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"Jacques, A"
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Interpretable machine learning for knowledge generation in heterogeneous catalysis
Most applications of machine learning in heterogeneous catalysis thus far have used black-box models to predict computable physical properties (descriptors), such as adsorption or formation energies, that can be related to catalytic performance (that is, activity or stability). Extracting meaningful physical insights from these black-box models has proved challenging, as the internal logic of these black-box models is not readily interpretable due to their high degree of complexity. Interpretable machine learning methods that merge the predictive capacity of black-box models with the physical interpretability of physics-based models offer an alternative to black-box models. In this Perspective, we discuss the various interpretable machine learning methods available to catalysis researchers, highlight the potential of interpretable machine learning to accelerate hypothesis formation and knowledge generation, and outline critical challenges and opportunities for interpretable machine learning in heterogeneous catalysis.
Most applications of machine learning in catalysis use black-box models to predict physical properties, but extracting meaningful physical insights from them is challenging. This Perspective discusses machine learning approaches for heterogeneous catalysis and classifies them in terms of their interpretability.
Journal Article
Tracking emissions in the US electricity system
Understanding electricity consumption and production patterns is a necessary first step toward reducing the health and climate impacts of associated emissions. In this work, the economic input–output model is adapted to track emissions flows through electric grids and quantify the pollution embodied in electricity production, exchanges, and, ultimately, consumption for the 66 continental US Balancing Authorities (BAs). The hourly and BA-level dataset we generate and release leverages multiple publicly available datasets for the year 2016. Our analysis demonstrates the importance of considering location and temporal effects as well as electricity exchanges in estimating emissions footprints. While increasing electricity exchanges makes the integration of renewable electricity easier, importing electricity may also run counter to climate-change goals, and citizens in regions exporting electricity from high-emission-generating sources bear a disproportionate air-pollution burden. For example, 40% of the carbon emissions related to electricity consumption in California’s main BA were produced in a different region. From 30 to 50% of the sulfur dioxide and nitrogen oxides released in some of the coal-heavy Rocky Mountain regions were related to electricity produced that was then exported. Whether for policymakers designing energy efficiency and renewable programs, regulators enforcing emissions standards, or large electricity consumers greening their supply, greater resolution is needed for electricsector emissions indices to evaluate progress against current and future goals.
Journal Article
Natural Killer Cell Signaling Pathways
Natural killer (NK) cells are lymphocytes of the innate immune system that are involved in the early defenses against foreign cells, as well as autologous cells undergoing various forms of stress, such as microbial infection or tumor transformation. NK cell activation is controlled by a dynamic balance between complementary and antagonistic pathways that are initiated upon interaction with potential target cells. NK cells express an array of activating cell surface receptors that can trigger cytolytic programs, as well as cytokine or chemokine secretion. Some of these activating cell surface receptors initiate protein tyrosine kinase (PTK)-dependent pathways through noncovalent associations with transmembrane signaling adaptors that harbor intracytoplasmic ITAMs (immunoreceptor tyrosine-based activation motifs). Additional cell surface receptors that are not directly coupled to ITAMs also participate in NK cell activation. These include NKG2D, which is noncovalently associated to the DAP10 transmembrane signaling adaptor, as well as integrins and cytokine receptors. NK cells also express cell surface inhibitory receptors that antagonize activating pathways through protein tyrosine phosphatases (PTPs). These inhibitory cell surface receptors are characterized by intracytoplasmic ITIMs (immunoreceptor tyrosine-based inhibition motifs). The tyrosine-phosphorylation status of several signaling components that are substrates for both PTKs and PTPs is thus key to the propagation of the NK cell effector pathways. Understanding the integration of these multiple signals is central to the understanding and manipulation of NK cell effector signaling pathways.
Journal Article
Life cycle comparison of industrial-scale lithium-ion battery recycling and mining supply chains
Recycling lithium-ion batteries (LIBs) can supplement critical materials and improve the environmental sustainability of LIB supply chains. In this work, environmental impacts (greenhouse gas emissions, water consumption, energy consumption) of industrial-scale production of battery-grade cathode materials from end-of-life LIBs are compared to those of conventional mining supply chains. Converting mixed-stream LIBs into battery-grade materials reduces environmental impacts by at least 58%. Recycling batteries to mixed metal products instead of discrete salts further reduces environmental impacts. Electricity consumption is identified as the principal contributor to all LIB recycling environmental impacts, and different electricity sources can change greenhouse gas emissions up to five times. Supply chain steps that precede refinement (material extraction and transport) contribute marginally to the environmental impacts of circular LIB supply chains (<4%), but are more significant in conventional supply chains (30%). This analysis provides insights for advancing sustainable LIB supply chains, and informs optimization of industrial-scale environmental impacts for emerging battery recycling efforts.
Battery recycling LCA shows that recycling can reduce 58% of environmental impacts of making mixed salt solutions compared to conventional mining. Electricity and hydrometallurgical processes dominate impacts and show improvement opportunities.
