted for global elimination as a public health problem by 2020. In order to contribute to this goal, countries should demonstrate reduction of disease prevalence below specified thresholds, after implementation of the SAFE strategy in areas with defined endemicity. Zimbabwe had not yet generated data on trachoma endemicity and no specific interventions against trachoma have yet been implemented.MethodsTwo trachoma mapping phases were successively implemented in Zimbabwe, with eight districts included in each phase, in September 2014 and October 2015. The methodology of the Global Trachoma Mapping Project was used.ResultsOur teams examined 53,211 people for trachoma in 385 sampled clusters. Of 18,196 children aged 1-9 years examined, 1526 (8.4%) had trachomatous inflammation-follicular (TF). Trichiasis was observed in 299 (1.0%) of 29,519 people aged ≥15 years. Of the 16 districts surveyed, 11 (69%) had TF prevalences ≥10% in 1-9-year-olds, indicative of active trachoma being a significant public health problem, requiring implementation of the A, F and E components of the SAFE strategy for at least 3 years. The total estimated trichiasis backlog across the 16 districts was 5506 people. The highest estimated trichiasis burdens were in Binga district (1211 people) and Gokwe North (854 people).ConclusionImplementation of the SAFE strategy is needed in parts of Zimbabwe. In addition, Zimbabwe needs to conduct more baseline trachoma mapping in districts adjacent to those identified here as having a public health problem from the disease.

BACKGROUND:Trachoma, a leading cause of blindness, is targeted for global elimination as a public health problem by 2020. In order to contribute to this goal, countries should demonstrate reduction of disease prevalence below specified thresholds, after implementation of the SAFE strategy in areas with defined endemicity. Zimbabwe had not yet generated data on trachoma endemicity and no specific interventions against trachoma have yet been implemented. METHODS:Two trachoma mapping phases were successively implemented in Zimbabwe, with eight districts included in each phase, in September 2014 and October 2015. The methodology of the Global Trachoma Mapping Project was used. RESULTS:Our teams examined 53,211 people for trachoma in 385 sampled clusters. Of 18,196 children aged 1-9 years examined, 1526 (8.4%) had trachomatous inflammation-follicular (TF). Trichiasis was observed in 299 (1.0%) of 29,519 people aged ≥15 years. Of the 16 districts surveyed, 11 (69%) had TF prevalences ≥10% in 1-9-year-olds, indicative of active trachoma being a significant public health problem, requiring implementation of the A, F and E components of the SAFE strategy for at least 3 years. The total estimated trichiasis backlog across the 16 districts was 5506 people. The highest estimated trichiasis burdens were in Binga district (1211 people) and Gokwe North (854 people). CONCLUSION:Implementation of the SAFE strategy is needed in parts of Zimbabwe. In addition, Zimbabwe needs to conduct more baseline trachoma mapping in districts adjacent to those identified here as having a public health problem from the disease.

BackgroundThe clinical sequencing of cancer genomes to personalize therapy is becoming routine across the world. However, concerns over patient re-identification from these data lead to questions about how tightly access should be controlled. It is not thought to be possible to re-identify patients from somatic variant data. However, somatic variant detection pipelines can mistakenly identify germline variants as somatic ones, a process called "germline leakage". The rate of germline leakage across different somatic variant detection pipelines is not well-understood, and it is uncertain whether or not somatic variant calls should be considered re-identifiable. To fill this gap, we quantified germline leakage across 259 sets of whole-genome somatic single nucleotide variant (SNVs) predictions made by 21 teams as part of the ICGC-TCGA DREAM Somatic Mutation Calling Challenge.ResultsThe median somatic SNV prediction set contained 4325 somatic SNVs and leaked one germline polymorphism. The level of germline leakage was inversely correlated with somatic SNV prediction accuracy and positively correlated with the amount of infiltrating normal cells. The specific germline variants leaked differed by tumour and algorithm. To aid in quantitation and correction of leakage, we created a tool, called GermlineFilter, for use in public-facing somatic SNV databases.ConclusionsThe potential for patient re-identification from leaked germline variants in somatic SNV predictions has led to divergent open data access policies, based on different assessments of the risks. Indeed, a single, well-publicized re-identification event could reshape public perceptions of the values of genomic data sharing. We find that modern somatic SNV prediction pipelines have low germline-leakage rates, which can be further reduced, especially for cloud-sharing, using pre-filtering software.

BackgroundThe phenotypes of cancer cells are driven in part by somatic structural variants. Structural variants can initiate tumors, enhance their aggressiveness, and provide unique therapeutic opportunities. Whole-genome sequencing of tumors can allow exhaustive identification of the specific structural variants present in an individual cancer, facilitating both clinical diagnostics and the discovery of novel mutagenic mechanisms. A plethora of somatic structural variant detection algorithms have been created to enable these discoveries; however, there are no systematic benchmarks of them. Rigorous performance evaluation of somatic structural variant detection methods has been challenged by the lack of gold standards, extensive resource requirements, and difficulties arising from the need to share personal genomic information.ResultsTo facilitate structural variant detection algorithm evaluations, we create a robust simulation framework for somatic structural variants by extending the BAMSurgeon algorithm. We then organize and enable a crowdsourced benchmarking within the ICGC-TCGA DREAM Somatic Mutation Calling Challenge (SMC-DNA). We report here the results of structural variant benchmarking on three different tumors, comprising 204 submissions from 15 teams. In addition to ranking methods, we identify characteristic error profiles of individual algorithms and general trends across them. Surprisingly, we find that ensembles of analysis pipelines do not always outperform the best individual method, indicating a need for new ways to aggregate somatic structural variant detection approaches.ConclusionsThe synthetic tumors and somatic structural variant detection leaderboards remain available as a community benchmarking resource, and BAMSurgeon is available at https://github.com/adamewing/bamsurgeon .

BackgroundThe phenotypes of cancer cells are driven in part by somatic structural variants. Structural variants can initiate tumors, enhance their aggressiveness, and provide unique therapeutic opportunities. Whole-genome sequencing of tumors can allow exhaustive identification of the specific structural variants present in an individual cancer, facilitating both clinical diagnostics and the discovery of novel mutagenic mechanisms. A plethora of somatic structural variant detection algorithms have been created to enable these discoveries; however, there are no systematic benchmarks of them. Rigorous performance evaluation of somatic structural variant detection methods has been challenged by the lack of gold standards, extensive resource requirements, and difficulties arising from the need to share personal genomic information.ResultsTo facilitate structural variant detection algorithm evaluations, we create a robust simulation framework for somatic structural variants by extending the BAMSurgeon algorithm. We then organize and enable a crowdsourced benchmarking within the ICGC-TCGA DREAM Somatic Mutation Calling Challenge (SMC-DNA). We report here the results of structural variant benchmarking on three different tumors, comprising 204 submissions from 15 teams. In addition to ranking methods, we identify characteristic error profiles of individual algorithms and general trends across them. Surprisingly, we find that ensembles of analysis pipelines do not always outperform the best individual method, indicating a need for new ways to aggregate somatic structural variant detection approaches.ConclusionsThe synthetic tumors and somatic structural variant detection leaderboards remain available as a community benchmarking resource, and BAMSurgeon is available at https://github.com/adamewing/bamsurgeon .

In situ spectroscopic techniques provide kinetic and chemical structure data for elucidation of reaction mechanisms and pathways during reactive separations.

BACKGROUND:The clinical sequencing of cancer genomes to personalize therapy is becoming routine across the world. However, concerns over patient re-identification from these data lead to questions about how tightly access should be controlled. It is not thought to be possible to re-identify patients from somatic variant data. However, somatic variant detection pipelines can mistakenly identify germline variants as somatic ones, a process called "germline leakage". The rate of germline leakage across different somatic variant detection pipelines is not well-understood, and it is uncertain whether or not somatic variant calls should be considered re-identifiable. To fill this gap, we quantified germline leakage across 259 sets of whole-genome somatic single nucleotide variant (SNVs) predictions made by 21 teams as part of the ICGC-TCGA DREAM Somatic Mutation Calling Challenge. RESULTS:The median somatic SNV prediction set contained 4325 somatic SNVs and leaked one germline polymorphism. The level of germline leakage was inversely correlated with somatic SNV prediction accuracy and positively correlated with the amount of infiltrating normal cells. The specific germline variants leaked differed by tumour and algorithm. To aid in quantitation and correction of leakage, we created a tool, called GermlineFilter, for use in public-facing somatic SNV databases. CONCLUSIONS:The potential for patient re-identification from leaked germline variants in somatic SNV predictions has led to divergent open data access policies, based on different assessments of the risks. Indeed, a single, well-publicized re-identification event could reshape public perceptions of the values of genomic data sharing. We find that modern somatic SNV prediction pipelines have low germline-leakage rates, which can be further reduced, especially for cloud-sharing, using pre-filtering software.