Journal Article
Measurement of Outflow Facility Using iPerfusion
Elevated intraocular pressure (IOP) is the predominant risk factor for glaucoma, and reducing IOP is the only successful strategy to prevent further glaucomatous vision loss. IOP is determined by the balance between the rates of aqueous humour secretion and outflow, and a pathological reduction in the hydraulic conductance of outflow, known as outflow facility, is responsible for IOP elevation in glaucoma. Mouse models are often used to investigate the mechanisms controlling outflow facility, but the diminutive size of the mouse eye makes measurement of outflow technically challenging. In this study, we present a new approach to measure and analyse outflow facility using iPerfusion™, which incorporates an actuated pressure reservoir, thermal flow sensor, differential pressure measurement and an automated computerised interface. In enucleated eyes from C57BL/6J mice, the flow-pressure relationship is highly non-linear and is well represented by an empirical power law model that describes the pressure dependence of outflow facility. At zero pressure, the measured flow is indistinguishable from zero, confirming the absence of any significant pressure independent flow in enucleated eyes. Comparison with the commonly used 2-parameter linear outflow model reveals that inappropriate application of a linear fit to a non-linear flow-pressure relationship introduces considerable errors in the estimation of outflow facility and leads to the false impression of pressure-independent outflow. Data from a population of enucleated eyes from C57BL/6J mice show that outflow facility is best described by a lognormal distribution, with 6-fold variability between individuals, but with relatively tight correlation of facility between fellow eyes. iPerfusion represents a platform technology to accurately and robustly characterise the flow-pressure relationship in enucleated mouse eyes for the purpose of glaucoma research and with minor modifications, may be applied in vivo to mice, as well as to eyes from other species or different biofluidic systems.
Journal Article
CD200R1-CD200 checkpoint inhibits phagocytosis differently from SIRPα-CD47 to suppress tumor growth
Targeting macrophage inhibitory receptors like signal regulatory protein α (SIRPα) is a promising avenue in cancer treatment. Whereas the ligand of SIRPα, CD47, is widely expressed on tumor cells, its simultaneous presence on all normal cells raises concerns about toxicity and efficacy. This study identifies CD200R1, which binds CD200 on specific tumor types and limited normal cells, as an alternative inhibitory checkpoint for phagocytosis. Blocking or removing CD200R1 from macrophages or CD200 from tumor cells increases phagocytosis and suppresses tumor growth. In humans, CD200R1 is mainly expressed in immunosuppressive macrophages and is induced by interleukin-4. Unlike SIRPα that utilizes phosphatases Src homology 2 domain phosphatase (SHP)−1 and SHP-2, CD200R1 mediates its inhibitory effect via the kinase Csk. Combined CD200R1-CD200 and SIRPα-CD47 blockade further boosts phagocytosis and reduces tumor growth of CD200-expressing tumors, compared to either blockade alone. Thus, targeting CD200R1-CD200 is a promising strategy for immune checkpoint blockade in macrophages, either alone or alongside blockade of other checkpoints.
CD200R1 is a transmembrane receptor expressed on macrophages. Here the authors report that the interaction of CD200R1 with its ligand CD200, expressed by tumor cells, suppresses phagocytosis, and that targeting CD200R1-CD200 promotes macrophage-mediated anti-tumor response.
Journal Article
Vitamin D Controls Tumor Growth and CD8+ T Cell Infiltration in Breast Cancer
Women with low levels of vitamin D have a higher risk of developing breast cancer. Numerous studies associated the presence of a CD8+ T cell infiltration with a good prognosis. As vitamin D may play a key role in the modulation of the immune system, the objective of this work was to evaluate the impact of vitamin D on the breast cancer progression and mammary tumor microenvironment. We show that vitamin D decreases breast cancer tumor growth. Immunomonitoring of the different immune subsets in dissociated tumors revealed an increase in tumor infiltrating CD8+ T cells in the vitamin D-treated group. Interestingly, these CD8+ T cells exhibited a more active T cell (T
) phenotype. However, in high-fat diet conditions, we observed an opposite effect of vitamin D on breast cancer tumor growth, associated with a reduction of CD8+ T cell infiltration. Our data show that vitamin D is able to modulate breast cancer tumor growth and inflammation in the tumor microenvironment
. Unexpectedly, this effect is reversed in high-fat diet conditions, revealing the importance of diet on tumor growth. We believe that supplementation with vitamin D can in certain conditions represent a new adjuvant in the treatment of breast cancers.
Journal Article
High-dimensional mass cytometry analysis of NK cell alterations in AML identifies a subgroup with adverse clinical outcome
Natural killer (NK) cells are major antileukemic immune effectors. Leukemic blasts have a negative impact on NK cell function and promote the emergence of phenotypically and functionally impaired NK cells. In the current work, we highlight an accumulation of CD56⁻CD16⁺ unconventional NK cells in acute myeloid leukemia (AML), an aberrant subset initially described as being elevated in patients chronically infectedwith HIV-1. Deep phenotyping of NK cells was performed using peripheral blood from patients with newly diagnosed AML (n = 48, HEMATOBIO cohort, NCT02320656) and healthy subjects (n = 18) by mass cytometry. We showed evidence of amoderate to drastic accumulation of CD56⁻CD16⁺ unconventional NK cells in 27% of patients. These NK cells displayed decreased expression of NKG2A as well as the triggering receptors NKp30 and NKp46, in line with previous observations in HIV-infected patients. High-dimensional characterization of these NK cells highlighted a decreased expression of three additional major triggering receptors required for NK cell activation, NKG2D, DNAM-1, and CD96. A high proportion of CD56⁻CD16⁺ NK cells at diagnosis was associated with an adverse clinical outcome and decreased overall survival (HR = 0.13; P = 0.0002) and event-free survival (HR = 0.33; P = 0.018) and retained statistical significance in multivariate analysis. Pseudotime analysis of the NK cell compartment highlighted a disruption of the maturation process, with a bifurcation from conventional NK cells toward CD56⁻CD16⁺ NK cells. Overall, our data suggest that the accumulation of CD56⁻CD16⁺ NK cells may be the consequence of immune escape from innate immunity during AML progression.
Journal Article