Developing fundamental insight for reactions between gas phase H2S and solid phase CuO has the potential to lead to improved materials and processes for natural gas purification. However, this insight requires detailed knowledge of the atomistic characteristics of the solid and how these characteristics influence the reaction mechanism and kinetics. Herein, we use fixed bed reactors, X-ray absorption spectroscopy, and transmission X-ray microscopy to simultaneously probe the fundamental kinetics of the reaction of CuO with H2S to form CuS, and thereby probe spatialoral chemical and structural changes of copper during this reaction. H2S removal reaction kinetics show similar trends in fixed bed reactors as in 10-20 μm sized particles. However, reaction fronts proceed through the entire diameter of particles heterogeneously, indicating the presence of pore diffusion resistance even at very small length scales. In addition, CuO sorbent samples with similar characteristics exhibit 3 times different sulfidation conversion with reaction rate constants that differ by a factor of 1.5. These differences in reaction kinetics and conversion indicate the critical impact of possible atomic scale differences and the formation of different copper sulfide products.

Cardiac β-adrenergic receptors (β-AR) and Ca2+-Calmodulin dependent protein kinase (CaMKII) regulate both physiological and pathophysiological Ca2+ signaling. Elevated diastolic Ca2+ leak from the sarcoplasmic reticulum (SR) contributes to contractile dysfunction in heart failure and to arrhythmogenesis. β-AR activation is known to increase SR Ca2+ leak via CaMKII-dependent phosphorylation of the ryanodine receptor. Two independent and reportedly parallel pathways have been implicated in this β-AR-CaMKII cascade, one involving exchange protein directly activated by cAMP (Epac2) and another involving nitric oxide synthase 1 (NOS1). Here we tested whether Epac and NOS function in a single series pathway to increase β-AR induced and CaMKII-dependent SR Ca2+ leak. Leak was measured as both Ca2+ spark frequency and tetracaine-induced shifts in SR Ca2+, in mouse and rabbit ventricular myocytes. Direct Epac activation by 8-CPT (8-(4-chlorophenylthio)-2'-O-methyl-cAMP) mimicked β-AR-induced SR Ca2+ leak, and both were blocked by NOS inhibition. The same was true for myocyte CaMKII activation (assessed via a FRET-based reporter) and ryanodine receptor phosphorylation. Inhibitor and phosphorylation studies also implicated phosphoinositide 3-kinase (PI3K) and protein kinase B (Akt) downstream of Epac and above NOS activation in this pathway. We conclude that these two independently characterized parallel pathways function mainly via a single series arrangement (β-AR-cAMP-Epac-PI3K-Akt-NOS1-CaMKII) to mediate increased SR Ca2+ leak. Thus, for β-AR activation the cAMP-PKA branch effects inotropy and lusitropy (by effects on Ca2+ current and SR Ca2+-ATPase), this cAMP-Epac-NOS pathway increases pathological diastolic SR Ca2+leak. This pathway distinction may allow novel SR Ca2+ leak therapeutic targeting in treatment of arrhythmias in heart failure that spare the inotropic and lusitropic effects of the PKA branch.

Cardiac β-adrenergic receptors (β-AR) and Ca2+-Calmodulin dependent protein kinase (CaMKII) regulate both physiological and pathophysiological Ca2+ signaling. Elevated diastolic Ca2+ leak from the sarcoplasmic reticulum (SR) contributes to contractile dysfunction in heart failure and to arrhythmogenesis. β-AR activation is known to increase SR Ca2+ leak via CaMKII-dependent phosphorylation of the ryanodine receptor. Two independent and reportedly parallel pathways have been implicated in this β-AR-CaMKII cascade, one involving exchange protein directly activated by cAMP (Epac2) and another involving nitric oxide synthase 1 (NOS1). Here we tested whether Epac and NOS function in a single series pathway to increase β-AR induced and CaMKII-dependent SR Ca2+ leak. Leak was measured as both Ca2+ spark frequency and tetracaine-induced shifts in SR Ca2+, in mouse and rabbit ventricular myocytes. Direct Epac activation by 8-CPT (8-(4-chlorophenylthio)-2'-O-methyl-cAMP) mimicked β-AR-induced SR Ca2+ leak, and both were blocked by NOS inhibition. The same was true for myocyte CaMKII activation (assessed via a FRET-based reporter) and ryanodine receptor phosphorylation. Inhibitor and phosphorylation studies also implicated phosphoinositide 3-kinase (PI3K) and protein kinase B (Akt) downstream of Epac and above NOS activation in this pathway. We conclude that these two independently characterized parallel pathways function mainly via a single series arrangement (β-AR-cAMP-Epac-PI3K-Akt-NOS1-CaMKII) to mediate increased SR Ca2+ leak. Thus, for β-AR activation the cAMP-PKA branch effects inotropy and lusitropy (by effects on Ca2+ current and SR Ca2+-ATPase), this cAMP-Epac-NOS pathway increases pathological diastolic SR Ca2+leak. This pathway distinction may allow novel SR Ca2+ leak therapeutic targeting in treatment of arrhythmias in heart failure that spare the inotropic and lusitropic effects of the PKA branch.

X-ray absorption spectroscopy is an element-specific technique for probing the local atomic-scale environment around an absorber atom. It is widely used to investigate the structures of liquids and solids, being especially valuable for characterization of solid-supported catalysts. Reported cell designs are limited in capabilities-to fluorescence or transmission and to static or flowing atmospheres, or to vacuum. Our goal was to design a robust and widely applicable cell for catalyst characterizations under all these conditions-to allow tracking of changes during genesis and during operation, both under vacuum and in reactive atmospheres. Herein, we report the design of such a cell and a demonstration of its operation both with a sample under dynamic vacuum and in the presence of gases flowing at temperatures up to 300 °C, showing data obtained with both fluorescence and transmission detection. The cell allows more flexibility in catalyst characterization than any reported.

X-ray absorption spectroscopy is an element-specific technique for probing the local atomic-scale environment around an absorber atom. It is widely used to investigate the structures of liquids and solids, being especially valuable for characterization of solid-supported catalysts. Reported cell designs are limited in capabilities-to fluorescence or transmission and to static or flowing atmospheres, or to vacuum. Our goal was to design a robust and widely applicable cell for catalyst characterizations under all these conditions-to allow tracking of changes during genesis and during operation, both under vacuum and in reactive atmospheres. Herein, we report the design of such a cell and a demonstration of its operation both with a sample under dynamic vacuum and in the presence of gases flowing at temperatures up to 300 °C, showing data obtained with both fluorescence and transmission detection. The cell allows more flexibility in catalyst characterization than any reported.

Identifying accurate biomarkers of cognitive decline is essential for advancing early diagnosis and prevention therapies in Alzheimer's disease. The Alzheimer's disease DREAM Challenge was designed as a computational crowdsourced project to benchmark the current state-of-the-art in predicting cognitive outcomes in Alzheimer's disease based on high dimensional, publicly available genetic and structural imaging data. This meta-analysis failed to identify a meaningful predictor developed from either data modality, suggesting that alternate approaches should be considered for prediction of cognitive performance.

ContextThe optimal pharmacologic treatment for early convulsive status epilepticus is unclear.ObjectiveTo analyze efficacy, tolerability and safety data for anticonvulsant treatment of children and adults with convulsive status epilepticus and use this analysis to develop an evidence-based treatment algorithm.Data sourcesStructured literature review using MEDLINE, Embase, Current Contents, and Cochrane library supplemented with article reference lists.Study selectionRandomized controlled trials of anticonvulsant treatment for seizures lasting longer than 5 minutes.Data extractionIndividual studies were rated using predefined criteria and these results were used to form recommendations, conclusions, and an evidence-based treatment algorithm.ResultsA total of 38 randomized controlled trials were identified, rated and contributed to the assessment. Only four trials were considered to have class I evidence of efficacy. Two studies were rated as class II and the remaining 32 were judged to have class III evidence. In adults with convulsive status epilepticus, intramuscular midazolam, intravenous lorazepam, intravenous diazepam and intravenous phenobarbital are established as efficacious as initial therapy (Level A). Intramuscular midazolam has superior effectiveness compared to intravenous lorazepam in adults with convulsive status epilepticus without established intravenous access (Level A). In children, intravenous lorazepam and intravenous diazepam are established as efficacious at stopping seizures lasting at least 5 minutes (Level A) while rectal diazepam, intramuscular midazolam, intranasal midazolam, and buccal midazolam are probably effective (Level B). No significant difference in effectiveness has been demonstrated between intravenous lorazepam and intravenous diazepam in adults or children with convulsive status epilepticus (Level A). Respiratory and cardiac symptoms are the most commonly encountered treatment-emergent adverse events associated with intravenous anticonvulsant drug administration in adults with convulsive status epilepticus (Level A). The rate of respiratory depression in patients with convulsive status epilepticus treated with benzodiazepines is lower than in patients with convulsive status epilepticus treated with placebo indicating that respiratory problems are an important consequence of untreated convulsive status epilepticus (Level A). When both are available, fosphenytoin is preferred over phenytoin based on tolerability but phenytoin is an acceptable alternative (Level A). In adults, compared to the first therapy, the second therapy is less effective while the third therapy is substantially less effective (Level A). In children, the second therapy appears less effective and there are no data about third therapy efficacy (Level C). The evidence was synthesized into a treatment algorithm.ConclusionsDespite the paucity of well-designed randomized controlled trials, practical conclusions and an integrated treatment algorithm for the treatment of convulsive status epilepticus across the age spectrum (infants through adults) can be constructed. Multicenter, multinational efforts are needed to design, conduct and analyze additional randomized controlled trials that can answer the many outstanding clinically relevant questions identified in this guideline.

The detection of somatic mutations from cancer genome sequences is key to understanding the genetic basis of disease progression, patient survival and response to therapy. Benchmarking is needed for tool assessment and improvement but is complicated by a lack of gold standards, by extensive resource requirements and by difficulties in sharing personal genomic information. To resolve these issues, we launched the ICGC-TCGA DREAM Somatic Mutation Calling Challenge, a crowdsourced benchmark of somatic mutation detection algorithms. Here we report the BAMSurgeon tool for simulating cancer genomes and the results of 248 analyses of three in silico tumors created with it. Different algorithms exhibit characteristic error profiles, and, intriguingly, false positives show a trinucleotide profile very similar to one found in human tumors. Although the three simulated tumors differ in sequence contamination (deviation from normal cell sequence) and in subclonality, an ensemble of pipelines outperforms the best individual pipeline in all cases. BAMSurgeon is available at https://github.com/adamewing/bamsurgeon/.

The detection of somatic mutations from cancer genome sequences is key to understanding the genetic basis of disease progression, patient survival and response to therapy. Benchmarking is needed for tool assessment and improvement but is complicated by a lack of gold standards, by extensive resource requirements and by difficulties in sharing personal genomic information. To resolve these issues, we launched the ICGC-TCGA DREAM Somatic Mutation Calling Challenge, a crowdsourced benchmark of somatic mutation detection algorithms. Here we report the BAMSurgeon tool for simulating cancer genomes and the results of 248 analyses of three in silico tumors created with it. Different algorithms exhibit characteristic error profiles, and, intriguingly, false positives show a trinucleotide profile very similar to one found in human tumors. Although the three simulated tumors differ in sequence contamination (deviation from normal cell sequence) and in subclonality, an ensemble of pipelines outperforms the best individual pipeline in all cases. BAMSurgeon is available at https://github.com/adamewing/bamsurgeon/.

ObjectiveTo determine whether a next-generation sequencing (NGS) panel of 34 cancer-associated genes would cost-effectively aid in the treatment selection for patients with metastatic melanoma, compared with a single-site BRAF V600 mutation test.MethodsA decision model was developed to estimate the costs and health outcomes of the two test strategies. The cost effectiveness of these two strategies was analyzed from a payer perspective over a 2-year time horizon with model parameters taken from the literature.ResultsIn the base case, the gene sequencing panel strategy resulted in a cost of US$120,022 and 0.721 quality-adjusted life years (QALYs) per patient, whereas the single-site mutation test strategy resulted in a cost of US$128,965 and 0.704 QALYs. Thus, the gene sequencing panel strategy cost US$8943 less per patient and increased QALYs by 0.0174 per patient. Sensitivity analyses showed that, compared with the single-site mutation test strategy, the gene sequencing panel strategy had a 90.9% chance of having reduced costs and increased QALYs, with the cost of the gene sequencing panel test having minimal effect on the incremental cost.ConclusionCompared with the single-site mutation test, the use of an NGS panel of 34 cancer-associated genes as an aid in selecting therapy for patients with metastatic melanoma reduced costs and increased QALYs. If the base-case results were applied to the 8900 patients diagnosed with metastatic melanoma in the USA each year, the gene sequencing panel strategy could result in an annual savings of US$79.6 million and a gain of 155 QALYs.

ObjectiveTo determine whether a next-generation sequencing (NGS) panel of 34 cancer-associated genes would cost-effectively aid in the treatment selection for patients with metastatic melanoma, compared with a single-site BRAF V600 mutation test.MethodsA decision model was developed to estimate the costs and health outcomes of the two test strategies. The cost effectiveness of these two strategies was analyzed from a payer perspective over a 2-year time horizon with model parameters taken from the literature.ResultsIn the base case, the gene sequencing panel strategy resulted in a cost of US$120,022 and 0.721 quality-adjusted life years (QALYs) per patient, whereas the single-site mutation test strategy resulted in a cost of US$128,965 and 0.704 QALYs. Thus, the gene sequencing panel strategy cost US$8943 less per patient and increased QALYs by 0.0174 per patient. Sensitivity analyses showed that, compared with the single-site mutation test strategy, the gene sequencing panel strategy had a 90.9% chance of having reduced costs and increased QALYs, with the cost of the gene sequencing panel test having minimal effect on the incremental cost.ConclusionCompared with the single-site mutation test, the use of an NGS panel of 34 cancer-associated genes as an aid in selecting therapy for patients with metastatic melanoma reduced costs and increased QALYs. If the base-case results were applied to the 8900 patients diagnosed with metastatic melanoma in the USA each year, the gene sequencing panel strategy could result in an annual savings of US$79.6 million and a gain of 155 QALYs.

Despite the knowledge of complex prokaryotic-transcription mechanisms, generalized rules, such as the simplified organization of genes into operons with well-defined promoters and terminators, have had a significant role in systems analysis of regulatory logic in both bacteria and archaea. Here, we have investigated the prevalence of alternate regulatory mechanisms through genome-wide characterization of transcript structures of approximately 64% of all genes, including putative non-coding RNAs in Halobacterium salinarum NRC-1. Our integrative analysis of transcriptome dynamics and protein-DNA interaction data sets showed widespread environment-dependent modulation of operon architectures, transcription initiation and termination inside coding sequences, and extensive overlap in 3' ends of transcripts for many convergently transcribed genes. A significant fraction of these alternate transcriptional events correlate to binding locations of 11 transcription factors and regulators (TFs) inside operons and annotated genes-events usually considered spurious or non-functional. Using experimental validation, we illustrate the prevalence of overlapping genomic signals in archaeal transcription, casting doubt on the general perception of rigid boundaries between coding sequences and regulatory elements.

Despite the knowledge of complex prokaryotic-transcription mechanisms, generalized rules, such as the simplified organization of genes into operons with well-defined promoters and terminators, have had a significant role in systems analysis of regulatory logic in both bacteria and archaea. Here, we have investigated the prevalence of alternate regulatory mechanisms through genome-wide characterization of transcript structures of approximately 64% of all genes, including putative non-coding RNAs in Halobacterium salinarum NRC-1. Our integrative analysis of transcriptome dynamics and protein-DNA interaction data sets showed widespread environment-dependent modulation of operon architectures, transcription initiation and termination inside coding sequences, and extensive overlap in 3' ends of transcripts for many convergently transcribed genes. A significant fraction of these alternate transcriptional events correlate to binding locations of 11 transcription factors and regulators (TFs) inside operons and annotated genes-events usually considered spurious or non-functional. Using experimental validation, we illustrate the prevalence of overlapping genomic signals in archaeal transcription, casting doubt on the general perception of rigid boundaries between coding sequences and regulatory elements.

BackgroundThe SCID-hu Thy/Liv mouse model of HIV-1 infection is a useful platform for the preclinical evaluation of antiviral efficacy in vivo. We performed this study to validate the model with representatives of all four classes of licensed antiretrovirals.Methodology/principal findingsEndpoint analyses for quantification of Thy/Liv implant viral load included ELISA for cell-associated p24, branched DNA assay for HIV-1 RNA, and detection of infected thymocytes by intracellular staining for Gag-p24. Antiviral protection from HIV-1-mediated thymocyte depletion was assessed by multicolor flow cytometric analysis of thymocyte subpopulations based on surface expression of CD3, CD4, and CD8. These mice can be productively infected with molecular clones of HIV-1 (e.g., the X4 clone NL4-3) as well as with primary R5 and R5X4 isolates. To determine whether results in this model are concordant with those found in humans, we performed direct comparisons of two drugs in the same class, each of which has known potency and dosing levels in humans. Here we show that second-generation antiretrovirals were, as expected, more potent than their first-generation predecessors: emtricitabine was more potent than lamivudine, efavirenz was more potent than nevirapine, and atazanavir was more potent than indinavir. After interspecies pharmacodynamic scaling, the dose ranges found to inhibit viral replication in the SCID-hu Thy/Liv mouse were similar to those used in humans. Moreover, HIV-1 replication in these mice was genetically stable; treatment of the mice with lamivudine did not result in the M184V substitution in reverse transcriptase, and the multidrug-resistant NY index case HIV-1 retained its drug-resistance substitutions.ConclusionGiven the fidelity of such comparisons, we conclude that this highly reproducible mouse model is likely to predict clinical antiviral efficacy in humans.

BackgroundThe SCID-hu Thy/Liv mouse model of HIV-1 infection is a useful platform for the preclinical evaluation of antiviral efficacy in vivo. We performed this study to validate the model with representatives of all four classes of licensed antiretrovirals.Methodology/principal findingsEndpoint analyses for quantification of Thy/Liv implant viral load included ELISA for cell-associated p24, branched DNA assay for HIV-1 RNA, and detection of infected thymocytes by intracellular staining for Gag-p24. Antiviral protection from HIV-1-mediated thymocyte depletion was assessed by multicolor flow cytometric analysis of thymocyte subpopulations based on surface expression of CD3, CD4, and CD8. These mice can be productively infected with molecular clones of HIV-1 (e.g., the X4 clone NL4-3) as well as with primary R5 and R5X4 isolates. To determine whether results in this model are concordant with those found in humans, we performed direct comparisons of two drugs in the same class, each of which has known potency and dosing levels in humans. Here we show that second-generation antiretrovirals were, as expected, more potent than their first-generation predecessors: emtricitabine was more potent than lamivudine, efavirenz was more potent than nevirapine, and atazanavir was more potent than indinavir. After interspecies pharmacodynamic scaling, the dose ranges found to inhibit viral replication in the SCID-hu Thy/Liv mouse were similar to those used in humans. Moreover, HIV-1 replication in these mice was genetically stable; treatment of the mice with lamivudine did not result in the M184V substitution in reverse transcriptase, and the multidrug-resistant NY index case HIV-1 retained its drug-resistance substitutions.ConclusionGiven the fidelity of such comparisons, we conclude that this highly reproducible mouse model is likely to predict clinical antiviral efficacy in humans.

Kaposi's sarcoma-associated herpesvirus (KSHV/HHV-8) is a novel human lymphotropic herpesvirus linked to several human neoplasms. To date, no animal model for infection by this virus has been described. We have examined the susceptibility of C.B-17 scid/scid mice implanted with human fetal thymus and liver grafts (SCID-hu Thy/Liv mice) to KSHV infection. KSHV virions were inoculated directly into the implants, and viral DNA and mRNA production was assayed using real-time quantitative polymerase chain reaction. This revealed a biphasic infection, with an early phase of lytic replication accompanied and followed by sustained latency. Ultraviolet irradiation of the inoculum abolished all DNA- and mRNA-derived signals, and infection was inhibited by ganciclovir. Viral gene expression was most abundant in CD19(+) B lymphocytes, suggesting that this model faithfully mimics the natural tropism of this virus. Short-term coinfection with HIV-1 did not alter the course of KSHV replication, nor did KSHV alter levels of HIV-1 p24 during the acute phase of the infection. Although no disease was evident in infected animals, SCID-hu Thy/Liv mice should allow the detailed study of KSHV tropism, latency, and drug susceptibility.

Kaposi's sarcoma-associated herpesvirus (KSHV/HHV-8) is a novel human lymphotropic herpesvirus linked to several human neoplasms. To date, no animal model for infection by this virus has been described. We have examined the susceptibility of C.B-17 scid/scid mice implanted with human fetal thymus and liver grafts (SCID-hu Thy/Liv mice) to KSHV infection. KSHV virions were inoculated directly into the implants, and viral DNA and mRNA production was assayed using real-time quantitative polymerase chain reaction. This revealed a biphasic infection, with an early phase of lytic replication accompanied and followed by sustained latency. Ultraviolet irradiation of the inoculum abolished all DNA- and mRNA-derived signals, and infection was inhibited by ganciclovir. Viral gene expression was most abundant in CD19(+) B lymphocytes, suggesting that this model faithfully mimics the natural tropism of this virus. Short-term coinfection with HIV-1 did not alter the course of KSHV replication, nor did KSHV alter levels of HIV-1 p24 during the acute phase of the infection. Although no disease was evident in infected animals, SCID-hu Thy/Liv mice should allow the detailed study of KSHV tropism, latency, and drug susceptibility.

Human herpesvirus 6 (HHV-6) is a potentially immunosuppressive agent that may act as a cofactor in the progression of AIDS. Here, we describe the first small animal model of HHV-6 infection. HHV-6 subgroup A, strain GS, efficiently infected the human thymic tissue implanted in SCID-hu Thy/Liv mice, leading to the destruction of the graft. Viral DNA was detected in Thy/Liv implants by quantitative polymerase chain reaction (PCR) as early as 4 d after inoculation and peaked at day 14. The productive nature of the infection was confirmed by electron microscopy and immunohistochemical staining. Atypical thymocytes with prominent nuclear inclusions were detected by histopathology. HHV-6 replication was associated with severe, progressive thymocyte depletion involving all major cellular subsets. However, intrathymic T progenitor cells (ITTPs) appeared to be more severely depleted than the other subpopulations, and a preferred tropism of HHV-6 for ITTPs was demonstrated by quantitative PCR on purified thymocyte subsets. These findings suggest that thymocyte depletion by HHV-6 may be due to infection and destruction of these immature T cell precursors. Similar results were obtained with strain PL-1, a primary isolate belonging to subgroup B. The severity of the lesions observed in this animal model underscores the possibility that HHV-6 may indeed be immunosuppressive in humans.

Human herpesvirus 6 (HHV-6) is a potentially immunosuppressive agent that may act as a cofactor in the progression of AIDS. Here, we describe the first small animal model of HHV-6 infection. HHV-6 subgroup A, strain GS, efficiently infected the human thymic tissue implanted in SCID-hu Thy/Liv mice, leading to the destruction of the graft. Viral DNA was detected in Thy/Liv implants by quantitative polymerase chain reaction (PCR) as early as 4 d after inoculation and peaked at day 14. The productive nature of the infection was confirmed by electron microscopy and immunohistochemical staining. Atypical thymocytes with prominent nuclear inclusions were detected by histopathology. HHV-6 replication was associated with severe, progressive thymocyte depletion involving all major cellular subsets. However, intrathymic T progenitor cells (ITTPs) appeared to be more severely depleted than the other subpopulations, and a preferred tropism of HHV-6 for ITTPs was demonstrated by quantitative PCR on purified thymocyte subsets. These findings suggest that thymocyte depletion by HHV-6 may be due to infection and destruction of these immature T cell precursors. Similar results were obtained with strain PL-1, a primary isolate belonging to subgroup B. The severity of the lesions observed in this animal model underscores the possibility that HHV-6 may indeed be immunosuppressive in humans.